title: HEART 8w 5AM MQ3

city: Bad Nauheim

first: Pieterjan

last: Dierickx

state: Hessen

address: Parkstrasse 1

department: Circadian Regulation of Cardiometabolism

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Sequencing was performed on NextSeq2000 instrument (Illumina) with 1x72bp single end setup.Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner). Alignments were filtered to remove: duplicates with Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5, multiple testing adjusted p-value < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample
Supplementary files format and content: tab-delimited txt file includes normlized counts for each sample

source_name: Heart

growth_protocol: Mice were kept under standard housing conditions approved by the IACUC of the University of Pennsylvania, including 12:12 light/dark cycles and ad libitum access to standard chow diet and water.

extract_protocol:
Total RNA was extracted from heart tissues (TRIZOL) using RNAeasy (Qiagen) according to the manufacturer’s instructions, and treated with DNase (Qiagen) before elution. Isolated mRNA quality and yield was tested using RNA integrity number (RIN) algorithm, using a Bioanalyzer (Agilent).
RNA and library preparation integrity were verified with LabChip Gx Touch 24 (Perkin Elmer). 1µg of total RNA was used as input for VAHTS Stranded mRNA-seq V6 Library preparation following manufacture’s protocol (Vazyme).

treatment_protocol: NR supplementation was provided by the addition of NR to clean drinking water to a concentration of 3g/L, then replacing original water bottles with 75mL foil-wrapped bottles. NR-treated water was checked daily and replaced at most every 3 days regardless of remaining volume. Mice at ZT22 harvests were euthanized and hearts collected with facility lights off under the use of red light headlamps.

value: Heart

value: 2 months

tag: time

value: MQ


title: Sample 18

status: Public on Feb 13 2026

type: SRA

city: Liverpool

first: Francesco

last: Del Carratore

address: Crown Street

department: Department of Biochemistry, Cell and Systems Biology

country: United Kingdom

institute: University of Liverpool

description: Library name: 3-2_1_S18

library_source: transcriptomic

data_processing:
Fastq files containing the raw reads were processed with the BBDuk and BBMap bioinformatics tools (B. Bushnell, sourceforge.net/projects/bbmap/). On a first run, BBDuk was used to trim the adapter sequences from the reads. On a second run, BBDuk was used to perform a rRNA decontamination step. For this step the SILVA  database62 was modified by including the rRNA sequence from the strains considered in this study.
The BBMap tool was then used to map the remaining reads to the four concatenated genomes considered in this study. Reads with ambiguous matches across the four genomes were discarded.
The alignment data obtained together with the concatenated genomes were then processed using the Bioconductor packages Rsamtools, GenomicFeatures and GenomicAlignments to obtain the raw counts data table.
Assembly: The genome assemblies for the 4 isolates are available on JGI at the following links:
Assembly: https://genome.jgi.doe.gov/portal/Strsp32123_FD/Strsp32123_FD.info.html
Assembly: https://genome.jgi.doe.gov/portal/Strsp32113_FD/Strsp32113_FD.info.html
Assembly: https://genome.jgi.doe.gov/portal/Strsp32124_FD/Strsp32124_FD.info.html
Assembly: https://genome.jgi.doe.gov/portal/Strsp3213_FD/Strsp3213_FD.info.html
Supplementary files format and content: Processed data are contained in the file named raw_counts.csv. The file contains the raw counts measured for all genes in the 4 concatenated genomes. Colums represent the samples as described above

molecule: total RNA

organism: unclassified Streptomyces

source_name: unclassified Streptomyces

growth_protocol: strains were incubated on SFM or ISP2 agar at 30 °C, conjugations were performed on SFM agar. All interaction, molecular profiling and desferrioxamine experiments were performed on ISP2 agar. SFM was prepared per litre tap water: 20 g soya flour (Holland & Barrett), 20 g mannitol (Fisher), 20 g agar (Fisher). ISP2 was prepared per litre distilled water:  4 g yeast extract (Oxoid), 10 g malt extract (Difco), 4 g d-glucose (Fisher), optionally 20 g agar, with the pH adjusted to 7.2 by strong NaOH. To culture the interacting bacteria for molecular profiling analysis, spores of each strain had first been standardised and aliquoted at 1 x 109 CFU ml-1 in 20% glycerol. Before use, these were diluted 10-fold to 1 x 108 CFU ml-1 in ISP2 broth, and 4 µl inoculated 1 cm apart in pairs on ISP2 agar. Each pairing was prepared in quadruplicate for each of the 5 timepoints (n=20 total for each pairing), to allow for the metabolite and RNA sampling in triplicate daily (with one spare). One set of quadruplicate plates was chosen at random to be photographed daily, such that the same four plates were imaged to capture phenotypes, considering our sampling on earlier timepoints is destructive. Images were captured daily on days 2 through to 6 of the quadruplicate set.

extract_protocol:
Streptomyces mycelia was scraped from the agar surface with a spatula, and frozen in liquid nitrogen before storage at -80 °C. Frozen cells were transferred to Lysing Matrix E 2ml tubes (MP Biomedicals LLC) before lysis with a FastPrep bead homogeniser (MP Biomedicals LLC) set to 6.0 m/s for 20 s. Trizol (1ml, ThermoFisher) was added to each tube, mixed by hand inversion and incubated for 5 minutes to allow dissociation of the nucleoproteins complex. Samples were centrifuged at 16,000 x g for 10 min, and 700 µl of supernatant was collected. To each, 140 µl of chloroform was added with incubation at room temperature for 3 min with occasional mixing by hand. After centrifugation for 15 min at 12,000 x g at 4 °C, samples separate to a lower red phenol-chloroform, interphase and colourless upper aqueous phase. The aqueous phase (2 x 140 µl) containing the RNA was transferred to a fresh tube, before removal of 200 µl with the tube tilted to avoid any contamination of the other phases. An equal volume of 200 µl 100% ethanol was added to each. RNA isolation from the resulting samples was performed using the Direct-zol RNA Miniprep kit (Zymo Research) with the manufacturer’s protocol, omitting the on-column DNAse treatment (that had proven ineffective in this experiment as indicated by qPCR). Samples were eluted in 50 µl autoclaved milli-Q water and concentration monitored by Qubit HS and BR RNA assay kits (Thermofisher). To remove residual gDNA in 50 µl samples, the manufacturer’s protocol was followed for TURBO DNase kit (Ambion), with 1 µl DNase per 50 µl input sample, including the DNase removal steps by kit reagent and centrifugation. RNA integrity was measured by recording RINs with a Bioanalyzer 2100 (Agilent).
Library preparation and sequencing was performed by Source Bioscience. The libraries were prepared with the NEBNext rRNA Depletion Kit for Bacteria (NEB) according to the manufacturer’s protocol. During this process, the libraries were indexed with NEBNext Multiplex Oligos for Illumina (NEB). Illumina sequencing was performed at depth 30 million read pairs per sample as 150 b.p. paired end reads. RNA samples were multiplexed before library generation and subsequent sequencing. To confirm our assertion that all four strains could be multiplexed without significant data loss, preliminary RNA-seq was performed with samples from strains B and C run individually, compared with the same samples mixed with each other and all four strains. No significant changes were observed in gene expression due to multiplexing, and therefore this strategy was applied to all further RNA-seq.

tag: cell type

value: unclassified Streptomyces

tag: day

tag: sits-a partner

value: SITS-C

tag: sits-b partner

value: SITS-A

tag: sits-c partner

value: SITS-B

tag: sits-d partner


title: BMDMs, KOCA(KO+Candida albicans)6

city: Hangzhou

first: Jiaqi

last: Huang

state: Zhejiang

address: No. 866 Yuhangtang Road

country: China

institute: Zhejiang University

description:
Library name: Sample 12
KOCA6A

data_processing:
The sequencing data was filtered with SOAPnuke;Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included;Expression level of gene was calculated by RSEM (v1.3.1).
Assembly: Reference Genome Version: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: txt files include FPKM values for each Sample

organism: Mus musculus

source_name: NO

extract_protocol:
Total RNA was extracted from tissues using TRIzol (Invitrogen, Carlsbad, California, USA) according to manual instruction.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).

tag: tissue

value: NO

tag: cell line

value: BMDM

value: Bone marrow-derived macrophages

tag: genotype


title: HEART 8w 5AM MQ2

country: Germany

tag: age

tag: Sex

value: female

tag: treatment


title: BMDMs, KOCA(KO+Candida albicans)5

description:
Library name: Sample 11
KOCA5A


title: Sample 19

description: Library name: 3-2_2_S19


title: human-derived periodontal ligament cell, LPS and DEIX treatment, rep3

city: Jeonbuk

first: JungChae

last: Lee

address: 567, Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, Republic of Korea

country: South Korea

institute: Jeonbuk National University

description: Library name: C3-III

data_processing:
Skewer ver 0.2.2 was used for trmming adaptor sequence.
Trimmed sequence reads were mapped to hg19 using STAR aligner ver 2.6
Read count extraction and normalization were performed using Cufflinks ver 2.2.1
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Homo sapiens

source_name: Human-originated periodontal ligament cells

extract_protocol:
The 1 ug of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.
RNA libraries for RNA-seq were prepared using MGIEasy RNA Directional Library Prep Kit following manufacture's protocols.

value: LPS and DEIX treatment


title: human-derived periodontal ligament cell, LPS and DEIX treatment, rep2

description: Library name: C3-II

value: Human-originated periodontal ligament cells


title: Sample 17

description: Library name: 3-1_3_S17

value: SITS-D


title: HEART 8w 5AM MQ1


title: BMDMs, KOCA(KO+Candida albicans)4

description:
Library name: Sample 10
KOCA4A


title: human-derived periodontal ligament cell, LPS and DEIX treatment, rep1

description: Library name: C3-I


title: BMDMs, KO3

description:
Library name: Sample 9
KO3A


title: Sample 15

description: Library name: 3-1_2b_S15


title: human-derived periodontal ligament cell, LPS treatment, rep3

description: Library name: C2-III

value: LPS treatment


title: BMDMs, KO2

description:
Library name: Sample 8
KO2A


title: Sample 14

description: Library name: 3-1_2_S14


title: human-derived periodontal ligament cell, LPS treatment, rep2

description: Library name: C2-II


title: HEART 8w 5PM MQ2


title: BMDMs, KO1

description:
Library name: Sample 7
KO1A


title: Sample 16

description: Library name: 3-1_2c_S16


title: HEART 8w 5PM MQ1


title: human-derived periodontal ligament cell, LPS treatment, rep1

description: Library name: C2-I


title: Sample 13

description: Library name: 3-1_1_S13


title: BMDMs, WTCA(WT+Candida albicans)6

description:
Library name: Sample 6
WTCA6A

value: Scapf/f


title: HEART 8w 5PM MQ3


title: HEART 1y 5AM NR2

value: 12 months

value: NR


title: Sample 12

description: Library name: 2-4_4_S12


title: BMDMs, WTCA(WT+Candida albicans)5

description:
Library name: Sample 5
WTCA5A


title: human-derived periodontal ligament cell, control, rep2

description: Library name: C1-II

value: control


title: BMDMs, WTCA(WT+Candida albicans)4

description:
Library name: Sample 4
WTCA4A


title: Sample 11

description: Library name: 2-4_3_S11


title: HEART 1y 5AM NR3

value: Heart


title: HEART 1y 5AM NR1


title: human-derived periodontal ligament cell, control, rep1

description: Library name: C1-I


title: HEART 1y 5AM MQ3

value: MQ


title: BMDMs, WT3

description:
Library name: Sample 3
WT3A


title: Sample 10

description: Library name: 2-4_2_S10

value: unclassified Streptomyces

value: SITS-C


title: BMDMs, WT2

description:
Library name: Sample 2
WT2A


title: Sample 9

description: Library name: 2-3_3_S9

value: SITS-B

value: SITS-A


title: HEART 1y 5AM MQ2


title: Sample 8

description: Library name: 2-3_2_S8


title: human-derived periodontal ligament cell, control, rep3

description: Library name: C1-III


title: SL-KM-SI infected with lentivirus carrying  shRNA for VCAN ( TRCN0000033638), rep2

city: Madrid

first: Yosra

last: Berrouayel

address: Arturo Duperier, 4

country: Spain

institute: Universidad Autónoma de Madrid

description: Library name: SKLMS1_shVCAN3_8

data_processing:
Assess sequence quality using FastQC.
Align the sequences to the human GRCh38 reference genome with HISAT2.
Quantify read counts with HTSeq-count.
Analyze the count data and perform differential expression analysis using edgeR and limma-voom in R.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

molecule: polyA RNA

growth_protocol: SK-LMS-1 cells were purchased from ATCC (LGC, Barcelona., Spain). Cells were maintained in 5% CO2 at 37 °C and grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1% glutamine plus antibiotics.

extract_protocol:
Total RNA was obtained by using Rnaeasy mini Kit (Quiagen) and following manufacturer instructions . and RNA integrity was determined by Agilent 2100 Bioanalyzer (RIN range, 9.1–9.9). Reverse stranded library preparation and RNA sequencing were conducted by BGI using the DNBSEQ platform, generating paired-end 100-bp reads.
RNA isolation, converting it to cDNA, ligating adapters, amplifying, circularizing the DNA, and forming DNA nanoballs (DNBs) for high-throughput sequencing.

treatment_protocol: SK-LM-S1 cells were infected with lentiviral particles (PlKO-Puro) produced in 293T cells carrying specifc  shRNA for MAP7 (shERK5-1 Human (TRCN0000010275) and shRNA VCAN-2 Human (TRCN0000033638). Lentiviral production and infections were performed as previously described (Pascual Serra et al., 2020.,  DOI: 10.1016/j.radonc.2020.12.008) . One day after infection, cells were selected with puromycin (Merck) for 72 h (SK-LMS-1: 1 µg/mL) Each sample l was collected from different infections and always 3-4 days after end of selection.


title: SL-KM-SI infected with lentivirus carrying  shRNA for VCAN ( TRCN0000033638), rep3

description: Library name: SKLMS1_shVCAN3_9


title: HEART 1y 5AM MQ1


title: Sample 7

description: Library name: 2-3_1_S7


title: SL-KM-SI infected with lentivirus carrying  shRNA for MAPK7 (TRCN0000010275), rep3

description: Library name: SKLMS1_455_8


title: SL-KM-SI infected with lentivirus carrying  shRNA for VCAN ( TRCN0000033638), rep1

description: Library name: SKLMS1_shVCAN3_6


title: Sample 6

description: Library name: 2-2_3_S6


title: HEART 1y 5PM NR3


title: SL-KM-SI infected with lentivirus carrying  shRNA for MAPK7 (TRCN0000010275), rep2

description: Library name: SKLMS1_455_5


title: BMDMs, WT1

description:
Library name: Sample 1
WT1A

value: NO

value: BMDM


title: Sample 5

description: Library name: 2-2_2_S5


title: HEART 1y 5PM NR2

value: female


title: Lats1-2_deficient_rep2

city: San Francisco

first: Pao-Tien

last: Chuang

address: 555 Mission Bay Blvd. South

country: USA

institute: University of California, San Francisco

data_processing:
remove adaptor with 'trim_galore'
align the reading to genome with 'Hisat2'
sort the SAM file and convert it to BAM file
create table counts with 'featurecounts'
generate DEG table with DeSeq2 in R
Assembly: mm10
Supplementary files format and content: csv file include log2 fold change and p value

source_name: lung

extract_protocol:
Embronic lungs were collected, snap freezed in liquid nitrogen, and RNAs were extracted with the RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: Embryonic lung

tag: developmental stage

value: Lats1f/f; Lats2f/f; SpcCre/+

tag: developmental state

value: mutant sample


title: Lats1-2_deficient_rep1


title: Lats1-2_deficient_rep3


title: HEART 1y 5PM NR1


title: SL-KM-SI infected with lentivirus carrying  shRNA for MAPK7 (TRCN0000010275), rep1

description: Library name: SKLMS1_455_2


title: Control_rep3

value: Control

value: control sample


title: Sample 4

description: Library name: 2-2_1_S4


title: SL-KM-SI infected with lentivirus carrying scramble shRNA, rep3

description: Library name: SKLMS1_EV_7


title: Sample 3

description: Library name: 2-1_3_S3

value: SITS-D


title: HEART 1y 5PM MQ3

value: 12 months


title: Control_rep2


title: Sample 2

description: Library name: 2-1_2_S2


title: SL-KM-SI infected with lentivirus carrying scramble shRNA, rep2

description: Library name: SKLMS1_EV_4


title: HEART 1y 5PM MQ2

value: Heart


title: HEART 1y 5PM MQ1

value: MQ


title: Control_rep1


title: Sample 1

description: Library name: 2-1_1_S1

value: unclassified Streptomyces


title: SL-KM-SI infected with lentivirus carrying scramble shRNA, rep1

description: Library name: SKLMS1_EV_1


title: WTG3.

status: Public on Feb 12 2026

city: Qingdao 266237

first: Kexuan

last: Ma

state: China

address: No. 72 Binhai Road

department: State Key Laboratory of Microbial Technology

institute: Shandong University

description: Library name: sample18

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 50-nt long tags.
Then low quality tags, one copy tags and tags which are not 50-nt long were removed to generate clean tags.
Reference 50-nt tag databases were created from predicted Penicillium oxalicum transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Assembly: Whole Genome Shotgun project in GenBank under the accession number AGIH00000000.1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Penicillium oxalicum

source_name: strain

growth_protocol: The germination of Penicillium oxalicum were inoculated in modifeid vogel's culture medium with 2% glucose as carbon resource for 24 h at 30℃ as the pre-culture, and then mycelia were transferred and grown in the modified Mendal’s medium with 2% glucose or 1% bran + 1% microcrystalline cellulose as carbon resources for 24h. Total RNA was extracted for DGE analysis.

extract_protocol:
Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 50bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: strain

value: 114-2(wild type)

value: Modified Mendal’s medium with 2% glucose as carbon resource


title: WTCW3.

description: Library name: sample15

value: Modified Mendal’s medium with 1percent bran + 1percent microcrystalline cellulose as carbon resource


title: WTG1.

description: Library name: sample16


title: WTCW2.

description: Library name: sample14


title: WTG2.

description: Library name: sample17


title: Dhap5G2

description: Library name: sample11

value: hap5 deletion strain


title: Dhap5CW3

description: Library name: sample9


title: WTCW1.

description: Library name: sample13


title: Dhap5G3

description: Library name: sample12


title: Dhap5G1

description: Library name: sample10


title: Dhap3G3

description: Library name: sample6

value: hap3 deletion strain


title: Dhap3G2

description: Library name: sample5


title: Dhap5CW1

description: Library name: sample7


title: Dhap3CW3

description: Library name: sample3


title: Dhap3CW2

description: Library name: sample2


title: Dhap3G1

description: Library name: sample4


title: Dhap3CW1

description: Library name: sample1


title: Female, YAP, Replicate 2

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: Female_YAP_JP1606
Female_YAP_JP1606

data_processing:
Sequencing reads were aligned to UCSC mouse genome mm10 using STAR aligner. Only uniquely mapped reads were retained for downstream analysis.
Read count mapped to each gene was measured using featureCounts with options ‘-O --fracOverlap 0.8’.
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample

source_name: kidney

extract_protocol:
Total RNA from P3 mouse kidneys were prepared using Single Cell RNA Purification Kit (Norgen). From total RNA, mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, New England Biolabs) following manufacturer’s instructions. Fragmentation of RNA followed by reverse transcription and second strand cDNA synthesis was done using NEBNext RNA First Strand Synthesis Module (E7525L) and NEBNext RNA Second Strand Synthesis Module (E6111L) following manufacturer’s instructions.
The resulting double-stranded cDNA’s were further processed to DNA sequencing libraries using ThruPLEX DNA-seq 12S Kit (R400428, Clontech Laboratories). Libraries were size-selected by gel purification for an average size of 350bp.

value: kidney

value: Slc12a3 Cre/+; C1 YAP/+


title: Male, YAP, Replicate 2

description:
Library name: Male_YAP_JP1604
Male_YAP_JP1604


title: Female, Ctrl, Replicate 2

description:
Library name: Female_Ctrl_JP1605
Female_Ctrl_JP1605


title: Male, Ctrl, Replicate 2

description:
Library name: Male_Ctrl_JP1603
Male_Ctrl_JP1603


title: Severe_MalariaSample_CerebralMalaria_4

type: RNA

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression Profiling

hyb_protocol: Labeled cRNA samples were fragmented at 60°C and hybridized onto an Agilent Custom Plasmodium vivax Gene Expression Microarray 8X15K using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5188-5242)

scan_protocol: The hybridized slides were scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2505C)

data_processing: Data extraction from Images was done using Feature Extraction software  and Quantile Normalization of the data was done in GeneSpring GX.

organism: Plasmodium vivax

source_name: Total RNA, Test Group 2, Sample 4

label_protocol: Samples were labeled using an Agilent Quick-Amp labeling Kit (p/n5190-0442). Total RNA was reverse transcribed at 40°C using an oligo dT primer tagged to a T7 polymerase promoter and converted to double-stranded cDNA. Synthesized double-stranded cDNA was used as the template for cRNA generation. cRNA was generated by in vitro transcription, and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C.

growth_protocol: Clinical samples collected from malaria patients

extract_protocol: RNA from enriched blood was isolated using TRIzol as per manufacture's protocols.

treatment_protocol: Total RNA was extracted from venous blood samples collected from malaria patients. The patients exhibited symptoms categorized as un-complicated (n =6), hepatic dysfunction (n=12), cerebral malaria (n=5).

value: Enriched blood sample

tag: clinical complication

value: Severe malaria - Cerebral Malaria


title: Dhap5CW2

description: Library name: sample8


title: Tissue - WT - Day 8 - Replicate 4

city: Ghent

first: Bruno

last: Verstraeten

state: Oost-Vlaanderen

address: Technologiepark 71

country: Belgium

institute: Ghent University

description: Library name: DSS11_42

data_processing:
The two sets of samples (Casp3/7 villin mice colon tissue and Casp3/7 villin mice colon IECs) were sequenced using paired end Illumina sequencing (150 nt). The set of Casp3/7 villin mice colon IEC samples (4 WT - control, 4 transgenic - control, 6 WT - DSS, 6 transgenic - DSS) was processed by trimming the reads using Trimmomatic (v0.39) with the following parameter settings: ILLUMINACLIP:"adapters.fa":3:30:10:2:True, SLIDINGWINDOW:5:20, MINLEN:36. The adapter sequences in the fasta file are F: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT and R:GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGATGACTATCTCGTATGCCGTCTTCTGCTTG.
Read mapping was performed using STAR  (v2.7.8a) on the GRCm39 mouse genome. Only uniquely mapped reads were kept by setting --outFilterMultimapNmax 1.
BAM files were read into an R (v4.4) environment and a count table was made using the summarizeOverlaps function (mode = "Union") of the GenomicAlignments  package and the GRCm39 gene annotation of Ensembl version 106. One WT – DSS and one transgenic – DSS (DSS_Seq1_12 and DSS_Seq1_15) sample were excluded based on principal component analysis.
The set of Casp3/7 villin mice colon tissue samples (5 Day 0 - WT, 6 Day 0 - transgenic, 5 Day 8 - WT, 6 Day 8 - transgenic) were processed similarly with the following changes: the trimming step was omitted and DESeq2 analysis was done per time point rather than on all samples at once.
Assembly: GRCm39
Supplementary files format and content: count tables

source_name: colon tissue

growth_protocol: Mice were bred in-house using heterozygous breeding pairs to obtain wild-type littermate controls in the VIB Center for Inflammation Research under specific pathogen-free (SPF) conditions. C57BL6/N wildtype mice were purchased from JANVIER LABS and acclimated for at least 1 week before the start of any experiment. All experiments on mice were conducted according to institutional, national, and European animal regulations. Animal protocols were approved by the ethics committee of Ghent University, (EC_LP0024_PVA_2022, EC2025-003). Sex-matched and age-matched co-housed littermates were used through the entire study, except further indicated.

extract_protocol:
For colon tissue RNA extraction, 5mm distal colon was placed in a 2 ml microcentrifuge tube containing one stainless steel bead (5mm mean diameter), add 150 μl Buffer RLT per tube and operate the TissueLyser II for 5 min at 20 Hz to generate tissue homogenate. Keep on ice for 10mins, centrifuge at 12000 g for 10 min at 4 °C, collect supernatant. For IECs, directly lysis with 150 μl Buffer RLT. Next, total RNA was isolated by using the RNeasy Micro Kit (74004, Qiagen) according to the manufacturer’s instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: DSS treatment pertaining to the colon tissue samples was performed by adding 3% DSS in the drinking water for 5 days followed by 3 days of no DSS drinking water. The DSS treatment pertaining to the IEC samples was performed by adding 3% DSS for 3 days to the drinking water of the mice.

value: colon tissue

value: Casp3/7 WT

value: DSS

tag: batch


title: Severe_MalariaSample_CerebralMalaria_1

description: Gene expression Profiling

source_name: Total RNA, Test Group 2, Sample 1


title: Control EC

city: Charlottesville

first: Andrew

middle: C

last: Dudley

state: VA

address: 1340 Jefferson Park Avenue

department: Dept. of Microbiology, Immunology, and Cancer Biology

institute: University of Virginia

description:
Library name: Sample 1
10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, alignment to the mouse reference genome (mm10; refdata-gex-mm10-2020-A), filtering, and UMI counting were performed using Cell Ranger Multi (v9.0.1) via the 10x Genomics Cloud platform (10x Genomics). Default parameters were used unless otherwise specified.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

growth_protocol: Mice were injected subcutaneously into the shaved shoulder with 5 x105 YUMMER1.7 melanoma cells suspended in 100 μl of PBS. Mice were monitored for the appearance of tumors to begin caliper measurements.

extract_protocol:
YUMMER1.7 tumors from control and Dnmt1iECKO mice were harvested and enzymatically dissociated into single-cell suspensions using collagenase II, dispase, and DNase I, followed by mechanical dissociation. Red blood cells were lysed and cells were stained with viability dye and antibodies against CD31 and CD45. Live CD31⁺CD45⁻ tumor endothelial cells were sorted by flow cytometry, washed, and resuspended in PBS supplemented with 0.04% BSA prior to single-cell library preparation.
Single-cell libraries were prepared using the 10x Genomics Chromium Single Cell 3′ Gene Expression GEM-X v4 kit according to the manufacturer’s instructions. Briefly, sorted cells were loaded onto the Chromium Controller for partitioning into GEMs, followed by reverse transcription, cDNA amplification, and library construction. Libraries were sequenced on an Illumina NextSeq 2000 using the P2 XLEAP-SBS 100-cycle kit in paired-end mode, targeting approximately 20,000–25,000 reads per cell.

value: Tumor

value: Melanoma cells

value: 8-10 weeks old

value: female


title: Severe_MalariaSample_HepaticDysfunction_11

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 11

value: Severe malaria - Hepatic Dysfunction


title: Severe_MalariaSample_CerebralMalaria_5

description: Gene expression Profiling

source_name: Total RNA, Test Group 2, Sample 5


title: Severe_MalariaSample_HepaticDysfunction_7

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 7


title: Severe_MalariaSample_HepaticDysfunction_8

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 8


title: Severe_MalariaSample_HepaticDysfunction_6

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 6


title: Severe_MalariaSample_CerebralMalaria_2

description: Gene expression Profiling

source_name: Total RNA, Test Group 2, Sample 2


title: Severe_MalariaSample_HepaticDysfunction_9

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 9


title: Severe_MalariaSample_HepaticDysfunction_4

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 4


title: Severe_MalariaSample_HepaticDysfunction_3

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 3


title: Severe_MalariaSample_HepaticDysfunction_5

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 5


title: Severe_MalariaSample_HepaticDysfunction_2

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 2


title: Severe_MalariaSample_CerebralMalaria_3

description: Gene expression Profiling

source_name: Total RNA, Test Group 2, Sample 3


title: Severe_MalariaSample_HepaticDysfunction_1

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 1


title: Uncomplicated_MalariaSample_4

description: Gene expression Profiling

source_name: Total RNA, Control Sample 4

value: Uncomplicated Malaria


title: Severe_MalariaSample_HepaticDysfunction_12

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 12


title: Uncomplicated_MalariaSample_5

description: Gene expression Profiling

source_name: Total RNA, Control Sample 5


title: 6M_pituitary

city: Nanjing

first: Shanglai

last: Li

address: Nanjing

institute: Nanjing agricultural university

description: Library name: Sample 2

data_processing:
The initial data obtained from sequencing were raw reads, which were then split into the Barcode, Unique molecular identifier (UMI), and inserted fragments of reads according to the unique library structure of scRNA-Seq. Next, the inserted fragment was compared to the reference genome (Ovis_aries, ARS-UI_Ramb_V2.0) used Cell Ranger(v5.0.0).
Assembly: Ovis_aries, ARS-UI_Ramb_V2.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Ovis aries

source_name: pituitary

extract_protocol:
The pituitaries were isolated and washed four times with DPBS (Gibco, Waltham, MA, USA). Based on pituitary tissue morphology, we separated the anterior and posterior pituitary. The anterior pituitary was cleaned using DMEM and immediately cut into 2–3 mm tissue blocks using a scalpel. The tissue blocks were transferred into a centrifuge tube filled with type IV collagenase and placed in a 37℃ water bath for digestion. After filtering the cell suspension through a 40 µm cell strainer, the cells were cleaned with DMEM and collected into a centrifuge tube. Red blood cell lysis buffer was added at room temperature to resuspend cells and lyse the red blood cells for 2–5 min. Equal amounts of PBS-BSA (0.04%) solution were added to stop the lysis of red blood cells. The cells were then washed using PBS-BSA (0.04%) to obtain a single-cell suspension.
The anterior pituitary was processed into a single-cell suspension, which was subjected to cell counting and viability assessments. Subsequently, the cells that met the quality inspection criteria were separated. The prepared single-cell suspension of the anterior pituitary was then divided into Gel Beads in Emulsions (GEMs) using an automated Chromium Controller, followed by the reverse transcription of mRNA into cDNA. Then, the cDNA was amplified and spliced. After library inspection, the cDNA was cyclized via PCR, whereas linear DNA molecules that were not cyclized were digested. Single-stranded circular DNA molecules were replicated via rolling cycle amplification, resulting in the generation of a DNA nanoball (DNB) containing multiple copies of DNA. DNBs of sufficient quality were then loaded onto patterned nanoarrays using the high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis.

value: pituitary


title: Old MOV 1

city: Fayetteville

first: Pieter

middle: Jan

last: Koopmans

state: AR

address: 155 N Stadium Drive

department: Cell and Molecular Biology

institute: University of Arkansas - Fayetteville

description:
Library name: OOV
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery

data_processing:
For total RNA-Seq, raw FASTQ files were imported into Partek Cloud Platfor aligned to mm39 with STAR 2.7.8a with default parameters. Aligned reads were quantified to annovation model and filtered to exclude genes with maximum count of less than 5. Normalized with DESeq2 median ratio. Tested for significance using DESeq2, with lowest average coverage filter of 1 prior to false discovery correction.
For myonuclear DNA RRBS (methylation), Base calling with Illumina Software. Raw FASTQ files were adapter, filled-in nucleotides, and quality trimmed using TrimGalore. The effect of trimming and overall quality distribution was determined using FastQC. Alignment was performed using Bismark. Read totals were called using Bismark Methylation Extractor. Bismark coverage data (.cov files) are generated from Bismark Methylation Extractor and contains the methylated count and total count at each position within the genome
Following library construction, libraries were sequenced on the Illumina Nova NextSeq X Plus System by Novogene to 200 million reads per sample. Raw FASTQ files were imported into Cell Ranger 9.0 for alignment to reference transcriptome, and report of UMIs/reads/nuclei barcodes. h5 files were exported and imported into Python environment, where ambient RNA correction tool CellBender was used. Processed files were imported into Seurat v5, and data quality control was performed by removing nuclei with <200 UMIs, nuclei with >5% of mitochondrial reads, and genes expressed in <3 nuclei.
Assembly: mm39
Supplementary files format and content: For total RNA-seq, DESeq2 Normalized Counts. For RRBS, bismark files.
Supplementary files format and content: For single myonucleus RNA-seq, .h5 Cell Ranger files

molecule: nuclear RNA

source_name: Plantaris, myonuclei

extract_protocol:
Total RNA was extracted via Trizol-Chloroform precpitiation of RNA using Zymo Direct-Zol RNA extraction kit. Genomic DNA was extracted from myonuclei isolated from the plantaris muscle via fluorescent activated nuclear sorting. The Quick-DNA™ Miniprep Plus kit (Zymo Research, D4068) was used as specified in the protocol. For single myonucleus RNA-seq, myonuclei were isolated from plantaris muscle chunks were minced with scissors in homogenization buffer (500 µl HEPES (1 M) 3 ml KCl (1 M) 250 µl spermidine (100 mM) 750 µl spermine tetrahydrochloride (10 mM) 10 ml EDTA (10 mM) 250 µl EGTA (100 mM) 2.5 ml MgCl (100 mM) 5.13 g sucrose, Dounce homogenized on ice with a plastic pestle in homogenization buffer, then passed through a 40 µm and 20 µm filter into directly into the MACSQuant High Speed Tyto Cardtridge. PI was added to label nuclei. Fluorescently labeled nuclei (GFP+/PI+) were purified via Fluorescence-activated nuclear sorting (FANS) and sorted into re-suspension buffer (1X PBS, 1% BSA, 0.2U/uL RNase inhibitors).
Total RNA-seq libraries were prepared for seqeuencing using standard Illumina protocols and underwent 150 bp PE sequencing. The DNA RRBS was rered to Zymo Research Corporation (RRBS Basic Srvise Package, 15-20 million read pairs per sample). Myouclei were mixed with reverse transcriptase buffer and loaded into the 10X Chromium system using the Single Cell 3’ Reagent Kit v4 according to the manufacturer’s protocol. Following library construction, libraries were sequenced on the Illumina NovaSeq X Plus System at the Novogene.

treatment_protocol: Mice were treated with doxycycline for 7 days to label myonuclei with green fluorescent protein, followed by a 7-13 day washout period. Then mice underwent 72 hours of ambulation after synergist ablation mechanical overload (MOV) surgery.

value: Plantaris, myonuclei

value: HSA-GFP

value: 72 Hour MOV


title: Young Sham 1

description:
Library name: YSH
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery

value: 72 hour Sham


title: Severe_MalariaSample_HepaticDysfunction_10

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 10


title: Old Sham 1

description:
Library name: OSH
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery


title: BAT, Full length Runx2, replicate 2, RNA-seq

city: Guangzhou

last: He

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China

department: Department of Basic Research

institute: Guangzhou National Laboratory

description: Library name: Runx2_control_rep2

data_processing:
Raw sequencing reads were processed by fastp with parameter "-q 20 --detect_adapter_for_pe --trim_poly_g" to trim the adapter and poly G end. Then reads were mapped to mouse reference genome (mm39) by STAR in 2-pass mode. Then, we use featureCounts to count expressed reads under each gene.
Assembly: mm39
Supplementary files format and content: count matrix

source_name: BAT

extract_protocol:
RNA are havested using RN28-EASYspin Plus kit
RNA libraries were constructed with VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (NR604-01/02) following the manufacture’s protocol and quantified by Qubit (invitrogen, USA) for cluster generation.

value: BAT

value: Mature brown adipocytes

value: Full length Runx2

value: Brown adipocyte differentiation


title: BAT, delete Runx2 IDR, replicate 2, RNA-seq

description: Library name: Runx2_delete_IDR_rep2

value: delete Runx2 IDR


title: BAT, Full length Runx2, replicate 1, RNA-seq

description: Library name: Runx2_control_rep1


title: Uncomplicated_MalariaSample_1

description: Gene expression Profiling

source_name: Total RNA, Control Sample 1

value: Enriched blood sample


title: 3M_pituitary

description: Library name: Sample 1


title: Uncomplicated_MalariaSample_2

description: Gene expression Profiling

source_name: Total RNA, Control Sample 2


title: Young MOV 1

description:
Library name: YOV
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery


title: HFD, WT, replicate 2, RNA-seq

description: Library name: HFD_control_rep2

source_name: IWAT

value: IWAT

value: WT


title: HFD, WT, replicate 3, RNA-seq

description: Library name: HFD_control_rep3


title: HFD, Knock out Runx1, replicate 1, RNA-seq

description: Library name: HFD_Runx1-KO_rep1

value: Knock out Runx1


title: HFD, Knock out Runx1, replicate 3, RNA-seq

description: Library name: HFD_Runx1-KO_rep3


title: HFD, WT, replicate 1, RNA-seq

description: Library name: HFD_control_rep1


title: BAT, delete Runx2 IDR, replicate 1, RNA-seq

description: Library name: Runx2_delete_IDR_rep1


title: BAT, WT, Runx2_delta_IDR_HA, CUT &Tag, replicate 2

description: Library name: Runx2_delta_IDR_HA_rep2

library_source: genomic

data_processing:
Raw sequencing reads were processed by fastp with parameter "-q 20 --detect_adapter_for_pe --trim_poly_g" to trim the adapter and poly G end. Then reads were mapped to mouse reference genome (mm39) by bowtie2 with default parameter. Properly mapped high MAPQ reads were remained by samtools view "-f 2 -q 20". Then PCR duplicates were removed by picard tools. Finally, we use macs2 with "-q 0.05 -B --nomodel -f BAMPE --keep-dup all" to call peaks.
Assembly: mm39
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
For ChIP-seq, brown preadipocytes or brown adipocytes were fixed with 1% formaldehyde for 10min and the reaction was quenched by 0.125M glycine. Cells were then washed with PBS for two times. Cells were lysed in ChIP buffer (1% SDS, 50 mM Tris-HCl, pH 8.0, 10 mM EDTA, and protease inhibitor cocktail) for 30 min at 4°C. The DNA was fragmented to 200-500bp by sonication and centrifuged at 12,000 g for 5min. The supernatant was diluted with ChIP IP buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl and protease inhibitor cocktail). For the CUT&Tag assay was performed using the NovoNGS® CUT &Tag 2.0 A High-Sensitivity Kit (for Illuina®) (Cat# N259-YH01-01A, Novoprotein Scientific, Inc.,) following the manufacturer's protocol.
The ChIP DNA library was constructed with VAHTS Turbo DNA Library Prep Kit for Illumina (Vazyme Biotech) according to the manufacturer’s instructions. For the CUT&Tag assay was performed using the NovoNGS® CUT &Tag 2.0 A High-Sensitivity Kit (for Illuina®) (Cat# N259-YH01-01A, Novoprotein Scientific, Inc.,) following the manufacturer's protocol.

value: Brown pre-adipocytes

value: Delat Runx2 IDR

tag: chip antibody

value: HA


title: BAT, WT, Runx2_HA, CUT &Tag, replicate 2

description: Library name: Runx2_HA_rep2

tag: cell type


title: BAT, WT, Runx2_delta_IDR_HA, CUT &Tag, replicate 1

description: Library name: Runx2_delta_IDR_HA_rep1


title: BAT, WT, Runx2_HA, CUT &Tag, replicate 1

description: Library name: Runx2_HA_rep1


title: HFD, Knock out Runx1, replicate 2, RNA-seq

description: Library name: HFD_Runx1-KO_rep2


title: BAT, Runx2 IDR delta, HDAC2, CUT &Tag, replicate 2

description: Library name: Cell_Runx2_delta_HDAC2_rep2


title: OOV5_GFP_2

description:
Library name: zr17671_39
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery


title: OOV6_GFP

description:
Library name: zr17671_35
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery


title: BAT, Runx2 IDR delta, EP300, CUT &Tag, replicate 2

description: Library name: Cell_Runx2_delta_IDR_Ep300_rep2


title: OOV4_GFP

description:
Library name: zr17671_31
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery


title: OSH5_GFP

description:
Library name: zr17671_25
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery


title: BAT, WT, HDAC2, CUT &Tag, replicate 2

description: Library name: Cell_Runx2_HDAC2_rep2


title: BAT, WT, EP300, CUT &Tag, replicate 2

description: Library name: Cell_Runx2_EP300_rep2


title: OSH7_GFP

description:
Library name: zr17671_29
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery


title: BAT, WT, HDAC2, CUT &Tag, replicate 1

description: Library name: Cell_Runx2_HDAC2_rep1


title: BAT, Runx2 IDR delta, HDAC2, CUT &Tag, replicate 1

description: Library name: Cell_Runx2_delta_HDAC2_rep1


title: YOV6_GFP

description:
Library name: zr17671_19
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery


title: YOV7_GFP

description:
Library name: zr17671_21
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery


title: WT_RNA-seq_GO_rep3

city: Davis

first: Satoshi

middle: H

last: Namekawa

state: CA

address: One Shields Avenue

department: Department of Molecular and Cellular Biology

institute: University of California, Davis

description: Library name: WT_RNA-seq_GO_rep3

data_processing:
Raw paired-end RNA-seq reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.7) were aligned to the mouse (GRCm38/mm10) genome using STAR (version STAR_2.5.4b) with following options: --outSAMtype BAM SortedByCoordinate; --twopassMode Basic; --outFilterType BySJout; --outFilterMultimapNmax 1; --winAnchorMultimapNmax 50; --alignSJoverhangMin 8; --alignSJDBoverhangMin 1; --outFilterMismatchNmax 999; --outFilterMismatchNoverReadLmax 0.04; --alignIntronMin 20; --alignIntronMax 1000000; --alignMatesGapMax 1000000 for unique alignments.
To quantify aligned reads in RNA-seq, aligned read counts for each gene were generated using featureCounts (v2.0.1), which is part of the Subread package based on annotated genes (GENCODE vM25: GRCm38.p6).
The transcripts per million (TPM) values of each gene were for comparative expression analyses.
De novo transcriptome assemblies from strand-specific RNA-seq libraries were generated using StringTie2 (v2.1.2) with default parameters.
Assembly: mm10
Supplementary files format and content: Gencode_vM25_TPM.txt

source_name: primary cells

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN, Cat # 74034) according to the manufacturer’s instructions and the External RNA Controls Consortium (ERCC) RNA Spike-In Mix (Invitrogen, 4456740) was added to total RNA.
Ribosomal RNA was depleted from total RNA using NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) (NEB, E7400L). Library preparation was performed with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB, E7760S) according to the manufacturer’s instruction. Prepared RNA-seq libraries were sequenced on the NovaSeq X Plus system (Illumina) with paired-ended 150-bp reads.

value: ovary

value: P6-7 growing oocytes


title: YOV5_GFP

description:
Library name: zr17671_17
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery

value: Plantaris, myonuclei

value: HSA-GFP


title: BAT, WT, EP300, CUT &Tag, replicate 1

description: Library name: Cell_Runx2_EP300_rep1


title: BAT, Runx2 IDR delta, EP300, CUT &Tag, replicate 1

description: Library name: Cell_Runx2_delta_IDR_Ep300_rep1


title: YOV4_GFP

description:
Library name: zr17671_15
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery

value: 72 Hour MOV


title: OSH4_GFP

description:
Library name: zr17671_23
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery

value: 72 hour Sham


title: YSH3_GFP

description:
Library name: zr17671_5
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery


title: WT_RNA-seq_GO_rep2

description: Library name: WT_RNA-seq_GO_rep2


title: WT_RNA-seq_NGO_rep3

description: Library name: WT_RNA-seq_NGO_rep3

value: P5-6 non-growing oocytes


title: WT_RNA-seq_NGO_rep1

description: Library name: WT_RNA-seq_NGO_rep1


title: DGH_NINT3

city: Parma

first: Ilaria

last: Minato

address: Parco Area delle Scienze 23/a

country: Italy

institute: Università di Parma

data_processing:
Reads were quality controlled using the FastQC tool
Reads were aligned to the Rattus norvegicus genome (v. 6) using STAR
Counts were calculated using the HTSeq Python package and the Ensembl annotation v. 103
Assembly: rn6
Supplementary files format and content: tab-delimited file includes raw counts for each sample

organism: Rattus norvegicus

source_name: Total Right Lung Homogenate

extract_protocol:
The fresh right lungs of each animal were rinsed and immediately collected in RNAlater™ (Sigma) for RNA preservation, and then they were homogenised in QIAzol® lysis reagent (QIAGEN) with gentleMACS™ Dissociator (Miltenyi Biotec). RNA was extracted from the lung homogenates using the QIAcube robotic workstation with the miRNeasy Mini Kit (QIAGEN), including the DNase digestion protocol.
The QuantSeq FWD (Lexogen) kit was used to prepare libraries for RNA-Seq, following manufacturer's protocol.

treatment_protocol:
Male Sprague-Dawley rats (Charles River) were intratracheally injected with BLM (1 U/kg/0.5 m; Baxter Oncology GmbH) at day 0 and after 4 days using a Penn Century Microsprayer (Penn-Century Inc.). The same procedure was performed to control animals using a saline solution.
Seven days after the first BLM dose, the animals treated with BLM were randomly divided into two groups, one of which was destined to receive the test substance, Nintedanib 100 mg/kg (Nintedanib free base – Carbosynth, Compton – UK; Group name: NINT) and the other to receive its vehicle (Methylcellulose 0.5% in water; Group name: BLM). The test substance and the vehicle were administered daily by oral gavage (per os, PO) for three weeks. For the weeks of treatment, the animals treated with SAL received the vehicle (Group name: SAL).

tag: strain

value: Sprague Dawley

value: male

value: Total Right Lung Homogenate

value: Bleomycin 1 U/kg/0.5 ml - IT administration (day 0 and day 4) + Nintedanib 100 mg/kg - PO administration (from day 7, daily for 3 weeks)

tag: termination day

value: Day 28


title: DGF_NINT1


title: DGI_NINT4


title: DGG_NINT2


title: WT_RNA-seq_P1O_rep3

description: Library name: WT_RNA-seq_P1O_rep3

value: P1 oocytes

value: WT


title: WT_RNA-seq_NGO_rep2

description: Library name: WT_RNA-seq_NGO_rep2


title: DGE_BLM4

value: Bleomycin 1 U/kg/0.5 ml - IT administration (day 0 and day 4) + Vehicle (Methylcellulose)- PO administration (from day 7, daily for 3 weeks)


title: WT_RNA-seq_P1O_rep1

description: Library name: WT_RNA-seq_P1O_rep1


title: WT_RNA-seq_E18O_rep3

description: Library name: WT_RNA-seq_E18O_rep3

value: E18.5 oocytes


title: WT_RNA-seq_E18O_rep2

description: Library name: WT_RNA-seq_E18O_rep2


title: DGB_BLM1


title: WT_RNA-seq_GO_rep1

description: Library name: WT_RNA-seq_GO_rep1


title: DGC_BLM2


title: DGA_SAL4

value: Saline Solution - IT administration (day 0 and day 4) + Vehicle (Methylcellulose)- PO administration (from day 7, daily for 3 weeks)


title: WT_RNA-seq_E18O_rep1

description: Library name: WT_RNA-seq_E18O_rep1

value: ovary


title: WT_CT_GO_S5P-PolII_rep2

description: Library name: WT_CT_GO_S5P-PolII_rep2

data_processing:
Raw paired-end CUT&Tag reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.7) were aligned to either the mouse (GRCm38/mm10) genomes using bowtie2 (version 2.3.3.1) with with options: --end-to-end --very-sensitive --no-mixed --no-discordant -I 10 -X 700.
The aligned reads were filtered to remove alignments mapped to multiple locations by calling grep with the -v option before being subjected to downstream analyses.
PCR duplicates were removed using the ‘MarkDuplicates’ command in Picard tools (version 2.23.8) (https://broadinstitute.github.io/picard/, Broad Institute).
Spike-in normalization was implemented using the exogenous scaling factor computed from the dm6 aligned files (scale factors = 10000/spike-in reads).
Biological replicates were pooled for visualization and other analyses after validation of reproducibility.
Peak calling for CUT&Tag data was performed using the Sparse Enrichment Analysis for CUT&RUN (SEACR) (https://seacr.fredhutch.org/ ) by selecting the top 1% enriched regions in stringent mode with parameters’-c 0.01 -n norm -m stringent’.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
FACS-sorted cells were isolated from ovaries and pooled as one replicate.
CUT&Tag libraries of oocytes were generated according to the protocol (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3) using CUTANA™ pAG-Tn5 (Epicypher, 15-1017). To perform quantitative spike-in CUT&Tag, Drosophila S2 cells were added to mouse oocytes at a fixed ratio (e.g. 5,000 S2 cells to 10,000 mouse oocytes) at the beginning of each reaction. CUT&Tag libraries were prepared using NEBNext HiFi 2x PCR Master mix (NEB, M0541L) according to the protocol (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3 ).

value: P6-7 growing oocytes


title: DFZ_SAL3


title: WT_CT_E18O_S5P-PolII_rep2

description: Library name: WT_CT_E18O_S5P-PolII_rep2


title: WT_CT_GO_S5P-PolII_rep1

description: Library name: WT_CT_GO_S5P-PolII_rep1


title: WT_CT_NGO_S5P-PolII_rep1

description: Library name: WT_CT_NGO_S5P-PolII_rep1


title: WT_RNA-seq_P1O_rep2

description: Library name: WT_RNA-seq_P1O_rep2


title: WT_CT_E18O_S5P-PolII_rep1

description: Library name: WT_CT_E18O_S5P-PolII_rep1


title: DGD_BLM3


title: WT_CT_NGO_S5P-PolII_rep2

description: Library name: WT_CT_NGO_S5P-PolII_rep2


title: DFY_SAL2


title: WT, Day3, replicate3

city: Los Angeles

first: Yiqian

last: Gu

address: 5000D Terasaki Life Sciences Building

institute: University of California Los Angeles

description: Library name: Wt3_d3

data_processing:
Utilizing STAR-2.7.11a, reads were aligned to the reference genome mm10. The "mappedReadsPerGene.out.tab" files were utilized to generate a count matrix combining all samples.
Assembly: mm10
Supplementary files format and content: .mappedReadsPerGene.out.tab

source_name: heart scar tissue

extract_protocol:
mice were anesthetized with isoflurane followed by cervical dislocation post cryo injury day 3. The heart was rapidly excised, and the injured region was dissected and snap-frozen in liquid nitrogen. The tissue was homogenized in 1 ml of TRIzol (Invitrogen, 15596026) using ceramic beads with a BEAD RUPTOR 24 homogenizer (Omni, 19-070). The aqueous phase was collected, mixed with ethanol, and processed using the Qiagen RNeasy Mini Kit (Qiagen, 74134) according to the manufacturer’s instructions."
KAPA mRNA HyperPrep kit

value: heart scar tissue

value: cryo injury


title: KO, Day3, replicate2

description: Library name: KO2_d3

value: KO


title: WT, Day3, replicate1

description: Library name: Wt1_d3


title: WT_CT_GO_S2P-PolII_rep1

description: Library name: WT_CT_GO_S2P-PolII_rep1


title: KO, Day3, replicate1

description: Library name: KO1_d3


title: DFX_SAL1


title: WT, Day3, replicate2

description: Library name: Wt2_d3


title: WT_CT_NGO_S2P-PolII_rep2

description: Library name: WT_CT_NGO_S2P-PolII_rep2


title: EF45

city: los angeles

first: Guoping

last: Fan

state: ca

address: 695 Charles E Young Drive South

department: Human Genetics

institute: university of california, los angeles

data_processing:
Library strategy: RNA-BS-Seq
All the sequenced raw reads were filtered and trimmed with Trim Galore (version 0.4.1)
the clean reads were mapped to the mouse genome (mm10) to determine the methylation level of cytosine by BS-RNAs tools
Genome_build: mm10
Supplementary_files_format_and_content: cov files with total counts as 4th column and methylated counts as 5th column

source_name: fibroblasts

growth_protocol: Fibroblast cell lines were isolated from the tails of WT, Het and Hom mice littermates of the same gender and cultured at 37 °C in fibroblast medium: DMEM medium containing 10% FBS, 1X NEAA and 1% (v/v) penicillin-streptomycin as described (Ilsley et al., 2018). Cell lines were validated by DNA sequencing and routinely tested for mycoplasma (Universal Mycoplasma Detection Kit, ATCC).

extract_protocol:
In vitro transcribed pTRI-Xef RNA was used as negative control in the amplicon-bsRNA-seq experiments. RNAs were transcribed using the MEGAscript® T7 Kit (Life Technologies) according to the manufacturer’s protocol. Total mRNA of mouse fibroblasts was extracted by the Dynabeads™ mRNA DIRECT™ Purification Kit (Thermo Fisher Scientific). Then 1 μg of the mRNA combined with 1 ng pTRI-Xef RNA were used for bisulfite treatment by EZ Methylation Kit (Zymo) following the protocols provided by the manufacturer.
After bisulfite conversion, the purified RNA was used for library construction by NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB).

tag: sirna

value: Dnmt1 siRNA treatment


title: WT_CT_GO_S2P-PolII_rep2

description: Library name: WT_CT_GO_S2P-PolII_rep2


title: WT_CT_NGO_S2P-PolII_rep1

description: Library name: WT_CT_NGO_S2P-PolII_rep1

value: P5-6 non-growing oocytes


title: KO, Day3, replicate3

description: Library name: KO3_d3


title: WT_CT_E18O_S2P-PolII_rep2

description: Library name: WT_CT_E18O_S2P-PolII_rep2


title: EF1

value: Control


title: WT_CT_E18O_S2P-PolII_rep1

description: Library name: WT_CT_E18O_S2P-PolII_rep1


title: WT_CT_NGO_Total-PolII_rep2

description: Library name: WT_CT_NGO_Total-PolII_rep2


title: DD1


title: WT_CT_GO_Total-PolII_rep2

description: Library name: WT_CT_GO_Total-PolII_rep2


title: DD4


title: cor  input

data_processing:
All the sequenced raw reads were filtered and trimmed with Trim Galore (version 0.4.1)
the clean reads were mapped to the mouse genome (mm10) using Hisat2
the number of reads uniquely mapped to each gene was determined using featurecount
Genome_build: mm10
Supplementary_files_format_and_content: reads count per gene

source_name: cortex

extract_protocol:
For Dnmt1 ripseq, 10 million  cells were collected and crosslinking was carried out by adding formaldehyde to a final concentration of 1%.  Rabbit anti-Dnmt1 antibody (Cosmo Bio, BAM-70-201) was used for immunoprecipitation.For RNA m5C immunoprecipitation, total mRNA was extracted by Dynabeads™ mRNA DIRECT™ Purification Kit (Thermo Fisher Scientific). Then 1 μg mRNA was incubated with anti-5-methylcytosine antibody (Diagenode, MAb-081-100). For the precipitated RNA, both ribosomal RNA (rRNA) depletion-based method and polyA enrichment- based method were used.
purfied mRNA were used for library construction by using the NEBNext® Ultra™ II RNA Library Prep Kit (NEB) following manufacturer’s recommendations.

value: input

tag: antibody

value: anti-IgG antibody


title: WT_CT_NGO_Total-PolII_rep1

description: Library name: WT_CT_NGO_Total-PolII_rep1


title: WT_CT_GO_Total-PolII_rep1

description: Library name: WT_CT_GO_Total-PolII_rep1


title: Hom cor m5C RIP

value: Hom

value: anti-5-Methylcytosine antibody


title: WT_CT_NGO_TCF12_rep2

description: Library name: WT_CT_NGO_TCF12_rep2


title: HOM fb m5C RIP

source_name: Fibroblast


title: WT_CT_E18O_Total-PolII_rep2

description: Library name: WT_CT_E18O_Total-PolII_rep2


title: Wt fb m5C RIP2


title: HET fb m5C RIP

value: Het


title: Het cor m5C RIP


title: WT_CT_E18O_Total-PolII_rep1

description: Library name: WT_CT_E18O_Total-PolII_rep1

value: WT


title: WT_CT_NGO_TCF12_rep1

description: Library name: WT_CT_NGO_TCF12_rep1


title: Wt fb m5C RIP1


title: WT_CT_NGO_TCF3_rep1

description: Library name: WT_CT_NGO_TCF3_rep1


title: fb input


title: Wt cor m5C RIP


title: WT_CT_NGO_TCF3_rep2

description: Library name: WT_CT_NGO_TCF3_rep2


title: Female, Ctrl, Replicate 1

description:
Library name: Female_Ctrl_JP1644
Female_Ctrl_JP1644

source_name: kidney

value: kidney


title: Hom Dnmt1 RIP2

value: anti-Dnmt1 antibody


title: Male, YAP, Replicate 1

description:
Library name: Male_YAP_JP1643
Male_YAP_JP1643

value: Slc12a3 Cre/+; C1 YAP/+


title: Female, YAP, Replicate 1

description:
Library name: Female_YAP_JP1642
Female_YAP_JP1642


title: Het Dnmt1 RIP1


title: Male, Ctrl, Replicate 1

description:
Library name: Male_Ctrl_JP1641
Male_Ctrl_JP1641


title: IWAT, Knock out Runx2, HDAC2 CUT&Tag, replicate 2

description: Library name: Tissue_KO_Runx2_HDAC2_rep2

source_name: White adipose

value: White adipose

value: Knock out Runx2

value: Adipoq-cre:Runx2 KO


title: Wt Dnmt1 RIP2


title: Wt Dnmt1 RIP1


title: peripheral blood 38

type: genomic

city: Cusano Milanino

first: Luciano

last: Calzari

state: MI

address: Via Zucchi 18

institute: IRCCS Istituto Auxologico Italiano

description: Case

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 850K EPIC Beadchip using standard Illumina protocol

scan_protocol: Fluorescence intensities were captured by using the fluorescent scanner Illumina HiScan SQ (Illumina).

data_processing: Quality control, pre-processing and generation of β-values matrix were performed by using the ChAMP package (release 2.32.0) package, implemented R environment (version 4.3.1): after the quality control/pre-processing step, 754964 probes and 38 samples were retained.

label: Cy5, Cy3

source_name: peripheral blood lymphocytes

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from peripheral blood lymphocytes of individuals (Automated Extractor, Tecan Group Ltd. and Wizard Genomic DNA Purification Kit (Ref: A1125), Promega). Quality control and quantification of DNA was assessed by visualization of genomic DNA (gDNA) on 1% agarose gel electrophoresis and by using NanoPhotometer Pearl (Implen GmbH).

value: Whole Blood

value: M


title: IWAT, Knock out Runx2, HDAC2 CUT&Tag, replicate 1

description: Library name: Tissue_KO_Runx2_HDAC2_rep1


title: IWAT, Knock out Runx1, HDAC2 CUT&Tag, replicate 2

description: Library name: Tissue_KO_Runx1_HDAC2_rep2

value: Knock out Runx1

value: Adipoq-cre:Runx1 KO


title: peripheral blood 36

description: Case


title: peripheral blood 37

description: Case


title: peripheral blood 35

description: Case


title: Hom Dnmt1 RIP1


title: IWAT, Knock out Runx1, HDAC2 CUT&Tag, replicate 1

description: Library name: Tissue_KO_Runx1_HDAC2_rep1


title: Het Dnmt1 RIP2


title: IWAT, Knock out Runx2, HDAC1 CUT&Tag, replicate 2

description: Library name: Tissue_KO_Runx2_HDAC1_rep2


title: IWAT, HDAC2 CUT&Tag, replicate 2

description: Library name: Tissue_HDAC2_rep2


title: IWAT, Knock out Runx2, HDAC1 CUT&Tag, replicate 1

description: Library name: Tissue_KO_Runx2_HDAC1_rep1


title: IWAT, Knock out Runx1, HDAC1 CUT&Tag, replicate 2

description: Library name: Tissue_KO_Runx1_HDAC1_rep2


title: IWAT, HDAC2 CUT&Tag, replicate 1

description: Library name: Tissue_HDAC2_rep1


title: peripheral blood 32

description: Case


title: IWAT, Knock out Runx1, HDAC1 CUT&Tag, replicate 1

description: Library name: Tissue_KO_Runx1_HDAC1_rep1


title: peripheral blood 29

description: Case


title: IWAT, HDAC1 CUT&Tag, replicate 2

description: Library name: Tissue_HDAC1_rep2


title: IWAT, HDAC1 CUT&Tag, replicate 1

description: Library name: Tissue_HDAC1_rep1


title: peripheral blood 30

description: Case


title: peripheral blood 28

description: Case


title: peripheral blood 27

description: Case


title: IWAT, Knock out Runx2, H3K27ac CUT&Tag, replicate 2

description: Library name: Tissue_KO_Runx2_H3K27ac_rep2


title: peripheral blood 26

description: Case


title: IWAT, Knock out Runx1, H3K27ac CUT&Tag, replicate 1

description: Library name: Tissue_KO_Runx1_H3K27ac_rep1


title: peripheral blood 25

description: Case


title: peripheral blood 24

description: Case


title: IWAT, Knock out Runx2, H3K27ac CUT&Tag, replicate 1

description: Library name: Tissue_KO_Runx2_H3K27ac_rep1


title: IWAT, Runx2 CUT&Tag, replicate 2

description: Library name: Tissue_Runx2_rep2


title: peripheral blood 23

description: Case


title: IWAT, Runx2 CUT&Tag, replicate 1

description: Library name: Tissue_Runx2_rep1


title: IWAT, Knock out Runx1, H3K27ac CUT&Tag, replicate 2

description: Library name: Tissue_KO_Runx1_H3K27ac_rep2


title: IWAT, Runx1 CUT&Tag, replicate 2

description: Library name: Tissue_Runx1_rep2


title: peripheral blood 22

description: Case


title: IWAT, Runx1 CUT&Tag, replicate 1

description: Library name: Tissue_Runx1_rep1


title: peripheral blood 20

description: Case


title: IWAT, H3K27ac CUT&Tag, replicate 1

description: Library name: Tissue_H3K27ac_rep1


title: peripheral blood 19

description: Case


title: BAT, OE Runx2, HDAC2 CUT&Tag, replicate 2

description: Library name: Cell_OE_Runx2_HDAC2_rep2

value: BAT

value: Mature brown adipocytes

value: over expression Runx2

value: Brown adipocyte differentiation


title: BAT, OE Runx2, HDAC2 CUT&Tag, replicate 1

description: Library name: Cell_OE_Runx2_HDAC2_rep1


title: peripheral blood 18

description: Case


title: BAT, OE Runx1, HDAC2 CUT&Tag, replicate 2

description: Library name: Cell_OE_Runx1_HDAC2_rep2

value: over expression Runx1


title: peripheral blood 15

description: Case


title: peripheral blood 17

description: Case


title: peripheral blood 16

description: Case


title: BAT, HDAC2 CUT&Tag, replicate 2

description: Library name: Cell_HDAC2_rep2


title: peripheral blood 14

description: Case


title: peripheral blood 13

description: Case


title: BAT, HDAC2 CUT&Tag, replicate 1

description: Library name: Cell_HDAC2_rep1


title: BAT, OE Runx1, HDAC2 CUT&Tag, replicate 1

description: Library name: Cell_OE_Runx1_HDAC2_rep1


title: peripheral blood 12

description: Case


title: peripheral blood 11

description: Case


title: BAT, OE Runx2, HDAC1 CUT&Tag, replicate 1

description: Library name: Cell_OE_Runx2_HDAC1_rep1


title: BAT, OE Runx2, HDAC1 CUT&Tag, replicate 2

description: Library name: Cell_OE_Runx2_HDAC1_rep2


title: peripheral blood 10

description: Case


title: BAT, OE Runx1, HDAC1 CUT&Tag, replicate 2

description: Library name: Cell_OE_Runx1_HDAC1_rep2


title: peripheral blood 8

description: Case


title: BAT, HDAC1 CUT&Tag, replicate 2

description: Library name: Cell_HDAC1_rep2


title: BAT, OE Runx1, HDAC1 CUT&Tag, replicate 1

description: Library name: Cell_OE_Runx1_HDAC1_rep1


title: peripheral blood 9

description: Case


title: peripheral blood 6

description: Case


title: BAT, OE Runx2, H3K27ac CUT&Tag, replicate 2

description: Library name: Cell_OE_Runx2_H3K27ac_rep2


title: peripheral blood 7

description: Case


title: BAT, HDAC1 CUT&Tag, replicate 1

description: Library name: Cell_HDAC1_rep1


title: BAT, OE Runx2, H3K27ac CUT&Tag, replicate 1

description: Library name: Cell_OE_Runx2_H3K27ac_rep1


title: BAT, OE Runx1, H3K27ac CUT&Tag, replicate 2

description: Library name: Cell_OE_Runx1_H3K27ac_rep2


title: BAT, OE Runx1, H3K27ac CUT&Tag, replicate 1

description: Library name: Cell_OE_Runx1_H3K27ac_rep1


title: peripheral blood 5

description: Case


title: peripheral blood 4

description: Case


title: peripheral blood 3

description: Case


title: BAT, H3K27ac CUT&Tag, replicate 2

description: Library name: Cell_H3K27ac_rep2


title: peripheral blood 1

description: Case


title: BAT, H3K27ac CUT&Tag, replicate 1

description: Library name: Cell_H3K27ac_rep1


title: peripheral blood 2

description: Case


title: Kelly, Erastin, rep3

city: Göteborg

first: Ganesh

last: Umapathy

address: Medicinaregatan 9 a-b

department: Sahlgrenska University Hospital

country: Sweden

institute: University of Gothenburg

description: Library name: Sample 12

data_processing:
Sequence reads were trimmed for adaptor/low-quality sequences using FASTX and Trimmomatic.
Trimmed reads were mapped to the human genome (GRCh38) and quantified per gene using HTSeq.
Differential gene expression analysis was performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: RNA-seq data are provided in merged comma-separated text files (CSV) for Kelly and AS
Supplementary files format and content: csv files include total counts for each Sample

source_name: KELLY

growth_protocol: Kelly and SK-N-AS cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics at 37C with 5% CO2.

extract_protocol:
RNA was harvested using ReliaPrep RNA Miniprep system (Promega #6111).
Purified RNA was sent to Novogene UK for library preparation and sequencing

treatment_protocol: KELLY and SK-N-AS neuroblastoma cell lines treated with 1 μM and 2 μM Erastin for 24 hours, respectively

value: KELLY

value: Neuronal

value: Erastin (Era)

tag: time

value: 24 hours


title: Kelly, Erastin, rep1

description: Library name: Sample 10


title: Kelly, Erastin, rep2

description: Library name: Sample 11


title: BAT, Runx2, ChIP-seq

description: Library name: Cell_Runx2

data_processing:
Raw sequencing reads were processed by fastp with parameter "-q 20 --detect_adapter_for_pe --trim_poly_g" to trim the adapter and poly G end. Then reads were mapped to mouse reference genome (mm39) by bowtie2 with default parameter. Properly mapped high MAPQ reads were remained by samtools view "-f 2 -q 20". Then PCR duplicates were removed by picard tools. Finally, we use macs2 with "-q 0.05 -B --nomodel -f BAMPE --keep-dup all" to call peaks.
Assembly: mm39
Supplementary files format and content: narrowPeak

value: Brown pre-adipocytes

value: WT


title: BAT, Runx2 input, ChIP-seq

description: Library name: Cell_Runx2_input

value: input


title: Kelly, Control, rep3

description: Library name: Sample 9

value: DMSO


title: BAT, Runx1 input, ChIP-seq

description: Library name: Cell_Runx1_input


title: BAT, Runx1, ChIP-seq

description: Library name: Cell_Runx1


title: Day 1, replicate 3, ATAC-seq

description: Library name: Day1_rep3

data_processing:
ATAC-seq raw reads were trimmed to remove low-quality reads and adapters using trim-galore (version 0.6.7). Next, trimmed reads were aligned to the mouse reference genome (mm10) using Bowtie2 (version 2.4.4) with the "--very-sensitive -X 1000" option; reads mapped to mitochondria were ignored. SAMtools (version 1.15.1) was applied to extract properly mapped reads and duplicated reads were removed by sambamba (version 0.8.2).
The Counts Per Million mapped reads (CPM) normalization method of deepTools bamCoverage (version 3.5.1) was used to transform alignment bam files into read coverage files in bigWig format. Peak calling was performed using MACS2 (version 2.2.7.1) with the parameter "--SPMR --nomodel --shift -100 --extsize 200" analysis.
Differentially accessible peaks were identified using the DiffBind R package (version 3.8.4), peaks with FDR of < 0.05, fold change >= 2 were identified as significant differentially accessible regions, and stable regions were identified with a fold change < 2.
Motif enrichment analysis was performed using the HOMER (version 4.11) function "findMotifsGenome.pl" with default options.
The Integrative Genomics Viewer (IGV, version 2.10.0) was used for data visualization.
Assembly: mouse reference genome mm10 (UCSC)
Supplementary files format and content: Peak files were generated using MACS2

extract_protocol:
The ATAC-Seq samples were prepared following TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme Biotech).
Library was then constructed by PCR amplification as instructed in the TruePrep DNA Library Prep Kit V2 protocol  (Vazyme Biotech), and purified by VAHTS DNA Clean Beads(Vazyme #N411).

value: Brown pre-adipocyte

value: Brown adipocyte differentiation, Day 1


title: Kelly, Control, rep2

description: Library name: Sample 8


title: Kelly, Control, rep1

description: Library name: Sample 7


title: Day 1, replicate 1, ATAC-seq

description: Library name: Day1_rep1


title: Day 0, replicate 3, ATAC-seq

description: Library name: Day0_rep3


title: AS, Erastin, rep2

description: Library name: Sample 5

source_name: SK-N-AS

value: SK-N-AS

value: neuroblast


title: Day 0, replicate 2, ATAC-seq

description: Library name: Day0_rep2

value: BAT


title: AS, Erastin, rep1

description: Library name: Sample 4


title: Day 1, replicate 2, ATAC-seq

description: Library name: Day1_rep2


title: Day 0, replicate 1, ATAC-seq

description: Library name: Day0_rep1


title: IWAT, Knock out Runx2, replicate 3, RNA-seq

description: Library name: Tissue_KO_Runx2_rep3

tag: tissue

value: White adipose

value: Knock out Runx2

value: Adipoq-cre:Runx2 KO


title: Uncomplicated_MalariaSample_6

description: Gene expression Profiling

data_processing: Data extraction from Images was done using Feature Extraction software  and Quantile Normalization of the data was done in GeneSpring GX.

source_name: Total RNA, Control Sample 6

value: Enriched blood sample

value: Uncomplicated Malaria


title: IWAT, Knock out Runx2, replicate 2, RNA-seq

description: Library name: Tissue_KO_Runx2_rep2


title: IWAT, Knock out Runx2, replicate 1, RNA-seq

description: Library name: Tissue_KO_Runx2_rep1


title: AS, Control, rep1

description: Library name: Sample 1

tag: cell line


title: Human hepatocellular carcinoma liver RNA-seq (HCC33)

city: Suita

first: Shuhei

last: Yamamoto

state: Osaka

address: 2-2 Yamadaoka, Suita, Osaka

country: Japan

institute: Osaka University, Graduate School of Medicine

description:
Library name: HCC33_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma

data_processing:
Reads were trimmed using Trimmomatic (v0.38) and aligned to hg19 with TopHat (v2.1.1). Gene-level counts were generated using featureCounts (Subread v2.0.0). Counts were normalized with DESeq2, filtered by CPM (0.5 or higher in at least one sample), and log2-transformed with a pseudocount of 1.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file containing a gene-level expression matrix. Rows represent genes and columns represent samples. Values are DESeq2-normalized, log2-transformed expression values.

source_name: liver

extract_protocol:
Total RNA was extracted from liver tumor biopsy using the Qiagen RNeasy Mini Kit following the manufacturer’s instructions.
RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s protocol, including poly(A) selection and fragmentation.

value: liver


title: Human hepatocellular carcinoma liver RNA-seq (HCC32)

description:
Library name: HCC32_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: IWAT, Knock out Runx2 control, replicate 2, RNA-seq

description: Library name: Tissue_Runx2_NC_rep2

tag: genotype

value: Runx2 flox


title: AS, Control, rep2

description: Library name: Sample 2

value: 24 hours


title: Human hepatocellular carcinoma liver RNA-seq (HCC31)

description:
Library name: HCC31_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: Human hepatocellular carcinoma liver RNA-seq (HCC30)

description:
Library name: HCC30_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: IWAT, Knock out Runx2 control, replicate 1, RNA-seq

description: Library name: Tissue_Runx2_NC_rep1


title: IWAT, Knock out Runx1, replicate 3, RNA-seq

description: Library name: Tissue_KO_Runx1_rep3

value: Knock out Runx1

value: Adipoq-cre:Runx1 KO


title: IWAT, Knock out Runx1, replicate 2, RNA-seq

description: Library name: Tissue_KO_Runx1_rep2


title: Human hepatocellular carcinoma liver RNA-seq (HCC29)

description:
Library name: HCC29_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: IWAT, Knock out Runx1, replicate 1, RNA-seq

description: Library name: Tissue_KO_Runx1_rep1


title: Uncomplicated_MalariaSample_3

description: Gene expression Profiling

source_name: Total RNA, Control Sample 3

extract_protocol: RNA from enriched blood was isolated using TRIzol as per manufacture's protocols.


title: Human hepatocellular carcinoma liver RNA-seq (HCC26)

description:
Library name: HCC26_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: IWAT, Knock out Runx1 control, replicate 2, RNA-seq

description: Library name: Tissue_Runx1_NC_rep2

value: WT

value: Runx1 flox


title: Human hepatocellular carcinoma liver RNA-seq (HCC27)

description:
Library name: HCC27_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: Human hepatocellular carcinoma liver RNA-seq (HCC25)

description:
Library name: HCC25_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: Human hepatocellular carcinoma liver RNA-seq (HCC28)

description:
Library name: HCC28_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: IWAT, Knock out Runx1 control, replicate 1, RNA-seq

description: Library name: Tissue_Runx1_NC_rep1


title: Human hepatocellular carcinoma liver RNA-seq (HCC24)

description:
Library name: HCC24_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: Human hepatocellular carcinoma liver RNA-seq (HCC23)

description:
Library name: HCC23_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: IWAT, Knock out Runx1 control, replicate 3, RNA-seq

description: Library name: Tissue_Runx1_NC_rep3


title: BAT, Double knock out Runx1 and Runx2, replicate 1, RNA-seq

description: Library name: Cell_DKO_rep1

source_name: BAT

value: Mature brown adipocytes

value: Double knock out, Runx1 and Runx2

value: Brown adipocyte differentiation


title: BAT, Double knock out Runx1 and Runx2, replicate 3, RNA-seq

description: Library name: Cell_DKO_rep3


title: Human hepatocellular carcinoma liver RNA-seq (HCC21)

description:
Library name: HCC21_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: BAT, Knock out Runx2, replicate 3, RNA-seq

description: Library name: Cell_KO_Runx2_rep3


title: BAT, Knock out Runx2, replicate 1, RNA-seq

description: Library name: Cell_KO_Runx2_rep1


title: BAT, Knock out Runx2, replicate 2, RNA-seq

description: Library name: Cell_KO_Runx2_rep2


title: BAT, Double knock out Runx1 and Runx2, replicate 2, RNA-seq

description: Library name: Cell_DKO_rep2


title: Human hepatocellular carcinoma liver RNA-seq (HCC19)

description:
Library name: HCC19_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: BAT, Knock out Runx1, replicate 3, RNA-seq

description: Library name: Cell_KO_Runx1_rep3


title: Human hepatocellular carcinoma liver RNA-seq (HCC18)

description:
Library name: HCC18_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: Human hepatocellular carcinoma liver RNA-seq (HCC20)

description:
Library name: HCC20_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: BAT, Knock out Runx1, replicate 2, RNA-seq

description: Library name: Cell_KO_Runx1_rep2


title: Human hepatocellular carcinoma liver RNA-seq (HCC17)

description:
Library name: HCC17_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: BAT, Knock out Runx1, replicate 1, RNA-seq

description: Library name: Cell_KO_Runx1_rep1


title: Human hepatocellular carcinoma liver RNA-seq (HCC15)

description:
Library name: HCC15_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: Human hepatocellular carcinoma liver RNA-seq (HCC16)

description:
Library name: HCC16_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: Human hepatocellular carcinoma liver RNA-seq (HCC14)

description:
Library name: HCC14_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: BAT, Knock out control, replicate 3, RNA-seq

description: Library name: Cell_KO_NC_rep3


title: BAT, Knock out control, replicate 2, RNA-seq

description: Library name: Cell_KO_NC_rep2


title: IWAT, Knock out Runx2 control, replicate 3, RNA-seq

description: Library name: Tissue_Runx2_NC_rep3


title: Human hepatocellular carcinoma liver RNA-seq (HCC12)

description:
Library name: HCC12_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: Human hepatocellular carcinoma liver RNA-seq (HCC22)

description:
Library name: HCC22_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: Human hepatocellular carcinoma liver RNA-seq (HCC11)

description:
Library name: HCC11_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: BAT, OE Runx2, replicate 3, RNA-seq

description: Library name: Cell_OE_Runx2_rep3

value: Over expression Runx2


title: BAT, OE Runx2, replicate 2, RNA-seq

description: Library name: Cell_OE_Runx2_rep2

value: BAT


title: BAT, OE Runx2, replicate 1, RNA-seq

description: Library name: Cell_OE_Runx2_rep1


title: BAT, Knock out control, replicate 1, RNA-seq

description: Library name: Cell_KO_NC_rep1


title: Human hepatocellular carcinoma liver RNA-seq (HCC13)

description:
Library name: HCC13_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: Human hepatocellular carcinoma liver RNA-seq (HCC10)

description:
Library name: HCC10_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: Human hepatocellular carcinoma liver RNA-seq (HCC09)

description:
Library name: HCC09_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: BAT, OE Runx1, replicate 3, RNA-seq

description: Library name: Cell_OE_Runx1_rep3

value: Over expression Runx1


title: BAT, OE Runx1, replicate 2, RNA-seq

description: Library name: Cell_OE_Runx1_rep2


title: Human hepatocellular carcinoma liver RNA-seq (HCC08)

description:
Library name: HCC08_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: Human hepatocellular carcinoma liver RNA-seq (HCC07)

description:
Library name: HCC07_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: BAT, OE Runx1, replicate 1, RNA-seq

description: Library name: Cell_OE_Runx1_rep1


title: BAT, OEV, replicate 3, RNA-seq

description: Library name: Cell_OEV_rep3


title: BAT, OEV, replicate 2, RNA-seq

description: Library name: Cell_OEV_rep2


title: Human hepatocellular carcinoma liver RNA-seq (HCC04)

description:
Library name: HCC04_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: BAT, OEV, replicate 1, RNA-seq

description: Library name: Cell_OEV_rep1


title: Human hepatocellular carcinoma liver RNA-seq (HCC03)

description:
Library name: HCC03_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: Human hepatocellular carcinoma liver RNA-seq (HCC06)

description:
Library name: HCC06_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: Human hepatocellular carcinoma liver RNA-seq (HCC02)

description:
Library name: HCC02_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: AB5075_vgrG2_ko_in_vitro_2

city: Hangzhou

first: xu

last: wenzeng

address: Department of Respiratory Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310016, China.

institute: Zhejiang University

description: Library name: Sample8

data_processing:
Data generated by the sequencer are referred to as raw reads or raw data, which are then subjected to quality control (QC) to determine their suitability for subsequent analyses. After QC, clean reads are obtained via filtration and aligned to the reference sequence using Rockhopper v2.0.3. Following the alignment, the distribution and coverage of reads across the reference sequence are quantified to evaluate whether the alignment results pass a second round of quality control (QC of alignment). If qualified, gene expression analysis is performed, from which differentially expressed genes (DEGs) between samples are screened out. Based on these DEGs, pathway enrichment analysis with statistical significance is subsequently conducted.
Assembly: A. baumannii AB5075 (GenBank assembly accession GCF_036601155.1)
Supplementary files format and content: FPKM values for each sample

organism: Acinetobacter baumannii

extract_protocol:
Total RNA was extracted using Total RNA Kit I (Omega) according to the manufacturer’s instructions, with additional on column DNase I (Takara) treatment to remove genomic DNA. RNA quality and concentration were assessed using a Bioanalyzer (Agilent Technologies).
Total RNA was extracted from the samples and treated with DNase I to digest genomic DNA. Eukaryotic mRNA was then enriched using magnetic beads conjugated with Oligo(dT); for prokaryotic samples, rRNA was removed with a commercial kit prior to the subsequent steps. mRNA fragmentation reagent was added to shear the mRNA into short fragments at an optimal temperature in a Thermomixer. The sheared mRNA was used as the template to synthesize first-strand cDNA, followed by the preparation of a second-strand synthesis reaction system for second-strand cDNA generation. The resulting cDNA was purified and recovered with a kit, subjected to end repair, dA-tailing at the 3’ ends, and adapter ligation, prior to fragment size selection and final PCR amplification. After the constructed libraries passed quality control using an Agilent 2100 Bioanalyzer and an ABI StepOnePlus Real-Time PCR System, high-throughput sequencing was performed on an Illumina NovaSeq 6000 platform.


title: Human hepatocellular carcinoma liver RNA-seq (HCC01)

description:
Library name: HCC01_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma


title: AB5075_vgrG2_ko_in_vitro_1

description: Library name: Sample7


title: T778, sgTDP2, 4nM dox, Rep 3

city: Amsterdam

first: Daniel

last: Peeper

state: Outside the US or Canada

address: Plesmalaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

description: Library name: 36_T778TDP2__4nM_doxorubicin_1dRep_3

data_processing:
Fastq files were mapped to the human reference genome (Homo.sapiens.GRCh38.102).
Assembly: Homo.sapiens.GRCh38.102
Supplementary files format and content: Gene-level RNA-seq counts matrix  generated using gensum

growth_protocol: Cultured in Advanced DMEM, 9% FCS, 1% Glutamax & 1% Pen/Strep

extract_protocol:
The total RNA was isolated using the RNeasy Mini Kit (Qiagen, 74104), including an on-column DNase digestion (Qiagen, 79254).
cDNA libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina, 20020594)

treatment_protocol: Cells were treated with Doxorubicin (4nM, 24h) +/- peposertib (0.5uM)

value: liposarcoma

value: TDP2 KO

value: Doxorubicin 4nM


title: T778, sgTDP2, 4nM dox, Rep 1

description: Library name: 34_T778TDP2__4nM_doxorubicin_1dRep_1


title: AB5075_in_vivo_3

description: Library name: Sample6


title: AB5075_in_vivo_1

description: Library name: Sample4


title: AB5075_vgrG2_ko_in_vitro_3

description: Library name: Sample9


title: T778, sgTDP2, 4nM dox, Rep 2

description: Library name: 35_T778TDP2__4nM_doxorubicin_1dRep_2


title: T778, sgTDP2, Rep 3

description: Library name: 33_T778TDP2__0nM_doxorubicin_1dRep_3


title: AB5075_in_vitro_3

description: Library name: Sample3


title: AB5075_in_vitro_2

description: Library name: Sample2


title: AB5075_in_vitro_1

description: Library name: Sample1


title: T778, sgTDP2, Rep 1

description: Library name: 31_T778TDP2__0nM_doxorubicin_1dRep_1


title: T778, 0.5uM Peposertib, 4nM dox, Rep 3

description: Library name: 30_T7780_5_uM_Peposertib_4nM_Doxorubicin_1d_Rep_3

value: Peposertib 0.5uM + Doxorubicin 4nM


title: T778, sgTDP2, Rep 2

description: Library name: 32_T778TDP2__0nM_doxorubicin_1dRep_2


title: T778, 0.5uM Peposertib, 4nM dox, Rep 2

description: Library name: 29_T7780_5_uM_Peposertib_4nM_Doxorubicin_1d_Rep_2


title: T778, 0.5uM Peposertib, 4nM dox, Rep 1

description: Library name: 28_T7780_5_uM_Peposertib_4nM_Doxorubicin_1d_Rep_1


title: T778, 0.5uM Peposertib, Rep 3

description: Library name: 27_T7780_5_uM_Peposertib_0nM_Doxorubicin_1d_Rep_3

value: Peposertib 0.5uM


title: si_ALDH18A1_2

city: Urumqi City

first: abulajiang·abudoukelimu

middle: abudoukelimu

last: abulajiang

address: 新疆医科大学第三临床医学院

institute: The Third Clinical Medical College of Xinjiang Medical University

description: Library name: Sample5

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped. After that, clean reads were aligned to the GRCm39 genome by tophat2 (Kim et al. 2013) allowing 4 mismatches. Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped) (Trapnell et al. 2010).
Assembly: GRCh38
Supplementary files format and content: expressed_gene_FPKM.txt
Supplementary files format and content: expressed_gene_reads.txt

growth_protocol: The  HGC-27 cells were acquired from Procell (Wuhan, China). AGS cells were cultured in Ham’s-F12 medium, whereas HGC-27 cells were incubated in RPMI 1640 medium. All cells were maintained at 37℃ in a humidified atmosphere of 5% CO2.

extract_protocol:
For each sample, 1 µg of total RNA was treated with RQ1 DNase (M6101, Promega, USA) to remove genomic DNA prior to library construction. Directional RNA-seq libraries were prepared using the VAHTS© Universal V8 RNA-seq Library Prep Kit (NR605, Vazyme, China). Poly(A)+ mRNAs were enriched using VAHTS mRNA Capture Beads (N401, Vazyme, China).
Fragmented RNAs were reverse-transcribed into double-stranded cDNA. Following end repair and A-tailing, the cDNA fragments were ligated to VAHTS RNA Multiplex Oligos Set 1 (N323, Vazyme, China). The ligated products were then amplified, purified, quantified, and stored at −80 °C prior to sequencing. The strand marked with dUTP (the second cDNA strand) was not amplified, enabling strand-specific sequencing.  For high-throughput sequencing, libraries were prepared according to the manufacturer’s instructions and sequenced on the DNBSEQ-T7 platform (MGI, China) to generate 150 bp paired-end reads.

treatment_protocol: HGC-27 cells were transfected with si-ALDH18A1 or si-NC. Plasmid transfection of cells was performed using Lipofectamine (Invitrogen, China) according to the manufacturer's protocol. Transfected cells were harvested after 48 h for RT-qPCR and Western blotting analysis.

value: ALDH18A1 knockdown transfected with si-ALDH18A2


title: NC_ALDH18A1_3

address: 新疆医科大学第三临床医学院

description: Library name: Sample3

value: Non-targeting control si-NC


title: si_ALDH18A1_1

address: 新疆医科大学第三临床医学院

description: Library name: Sample4

value: ALDH18A1 knockdown transfected with si-ALDH18A1


title: Human hepatocellular carcinoma liver RNA-seq (HCC05)

description:
Library name: HCC05_liver_RNAseq
Tumor liver biopsy from a patient with hepatocellular carcinoma

value: liver


title: T778, 0.5uM Peposertib, Rep 2

description: Library name: 26_T7780_5_uM_Peposertib_0nM_Doxorubicin_1d_Rep_2

value: WT


title: NC_ALDH18A1_2

address: 新疆医科大学第三临床医学院

description: Library name: Sample2


title: T778, 0.5uM Peposertib, Rep 1

description: Library name: 25_T7780_5_uM_Peposertib_0nM_Doxorubicin_1d_Rep_1


title: AB5075_in_vivo_2

description: Library name: Sample5


title: NC_ALDH18A1_1

address: 新疆医科大学第三临床医学院

description: Library name: Sample1


title: human embryo, CUT&Tag, WT, 8C, rep2

city: hangzhou

first: Hao

last: Jin

address: Nongshenghuan Building E, Zhejiang University, Hangzhou, Zhejiang

description: Library name: h_CUT_Tag_WT_8C_rep2

data_processing:
Bulk RNA-Seq data were trimmed and then aligned to the bovine (ARS-UCD1.2) or human (hg19) reference genome by HISAT2 (Version 2.2.1). For scRNA-Seq data, bases 1 - 8 of read 2 were extracted as cell barcodes by UMI-tools (version 1.1.2). Read 1 was trimmed to remove adapter and template switching oligo (TSO) sequences at the 5′ end and poly(A) tails at the 3′ end. Then, aligned reads were split based on their corresponding cell barcodes using Picard (version 2.26.3). The read counts and FPKM values of each gene were calculated by FeatureCounts (version 2.0.1) and StringTie (version 2.1.2).
For CUT&Tag, ChIP-seq, and ATAC-seq data,  Paired end CUT&Tag, ChIP-seq, and ATAC-seq reads were trimmed and then aligned to bovine (ARS-UCD1.2) or human (hg19) genome with Bowtie (version 2.2.5). Low quality reads (MAPQ <20) and PCR duplicated were removed by samtools (version 1.10) and sambamba (version 0.6.6). For downstream analysis, read counts were normalized to RPKM in a 50bp bin by bamCoverage from deepTools (version 3.5.3).
Assembly: bovine (ARS-UCD1.2) or human (hg19)
Supplementary files format and content: excel files include raw counts for scRNA-Seq and FPKM values for bulk RNA-Seq
Supplementary files format and content: bigwig for CUT-Tag, ChIP-Seq and ATAC-Seq signals

source_name: human embryo

extract_protocol:
The zona pellucidae of embryos were removed using 0.5% pronase E (Sigma- Aldrich, 107433). Then the embryos were washed in 0.5% BSA (Sigma- Aldrich, SRE0098) and manually transfer into PCR tubes
For RNA-Seq, library construction were performed according to the protocol described previously (Hu et al., 2024). For ChIP-Seq, library construction were performed according to the protocol described previously (Brind’Amour et.al 2015). For ATAC-Seq, library construction were performed according to the protocol described previously (Wu et al., 2018). For CUT-Tag, library construction were performed according to the protocol of Vazyme TD904 kit.

value: 8-cell human embryos

value: wild type


title: T778, sgNTC, 4nM dox, Rep 2

description: Library name: 23_T778NTC_4nM_Doxorubicin_1d_Rep_2

value: NTC


title: human embryo, CUT&Tag, WT, 8C, rep1

description: Library name: h_CUT_Tag_WT_8C_rep1


title: human embryo, RNA-Seq, siCtrl, 8C, 6

description: Library name: h_RNA_siCtrl_8C_6

value: siCtrl


title: T778, sgNTC, 4nM dox, Rep 3

description: Library name: 24_T778NTC_4nM_Doxorubicin_1d_Rep_3


title: human embryo, RNA-Seq, siCtrl, 8C, 5

description: Library name: h_RNA_siCtrl_8C_5


title: T778, sgNTC, Rep 2

description: Library name: 20_T778NTC_0nM_Doxorubicin_1d_Rep_2


title: T778, sgNTC, 4nM dox, Rep 1

description: Library name: 22_T778NTC_4nM_Doxorubicin_1d_Rep_1


title: LPS853, sgTDP2, 4nM dox, Rep 3

description: Library name: 18_LPS853TDP2__4nM_doxorubicin_1dRep_3


title: human embryo, RNA-Seq, siCtrl, 8C, 3

description: Library name: h_RNA_siCtrl_8C_3


title: human embryo, RNA-Seq, siCtrl, 8C, 4

description: Library name: h_RNA_siCtrl_8C_4


title: human embryo, RNA-Seq, siCtrl, 8C, 1

description: Library name: h_RNA_siCtrl_8C_1


title: T778, sgNTC, Rep 1

description: Library name: 19_T778NTC_0nM_Doxorubicin_1d_Rep_1


title: T778, sgNTC, Rep 3

description: Library name: 21_T778NTC_0nM_Doxorubicin_1d_Rep_3


title: human embryo, RNA-Seq, siCtrl, 8C, 2

description: Library name: h_RNA_siCtrl_8C_2