title: PC-3AcT cells, replicate 3

city: Cheonan-si

first: Dongsic

last: Choi

address: 31 Suncheonhyang 6-gil, Bongmyeong-dong

department: Department of Biochemistry

country: South Korea

institute: Soonchunhyang University, College of Medicine

description: Library name: Sample9

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to rn6 whole genome by using STAR version 2.6.0c with parameter --twopassMode Basic
Removed PCR duplicates using SAMBAMBA markdup (v0.6.6).
Variant calling was done using SplitNCigarReads, FixMateInformation, BaseRecalibrator, ApplyBQSR, and HaplotypeCaller from the GTAK v4.2.0.0 package. Filtered out variants with “FS > 30.0” and “QD < 2.0” using GTAK's VariantFiltration, and additionally filtered out variants with “DP < 10” using an in-house script.
Assembly: GRCh38
Supplementary files format and content: text files include SNV for each sample

growth_protocol: PC-3 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) (Welgene, Republic of Korea) supplemented with 5% fetal bovine serum (FBS) (Welgene), 1% L-glutamine (Hyclone, Logan, USA), and 1% penicillin-streptomycin (Hyclone). Acidic pre-adapted PC-3 cells termed as PC-3AcT cells were established by continuously exposing PC-3 cells to 3.8 μM lactic acid with four serial passages during 15 days.

extract_protocol:
Homogenizing Samples 1. Add 750 uL Trizol directly to the maximum of 1x10^7 cells. 2. Pipette this mixture tenderly. 3. Incubate for 5 minutes at room temperature for lysis.  Phase separation 1. Add 150 uL of chloroform per 750 uL of Trizol used for homogenization. 2. Shake tube vigorously by vortex for 15 seconds. 3. Incubate for 2–3 minutes at room temperature. 4. Centrifuge the sample at 12,000 × g for 15 minutes at 4°C. 5. Transfer the upper aqueous phase to a new tube.
Total RNA concentration was calculated by Quant-IT RiboGreen (Invitrogen, #R11490). To assess the integrity of the total RNA, samples are run on the TapeStation RNA screentape (Agilent, #5067-5576). Only high-quality RNA preparations, with RIN greater than 7.0, were used for RNA library construction. A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #20020595). The first step in the workflow involves purifying the poly‐A containing mRNA molecules using poly‐T‐attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using SuperScript II reverse transcriptase (Invitrogen, #18064014) and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I, RNase H and dUTP. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.The libraries were quantified using KAPA Library Quantification kits for Illumina Sequencing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, #KK4854) and qualified using the TapeStation D1000 ScreenTape (Agilent Technologies, # 5067-5582). Indexed libraries were then submitted to an Illumina NovaSeqX (Illumina, Inc., San Diego, CA, USA), and the paired-end (2×100 bp) sequencing was performed by the Macrogen Incorporated.

value: Prostate cancer cells

value: PC-3 subpopulation, lactic acid adaptation

value: Lactic acid


title: mrps-5 + C32E8.9 RNAi sample-5

status: Public on Apr 23 2025

type: SRA

city: Amsterdam

first: Man

middle: Iman

last: Hu

address: Meibergdreef 9

department: Laboratory Genetic Metabolic Diseases

country: Netherlands

institute: Amsterdam UMC Location University of Amsterdam

description: N2 worms treated with mrps-5 + C32E8.9 RNAi sample-5

library_source: transcriptomic

data_processing:
Reads were subjected to quality control FastQC and trimmed using fastp (version 0.23.2) and aligned to the C. elegans genome obtained from Ensembl (wbcel235), using STAR2 (version 2.5.4)
Assembly: Ensembl (wbcel235)
Supplementary files format and content: table delimited row counts

molecule: total RNA

organism: Caenorhabditis elegans

source_name: Whole body

growth_protocol: N2 worms were synchronized by hypochlorite treatment, then plated on NGMi plates (NGM plates with 2 mM IPTG and 25 mg/mL carbenicillin) with a bacterial lawn of either E. coli HT115 (RNAi control strain, containing an empty vector), mrps-5, C32E8.9, or mrps-5 + C32E8.9.

extract_protocol:
Total RNA was extracted as described above in the “RNA Isolation” section. Contaminating genomic DNA was removed using RNaseFree DNase (QIAGEN). RNA was quantified with a NanoDrop 2000 spectrophotometer (Thermo Scientific; Breda, The Netherlands). The qualities of RNA samples were checked with TapeStation (Agilent, CA, USA).
Sequencing libraries were constructed by using KAPA mRNA HyperPrep Kit (Roche, Switzerland)
Paired-end sequencing of Illumina NovaSeq was performed (Macrogen, Seoul, South Korea)

tag: tissue

value: Whole body

tag: genotype

tag: treatment

value: mrps-5 + C32E8.9 RNAi


title: mrps-5 + C32E8.9 RNAi sample-4

description: N2 worms treated with mrps-5 + C32E8.9 RNAi sample-4


title: Day_2_Cytoplasmic_fraction_replicate_3

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

country: Australia

institute: Adelaide University

description: Fractionation method: https://doi.org/10.1038/nprot.2014.138

data_processing:
Illumina bcl2fastq Conversion Software v2.20 used for basecalling
Raw reads were adapter trimmed using cutadapt v2.8. adapter sequence = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, minimum length = 28, error rate = 0.2, overlap - 5
A 12 base UMI sequence was removed from the 3' end of the each read using UMI-tools v1.0.1m "extract" method.
A 3' spacer sequence was removed using cutadapt v2.8. Adapter: AACTGTAGGCACCATCAAT, minimum length: 18, error rate: 0.2, overlap: 5
Reads were mapped against the human reference genome (build hg19) using the BWA v0.7.17 alignment algorithm (~84% alignment rate)
PCR duplicate reads were collapsed based on the 12 nt UMI using the UMI-tools ‘dedup’ method (using --method=percentile)
Annotation obtained from miRBase was used to obtain miR-level read counts using python scripts described in https://doi.org/10.1038/s41598-020-71323-0
Counts were TMM and log2 transformed using edgeR (version 3.34.0)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file of raw counts for all microRNAs for 1 sample
Supplementary_files_format_and_content: Comma-delimited matrix table with raw gene counts for every microRNA and every sample

organism: Homo sapiens

source_name: Human mammary epithelial cells

growth_protocol: HMLE cells were grown in HuMEC Ready Media (HuMEC Basal Serum-Free Medium (Gibco, #12753018) supplemented with HuMEC Supplement Kit (Gibco, #12755013)) at 37°C with 5% CO2.

extract_protocol:
RNA was extracted using Trizol (Ambion, #15596018) according to the manufacturer's protocol
The quantity and quality of the RNA samples were checked using nanodrop Qubit HS RNA (Invitrogen, # Q32852) and Bioanalyzer small RNA assay (Agilent, #5067-1548). Libraries were generated using 1 ug of the total RNA via QIAseq miRNA kit (Qiagen, # 331502) with 14 cycles of amplification. Amplified barcoded libraries were then size selected using auto gel-purification Pippin prep 3% agarose (SAGE science) which targets ranges from 100-250bp. Libraries (size between 180-190bp) were then confirmed by Qubit HS DNA and Bioanalyzer HS DNA assay for size and concentration.
small RNA, 1x75 bp sequencing (Illumina NextSeq 500)

treatment_protocol: A HMLE subline with a mesenchymal phenotype (mesHMLE) was achieved by culturing in DMEM:F12 media (Gibco, #11320033) supplemented with 10 mg/ml insulin (Actrapid HM 100IU/ml Penfill), 20 ng/ml EGF (R&D systems, #RDS236EG01M), 0.5 mg/ml hydrocortisone (Sigma Aldrich, # H0888), and 5% fetal Bovine serum (Hyclone, #SH300084) and treatment with 2.5 ng/ml of recombinant Human TGF-β 1 Protein (R&D systems, #RDS240B002) for maximum of 18 days. MesHMLEs were then maintained in this supplemented media without TGFβ1.

tag: cell line

value: HMLE

value: 2.5 ng/mL TGF-Beta

tag: time point

value: 2 days

tag: cellular fraction

value: Cytoplasm


title: Liver8

city: Måløv

first: Jens

last: Halling

address: Novo Nordisk Park 1

country: Denmark

institute: Novo Nordisk

description: Library name: Liver8

data_processing:
Trimming of sequence reads to remove potential adapter sequences and low-quality nucleotides using fastp v.0.23.1
UMI-based de-duplication was carried out using fastp v.0.23.1
Assembly: Rattus norvegicus Rnor6.0 reference genome - aligned using the STAR aligner v.2.5.2b
Supplementary files format and content: Raw counts csv file containing counts for each sample

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
RNeasy Minikit
Twist UMI system

value: Liver

value: WT

value: Vehicle


title: Liver7

description: Library name: Liver7


title: mrps-5 + C32E8.9 RNAi sample-3

description: N2 worms treated with mrps-5 + C32E8.9 RNAi sample-3


title: PC-3AcT cells, replicate 1

description: Library name: Sample7

tag: cell type


title: Day_2_Cytoplasmic_fraction_replicate_1

description: Fractionation method: https://doi.org/10.1038/nprot.2014.136


title: Day_2_Cytoplasmic_fraction_replicate_2

description: Fractionation method: https://doi.org/10.1038/nprot.2014.137


title: mrps-5 + C32E8.9 RNAi sample-2

description: N2 worms treated with mrps-5 + C32E8.9 RNAi sample-2


title: Liver5

description: Library name: Liver5


title: Day_0_Nuclear_fraction_replicate_3

description: Fractionation method: https://doi.org/10.1038/nprot.2014.135

value: Untreated

value: Nucleus


title: PC-3 cells, PC-3AcT EV treatment, replicate 3

description: Library name: Sample6

value: Lactic acid, PC-3AcT EV


title: PROP-CD45

city: Daejeon

first: Chae Won

last: Kim

address: 291, Daehak-ro, Yuseong-gu  E7 Rm 5101

department: Graduate School of Medical Science and Engineering

institute: Korea Advanced Institute of Science and Technology

description: NaP

library_source: transcriptomic single cell

data_processing:
Using cellranger 'mkfastq' module to demultiplexes raw base call files generated by Illumina sequencers into FASTQ files
Using cellranger 'count' to perform alignment, filtering, barcode counting and UMI counting
Assembly: Mm10
Supplementary files format and content: h5 file including matrix, barcodes, and features

organism: Mus musculus

source_name: brain

extract_protocol:
Isolate single cells from mouse brain tissues by using percoll gradient and sort CD45-positive immune cells or GFP-positive tumor cells by FACS
Chromiun Single Cell 3' RNA library v3

treatment_protocol: In our experimental design, we utilized 4-week-old mice and administered either sodium chloride or propionate through drinking water supplementation. For immune cell sorting experiments, we intracranially injected GL261 cells, while for sorting GFP-positive tumor cells, we used GL261-GFP cells. Brain tissues were collected at day 20 after tumor injection.

value: brain

tag: strain

value: sodium propionate


title: Day_0_Nuclear_fraction_replicate_2


title: PC-3 cells, PC-3AcT EV treatment, replicate 2

description: Library name: Sample5

value: Prostate cancer cells


title: Liver4

description: Library name: Liver4


title: Liver3

description: Library name: Liver3


title: PC-3 cells, PC-3AcT EV treatment, replicate 1

description: Library name: Sample4


title: Day_0_Nuclear_fraction_replicate_1


title: CTRL-CD45

description: NaCl

value: sodium chloride


title: Liver2

description: Library name: Liver2


title: PROP-GL261

description: PROP


title: Day_0_Cytoplasmic_fraction_replicate_3


title: PC-3 cells, replicate 1

description: Library name: Sample1

value: Lactic acid


title: Liver1

description: Library name: Liver1


title: CTRL-GL261

description: CTRL


title: Day_0_Cytoplasmic_fraction_replicate_2


title: PC-3AcT cells, replicate 2

description: Library name: Sample8

value: PC-3 subpopulation, lactic acid adaptation


title: PC-3 cells, replicate 2

description: Library name: Sample2


title: Day_0_Cytoplasmic_fraction_replicate_1


title: Liver6

description: Library name: Liver6


title: MP46 cells, 24 hour Mivebresib treatment, sample 1

status: Public on Apr 22 2025

city: Miami

first: Stefan

last: Kurtenbach

state: FL

address: 1501 NW 10th Ave

department: Ophthalmology

country: USA

institute: University of Miami

description:
Library name: MP46 Mivebresib 1
Column Name in MP46_RawReadCounts.txt: Mivebresib 1
Column Name in MP46_LogCPM.txt: Mivebresib 1
Column Name in MP46_QuantileNormalization.txt: Mivebresib.1
Row Name in MP46_Clean_stat.txt: M1

data_processing:
uploaded concatonated files to BioJupies for paired-end analysis
Assembly: hg38
Supplementary files format and content: MP41_RawReadCounts.txt: Raw read counts of each concatonated MP41 cell line sample
Supplementary files format and content: MP41_LogCPM.txt: Log counts per million for each MP41 cell line sample
Supplementary files format and content: MP41_QuantileNormalization.txt: Normalized gene expression for each MP41 cell line sample
Supplementary files format and content: MP41_Clean_stat.txt: Quality check for each MP41 cell line sample, including number of clean reads, clean bases, read length, Q20(%), Q30(%), and GC(%)
Supplementary files format and content: MP46_RawReadCounts.txt: Raw read counts of each concatonated MP46 cell line sample
Supplementary files format and content: MP46_LogCPM.txt: Log counts per million for each MP46 cell line sample
Supplementary files format and content: MP46_QuantileNormalization.txt: Normalized gene expression for each MP46 cell line sample
Supplementary files format and content: MP46_Clean_stat.txt: Quality check for each MP46 cell line sample, including number of clean reads, clean bases, read length, Q20(%), Q30(%), and GC(%)

source_name: uveal

growth_protocol: Cells maintained in D-MEM/F-12 media supplemented with 10% heat-inactivated FBS, 2 mmol/L Glutamax, 1mmol/L Non-Essential Amino Acid (NEAA) cell culture supplement, 0.5x Insulin-Transferin-Selenium (ITS), and 1x Pen-Strep. Growth conditions were 37 C° and 5.0% CO2.

extract_protocol:
Media was aspirated out and RNA was extracted from cells according to the Quick-RNA MiniPrep (Zymo Research, R1054) protocol.
Eukaryotic Strand-specific mRNA library with sequencing read length PE150 and clean fastq phred quality score encoding Phred+33

treatment_protocol: Drugs were obtained from TargetMol (Romidepsin T6006, Quisinostat T6055, Mivebresib T3712) and dissolved in sterile DMSO to yeild 10 mM stock concentration. Stocks were dissolved in cell media to yield above conctentrations. Cells were grown in drug media for 24 hours.

value: uveal

value: uveal melanoma

value: 1200 nM Mivebresib


title: MP46 cells, 24 hour Quisinostat treatment, sample 2

description:
Library name: MP46 Quisinostat 2
Column Name in MP46_RawReadCounts.txt: Quisinostat 2
Column Name in MP46_LogCPM.txt: Quisinostat 2
Column Name in MP46_QuantileNormalization.txt: Quisinostat.2
Row Name in MP46_Clean_stat.txt: Q2

value: 40 nM Quisinostat


title: MP46 cells, 24 hour Romidepsin treatment, sample 2

description:
Library name: MP46 Romidepsin 2
Column Name in MP46_RawReadCounts.txt: Romidepsin 2
Column Name in MP46_LogCPM.txt: Romidepsin 2
Column Name in MP46_QuantileNormalization.txt: Romidepsin.2
Row Name in MP46_Clean_stat.txt: R2

value: 40 nM Romidepsin


title: MP46 cells, 24 hour Romidepsin treatment, sample 3

description:
Library name: MP46 Romidepsin 3
Column Name in MP46_RawReadCounts.txt: Romidepsin 3
Column Name in MP46_LogCPM.txt: Romidepsin 3
Column Name in MP46_QuantileNormalization.txt: Romidepsin.3
Row Name in MP46_Clean_stat.txt: R3


title: MP46 cells, 24 hour Quisinostat treatment, sample 3

description:
Library name: MP46 Quisinostat 3
Column Name in MP46_RawReadCounts.txt: Quisinostat 3
Column Name in MP46_LogCPM.txt: Quisinostat 3
Column Name in MP46_QuantileNormalization.txt: Quisinostat.3
Row Name in MP46_Clean_stat.txt: Q3


title: MP46 cells, 24 hour Mivebresib treatment, sample 3

description:
Library name: MP46 Mivebresib 3
Column Name in MP46_RawReadCounts.txt: Mivebresib 3
Column Name in MP46_LogCPM.txt: Mivebresib 3
Column Name in MP46_QuantileNormalization.txt: Mivebresib.3
Row Name in MP46_Clean_stat.txt: M3


title: MP46 cells, 24 hour Mivebresib treatment, sample 2

description:
Library name: MP46 Mivebresib 2
Column Name in MP46_RawReadCounts.txt: Mivebresib 2
Column Name in MP46_LogCPM.txt: Mivebresib 2
Column Name in MP46_QuantileNormalization.txt: Mivebresib.2
Row Name in MP46_Clean_stat.txt: M2


title: MP46 cells, 24 hour Quisinostat treatment, sample 1

description:
Library name: MP46 Quisinostat 1
Column Name in MP46_RawReadCounts.txt: Quisinostat 1
Column Name in MP46_LogCPM.txt: Quisinostat 1
Column Name in MP46_QuantileNormalization.txt: Quisinostat.1
Row Name in MP46_Clean_stat.txt: Q1


title: MP46 cells, 24 hour 0.1% DMSO treatment, sample 2

description:
Library name: MP46 Control 2
Column Name in MP46_RawReadCounts.txt: control 2
Column Name in MP46_LogCPM.txt: control 2
Column Name in MP46_QuantileNormalization.txt: control.2
Row Name in MP46_Clean_stat.txt: C2

value: 0.1% DMSO


title: MP46 cells, 24 hour 0.1% DMSO treatment, sample 3

description:
Library name: MP46 Control 3
Column Name in MP46_RawReadCounts.txt: control 3
Column Name in MP46_LogCPM.txt: control 3
Column Name in MP46_QuantileNormalization.txt: control.3
Row Name in MP46_Clean_stat.txt: C3


title: MP46 cells, 24 hour 0.1% DMSO treatment, sample 1

description:
Library name: MP46 Control 1
Column Name in MP46_RawReadCounts.txt: control 1
Column Name in MP46_LogCPM.txt: control 1
Column Name in MP46_QuantileNormalization.txt: control.1
Row Name in MP46_Clean_stat.txt: C1


title: PC-3 cells, replicate 3

description: Library name: Sample3

value: WT


title: MP41 cells, 24 hour Romidepsin treatment, sample 3

description:
Library name: MP41 Romidepsin 3
Column Name in MP41_RawReadCounts.txt: Romi3
Column Name in MP41_LogCPM.txt: Romi3
Column Name in MP41_QuantileNormalization.txt: Romi3
Row Name in MP41_Clean_stat.txt: R3


title: mrps-5 + C32E8.9 RNAi sample-1

description: N2 worms treated with mrps-5 + C32E8.9 RNAi sample-1

value: Whole body

value: mrps-5 + C32E8.9 RNAi


title: MP41 cells, 24 hour Mivebresib treatment, sample 3

description:
Library name: MP41 Mivebresib 3
Column Name in MP41_RawReadCounts.txt: Miveb3
Column Name in MP41_LogCPM.txt: Miveb3
Column Name in MP41_QuantileNormalization.txt: Miveb3
Row Name in MP41_Clean_stat.txt: M3


title: MP41 cells, 24 hour Mivebresib treatment, sample 2

description:
Library name: MP41 Mivebresib 2
Column Name in MP41_RawReadCounts.txt: Miveb2
Column Name in MP41_LogCPM.txt: Miveb2
Column Name in MP41_QuantileNormalization.txt: Miveb2
Row Name in MP41_Clean_stat.txt: M2


title: MP41 cells, 24 hour Romidepsin treatment, sample 2

description:
Library name: MP41 Romidepsin 2
Column Name in MP41_RawReadCounts.txt: Romi2
Column Name in MP41_LogCPM.txt: Romi2
Column Name in MP41_QuantileNormalization.txt: Romi2
Row Name in MP41_Clean_stat.txt: R2


title: MP41 cells, 24 hour Romidepsin treatment, sample 1

description:
Library name: MP41 Romidepsin 1
Column Name in MP41_RawReadCounts.txt: Romi1
Column Name in MP41_LogCPM.txt: Romi1
Column Name in MP41_QuantileNormalization.txt: Romi1
Row Name in MP41_Clean_stat.txt: R1


title: MP41 cells, 24 hour Mivebresib treatment, sample 1

description:
Library name: MP41 Mivebresib 1
Column Name in MP41_RawReadCounts.txt: Miveb1
Column Name in MP41_LogCPM.txt: Miveb1
Column Name in MP41_QuantileNormalization.txt: Miveb1
Row Name in MP41_Clean_stat.txt: M1


title: MP41 cells, 24 hour Quisinostat treatment, sample 2

description:
Library name: MP41 Quisinostat 2
Column Name in MP41_RawReadCounts.txt: Quis2
Column Name in MP41_LogCPM.txt: Quis2
Column Name in MP41_QuantileNormalization.txt: Quis2
Row Name in MP41_Clean_stat.txt: Q2


title: MP41 cells, 24 hour Quisinostat treatment, sample 3

description:
Library name: MP41 Quisinostat 3
Column Name in MP41_RawReadCounts.txt: Quis3
Column Name in MP41_LogCPM.txt: Quis3
Column Name in MP41_QuantileNormalization.txt: Quis3
Row Name in MP41_Clean_stat.txt: Q3


title: MP41 cells, 24 hour 0.1% DMSO treatment, sample 3

description:
Library name: MP41 Control 3
Column Name in MP41_RawReadCounts.txt: Control3
Column Name in MP41_LogCPM.txt: Control3
Column Name in MP41_QuantileNormalization.txt: Control3
Row Name in MP41_Clean_stat.txt: C3


title: MP41 cells, 24 hour 0.1% DMSO treatment, sample 2

description:
Library name: MP41 Control 2
Column Name in MP41_RawReadCounts.txt: Control2
Column Name in MP41_LogCPM.txt: Control2
Column Name in MP41_QuantileNormalization.txt: Control2
Row Name in MP41_Clean_stat.txt: C2


title: ATAC_BCG_R2

city: New York City

first: Andrew

middle: Wayne

last: Daman

state: NY

address: 1300 York Avenue

department: Pathology

institute: Weill Cornell Medical College

description: Library name: M6_ATAC

library_source: genomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the cell ranger software.
Paired-end ATAC-seq reads were quality trimmed using Trimmomatic.
After preprocessing and quality filtering, peaks were called on alignments with MACS2 using the BAMPE option.
For differential accessibility analyses the consensus peak set was generated using the R package DiffBind. The consensus peakset was generated per celltype.
Assembly: mm10
Supplementary files format and content: rds project files for RNA, and ATAC fragment files for ATAC data.

molecule: genomic DNA

source_name: Lineage- Bone Marrow Cells

extract_protocol:
Cells were sorted into FACS buffer  using a BD Aria II.
The library was performed according to the manufacturers instructions (single cell multiomics 10x genomics)

treatment_protocol: Mice treated with 3 doses of BCG and then

value: Lineage- Bone Marrow Cells

value: BCG


title: ATAC_BCG_R1

description: Library name: M5_ATAC


title: MP41 cells, 24 hour 0.1% DMSO treatment, sample 1

description:
Library name: MP41 Control 1
Column Name in MP41_RawReadCounts.txt: Control1
Column Name in MP41_LogCPM.txt: Control1
Column Name in MP41_QuantileNormalization.txt: Control1
Row Name in MP41_Clean_stat.txt: C1


title: ATAC_PBS_R2

description: Library name: M2_ATAC

value: PBS


title: MP41 cells, 24 hour Quisinostat treatment, sample 1

description:
Library name: MP41 Quisinostat 1
Column Name in MP41_RawReadCounts.txt: Quis1
Column Name in MP41_LogCPM.txt: Quis1
Column Name in MP41_QuantileNormalization.txt: Quis1
Row Name in MP41_Clean_stat.txt: Q1


title: MP46 cells, 24 hour Romidepsin treatment, sample 1

description:
Library name: MP46 Romidepsin 1
Column Name in MP46_RawReadCounts.txt: Romidepsin 1
Column Name in MP46_LogCPM.txt: Romidepsin 1
Column Name in MP46_QuantileNormalization.txt: Romidepsin.1
Row Name in MP46_Clean_stat.txt: R1


title: ATAC_PBS_R1

description: Library name: M1_ATAC


title: RNA_BCG_R2

description: Library name: M6_RNA

molecule: polyA RNA


title: LSK ATAC BCG Rep 2

description: Library name: LSK ATAC BCG Replicate 2

library_source: genomic

data_processing:
Samples were processed using a nextflow-based pipeline available at https://github.com/michaelbale/jlabflow.
Paired ends were Trimmed with CutAdapt
Mapped using Bowtie2
Assembly: MM10
Supplementary files format and content: .bw

source_name: Sorted LSK

extract_protocol:
Illumina Nextera ATACseq Kit
Omni-ATAC library contrustion protoocl

value: Sorted LSK


title: LSK ATAC BCG Rep 1

description: Library name: LSK ATAC BCG Replicate 1


title: LSK ATAC PBS Rep 2

description: Library name: LSK ATAC PBS Replicate 2


title: LSK ATAC PBS Rep 4

description: Library name: LSK ATAC PBS Replicate 4


title: RNA_BCG_R1

description: Library name: M5_RNA


title: RNA_PBS_R2

description: Library name: M2_RNA


title: LSK ATAC BCG Rep 3

description: Library name: LSK ATAC BCG Replicate 3


title: Tumor_CD45_BCG

description: Library name: Sorted_CD45_BCG

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the cell ranger software.
Assembly: mm10
Supplementary files format and content: h5ad anndata files.

source_name: Tumor infiltrating CD45

extract_protocol:
CD45+ Cells were sorted into FACS buffer  using a BD Aria II.
The library was performed according to the manufacturers inscrutions (single cell 3' protocol 10x genomics)

treatment_protocol: Bladder administration of BCG for 2 hours, 3 weeks in a row.

value: Tumor infiltrating CD45


title: Tumor_CD45_PBS

description: Library name: Sorted_CD45_PBS


title: RNA_PBS_R1

description: Library name: M1_RNA


title: Nrl(f/f);Cag-CreERT(+)_rep2

type: RNA

city: Saint Louis

first: Daniel

last: Murphy

state: MO

address: 660 S. Euclid

institute: Washington University School of Medicine

description: RNA isolated from acute Nrl knockout retinas at p63

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized on MoGene 1.0 ST Array in the GeneChip Hybridization Oven 640 for 18 hr at 45C. GeneChip were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G 3000.

data_processing: The single-channel .CEL output files were processed using the limma and affy packages in R with Affymetrix mogene10 annotation data. Data files were loaded using the affy function justRMA, and the differentially expressed genes were determined with the limma functions linear model fit (lmFit) and empirical Bayes statistics (eBayes)

label: biotin

source_name: Whole retina RNA from two Nrlflox/flox mice treated with 4-hydroxytamoxifen from P42 to P44 to induce recombination of both Nrlflox alleles

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen Pico SL-Ovation RNA Amplification system for starting materials from 500pg-50 ng total RNA..

extract_protocol: Total RNA was extracted from retinas using TRIzol LS reagent (Thermo Fisher Scientific; Waltham, MA) and purified using the RNeasy kit (Qiagen; Germantown, MD). Two biological replicates, each consisting of total RNA from four retinas (two animals), for each genotype were analyzed.

treatment_protocol: Mice were injected intraperitoneally on a daily basis from P42 to P44 with 4-hydroxytamoxifen (dissolved in 15% ethanol/85% corn oil; Sigma Aldrich, St. Louis, MO) to induce recombination of the Nrlflox alleles, and retinas were then harvested at P63 for microarray analysis.

value: Nrl(f/f);Cag-CreERT(+)


title: EACBEko-DP-Trav14-HTGTS-rep3

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

country: China

institute: Southern Medical University

description: Library name: Sample 7

data_processing:
Illumina Casava1.7 software used for basecalling.
3C-HTGTS data processing for pairwise chromatin interactions. Paired-end Illumina sequencing fastq data were filtered by removing adapters and low-quality reads with using fastp (v0.20.0). Trimmed reads again were extracted from the sequence file after quality control with Cutadapt (v1.18). Paired-end reads containing nested primer or adapter primer were merged manually using restriction enzyme recognition sequences into single reads with Pear (v0.9.6), then the first digested fragment behind the bait was obtained by splitting the single reads into fragments according to restriction enzyme recognition sequences. The remaining single-end reads were aligned to the enzyme-digested mm10 reference genome with Bowtie2 (v2.4.5, parameter: -p 8 --sensitive), and mouse genome sequence (mm10) was retrieved from the UCSC and we extracted concordantly exact alignments using SAMtools (v1.9). Self-ligation reads and off-targeted reads were filtered after mapping. For visualization, we converted the final bam files into bedGraph files using Bedtools (v2.29.2). The signal peak bedGraph file was obtained by post-comparison filtering, signal statistics, and standardization. We normalized bedGraph files using the CPM (Counts Per Million in cis) normalization method and visualized them on the IGV genome browser. Differential pair-wise interactions were identified by the R package R.4Cker (v1.0.0, k=30) with the function nearBaitAnalysis called to define domains of interaction with the bait and DESeq2 (v1.34.0, p < 0.05). Finally, we organized the results report and visualized it with the Bioconductor package ggplot2 (v3.3.6).
3C-HTGTS data processing for three-way chromatin interactions. Paired-end Illumina sequencing reads were filtered by removing adapters and low-quality reads with using fastp (v0.20.0). Trimmed reads were extracted from the file after quality control with Cutadapt (v1.18). Paired-end reads containing nested primer or adapter primer were merged at restriction enzyme cut sites into single reads with Pear (v0.9.6), then fragments with multiple MboI cut sites were split and each fragment was aligned to the enzyme-digested mm10 reference genome by Bowtie2 (v2.4.5, parameter: -p 8 --sensitive). We extracted concordantly exact alignments using SAMtools (v1.9). We converted the final bam files into bed files using Bedtools (v2.29.2). Self-ligation and off-targeted fragments were filtered. Subsequently, we put all fragments retrieved from the same read according to the unique ID of each read on one line, then removed the continuous fragments. To create contact matrices, we extracted the first two digested fragments after the bait fragment, or a variety of combinations of three fragments were obtained by arranging all fragments from the same read. Raw contact matrices were generated at 3 kb, 5 kb, and 10 kb resolutions. For raw contact matrices correction, these interaction counts were normalized for a total of 1,000,000 interactions at the same resolutions. Similar to a Hi-C matrix, coverage was represented in a 2-dimensional matrix where each point represented the number of interactions found between two bins meaning a specific resolution. Differential analysis and visualization of local interactions from three-way interactions were obtained using the R package GENOVA (v1.0.0). Loops seen on the IGV genome browser were called using fixed-size bin resolutions from 3 kb to 10 kb. Briefly, interaction loops (contact frequencies >= 5) were identified by using raw contact frequencies.
ChIP-Seq data process pipline. The raw data were processed and analyzed according to the following procedure. First, SRA files were converted to fastq format, then aligned to mouse genome (mm10) using Bowtie2 (v2.4.5, parameter: -p 8 --sensitive). PCR duplicated fragments were filtered by Picard (v2.22.8) (http://broadinstitute.github.io/picard). Then, we filtered the unmapped, multi-mapped reads and mapping to the reads on chrM. Peaks were identified by HOMER (v4.10.4) . FRiP (Fragments Ratio in Peaks) value was calculated using Bedtools (v2.29.2) and awk (v4.0.2). We used deepTools (v3.5.0) (https://github.com/deeptools/deepTools) to generate bigWig file with CPM normalization. Profiles were obtained on a region of ±0.2 Mb from the center of peaks, and average scores were plotted to generate averaged read density around peaks using deepTools(v3.5.0) plotProfile.
Assembly: mm10
Supplementary files format and content: BedGraph files were generated using Bedtools (v2.29.2) with normalized values for each sample.
Supplementary files format and content: BigWig files were generated using bamCoverage with normalized values for each sample.

source_name: Thymus

growth_protocol: All experiments involving mice were performed using protocols approved by  Southern Medical University Animal Studies Committee. Mice were on a C57Bl/6 genetic background . Animals were housed and bred in a specific pathogen-free animal facility.

extract_protocol:
For 3C-HTGTS, mouse thymus were removed, cells were filtered through nylon mech.10 million cells were cross-linked with 1% formaldehyde. Cell were lysed and digest with 200U MboI overnight at 37°C. The sample was ligated with T4 DNA ligase overnight at 16°C. Crosslinks were reversed by Proteinase K and RNase A prior to DNA extraction with 1:1 phenol-chloroform and precipitation with ethanol. The 10ug 3C DNA was sonicated to 300-500bp and was linearly amplified with a biotinylated primer. The biotin-labeled single-stranded DNA products were enriched with streptavidin C1 beads, and followed by 3’ ends ligation with the bridge adaptor. The adaptor-ligated products were amplified via nested PCR using a nested primer and an adaptor-complementary primer.The detailed primers used in this study are also listed in Supplementary information, Table S1.  And a final PCR for another 5-10 cycles with P5 and P7 was performed. After purification of the PCR products, the final libraries were sequenced on an Illumina NovaSeq 6000 platform to obtain 150 bp paired-end reads.
For ChIP-Seq, Chromatin immunoprecipitation (ChIP) was performed on DN thymocytes from 3-4 Rag1-/- mice and 10 million anti-CD3 antibody-stimulated DP thymocytes from Rag1-/- mice per experiment. Cells were crosslinked with a final concentration of 1% formaldehyde on ice for 10 minutes and quenched with glycine (final concentration 0.125 M) on ice for 5 minutes. Cells were washed in 1x PBS once. The subsequent steps were carried out as ABclonal Sonication ChIP Kit (RK20258) with some modifications. After lysed and sonicated, chromosomal DNA was incubated with 5μg of specific antibody (anti-CTCF 07-729 from Millipore, anti-Rad21 Ab992 from Abcam) or isotype-matched IgG for 5 hours at 4°C, followed by addition of 15μl protein A/G magnetic beads for an additional 2 hours at 4°C. After washing and reversal of cross-linking, Immunoprecipitates place tube on magnet and collect supernatant to a new tube.The product was purified by PCR purification kit. Immunoprecipitated and input DNAs were quantified by real time PCR or sequenced on an Illumina NovaSeq 6000 platform to obtain 150 bp pair-end reads.
Construction of libraries were described as the above extract protocol

treatment_protocol: Three week-old mice were intraperitoneally injected with 150ug of CD3 antibody and thymic DP cells were taken 10 days later.

value: Thymus

value: T-cell

value: DP thymocytes

value: EACBE-/-


title: EACBEko-DP-Trav14-HTGTS-rep1

description: Library name: Sample 5


title: EACBEko-Rag1ko-DN-GT-RNA-Seq-rep2

description: Library name: Sample 1

value: DN thymocytes


title: EACBEko-DP-Trav14-HTGTS-rep2

description: Library name: Sample 6


title: EACBEwt-DP-Trav14-HTGTS-rep2

description: Library name: Sample 3

value: EACBE+/+


title: EACBEwt-DP-Trav14-HTGTS-rep1

description: Library name: Sample 2


title: Nrl(f/f);Cag-CreERT(+)_rep1


title: EACBEwt-DP-Trav14-HTGTS-rep3

description: Library name: Sample 4


title: Adult mouse bone marrow monocytes, ATAC

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

description:
Library name: BM_monocytes_snATACseq
ATACseq (v2 10x Genomics): read1 and read3 contain the transposed DNA sequence, while read2 contains the cell barcode
BM_monocytes_snATACseq_JBA1_filtered_peak_bc_matrix.h5
BM_monocytes_snATACseq_JBA1_fragments.tsv.gz
Metadata_FL.monocytes.BM.monocytes_snATACseq.csv

data_processing:
Raw data bcl files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
Assembly: mm10, GRCh38
Supplementary files format and content: Compressed .h5/tar.gz files containing UMI RNA/ADT/ATAC peak counts in Cellranger output format, ATAC fragment (.tsv.gz) files, and comma-delimited text files including metadata per cell

source_name: bone marrow monocytes

extract_protocol: All methods listed in Bastos et al. Monocytes can efficiently replace all brain macrophages and instruct different microglial identities depending on their origin. Immunity. 2025

value: bone marrow monocytes


title: Mouse brains after injection of human cord blood monocytes, donor 1

description:
Library name: hCSF1_brain_human_cord_monocytes_donor1
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
hCSF1_brain_human_cord_monocytes_donor1_MVP7_raw_feature_bc_matrix.tar.gz
Metadata_hCSF1_brain_human.cord.monocytes.adult.monocytes.csv
Metadata_hCSF1_brain_human.cord.monocytes.adult.monocytes_Macrophage_subset.csv

value: brain

value: hCSF1:Rag2-/-:gamma c-/-

value: intracerebrally injected with human cord blood monocytes


title: Mouse brains after injection of human cord blood monocytes, donor 2

description:
Library name: hCSF1_brain_human_cord_monocytes_donor2
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
hCSF1_brain_human_cord_monocytes_donor2_MVP8_raw_feature_bc_matrix.h5
Metadata_hCSF1_brain_human.cord.monocytes.adult.monocytes.csv
Metadata_hCSF1_brain_human.cord.monocytes.adult.monocytes_Macrophage_subset.csv


title: Nrl(+/f);Cag-CreERT(+)_rep1

description: RNA isolated from control retinas at p63

source_name: Whole retina RNA from two Nrlflox/+ mice treated with 4-hydroxytamoxifen from P42 to P44. Control mice in which there is an intact Nrl allele

value: Nrl(+/f);Cag-CreERT(+)


title: Mouse brains after injection of adult human blood monocytes, donor 1

description:
Library name: hCSF1_brain_human_adult_monocytes_donor1
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
hCSF1_brain_human_adult_monocytes_donor1_MVP9_raw_feature_bc_matrix.h5
Metadata_hCSF1_brain_human.cord.monocytes.adult.monocytes.csv
Metadata_hCSF1_brain_human.cord.monocytes.adult.monocytes_Macrophage_subset.csv

value: intracerebrally injected with adult human blood monocytes


title: Mouse fetal liver monocytes, ATAC

description:
Library name: FL_monocytes_snATACseq
ATACseq (v2 10x Genomics): read1 and read3 contain the transposed DNA sequence, while read2 contains the cell barcode
FL_monocytes_snATACseq_JBA2_filtered_peak_bc_matrix.h5
FL_monocytes_snATACseq_JBA2_fragments.tsv.gz
Metadata_FL.monocytes_snATACseq_Monocyte.macrophage.subset.csv
Metadata_FL.monocytes.BM.monocytes_snATACseq.csv

source_name: fetal liver monocytes

value: fetal liver monocytes


title: Mouse brains after injection of CD177+ monocytes

description:
Library name: Brain_GDP-monocytes
3’ mRNA (v4 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
Brain_GDP-monocytes_JBA4_raw_feature_bc_matrix.h5
MetadataBrain_Brain_MDP-mono.GMP-mono_JBA3.4.csv

value: CD45+ CD11b+ GFP+

value: intracerebrally injected with CD177+ (GDP-derived)  monocytes from Cx3cr1 GFP/+ mice


title: LSK ATAC PBS Rep 3

description: Library name: LSK ATAC PBS Replicate 3

value: Sorted LSK

value: WT

value: PBS


title: Mouse brains after injection of CD319+ monocytes

description:
Library name: Brain_MDP-monocytes
3’ mRNA (v4 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
Brain_MDP-monocytes_JBA3_raw_feature_bc_matrix.h5
MetadataBrain_Brain_MDP-mono.GMP-mono_JBA3.4.csv

value: intracerebrally injected with CD319+ (MDP-derived)  monocytes from Cx3cr1 GFP/+ mice


title: Mouse brains after injection of fetal liver monocytes, sample 2, GFP- fraction

description:
Library name: Brain_FL_monocytes_GFPneg_sample2
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
Brain_FL_monocytes_GFPneg_sample2_IPJ24_raw_feature_bc_matrix.h5
MetadataBrain_FL_monocytes_GFPneg.GFPpos_IPJ22.23.24.25.csv

value: CD45+ CD11b+, GFP-

value: intracerebrally injected with Cx3cr1 GFP/+  E14 fetal liver monocytes


title: Mouse brains after injection of fetal liver monocytes, sample 2, GFP+ fraction

description:
Library name: Brain_FL_monocytes_GFPpos_sample2
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
Brain_FL_monocytes_GFPpos_sample2_IPJ25_raw_feature_bc_matrix.h5
MetadataBrain_FL_monocytes_GFPneg.GFPpos_IPJ22.23.24.25.csv

value: CD45+ CD11b+, GFP+


title: Mouse brains after injection of fetal liver monocytes, sample 1, GFP+ fraction

description:
Library name: Brain_FL_monocytes_GFPpos_sample1
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
Brain_FL_monocytes_GFPpos_sample1_IPJ23_raw_feature_bc_matrix.h5
MetadataBrain_FL_monocytes_GFPneg.GFPpos_IPJ22.23.24.25.csv


title: Subdural leptomeninges of control mice

description:
Library name: Subdura_Ctrl
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
Subdura_Ctrl_IPJ20_raw_feature_bc_matrix.h5
Metadata_Subdura_PLX.Ctrl_IPJ20.21.csv

source_name: Subdural leptomeninges

value: Subdural leptomeninges

value: CD45+, CD11b+, CX3CR1-mid, CLEC12A-high

value: Flt3-Cre R26-YFP

value: 9 weeks on control chow


title: Mouse brains after injection of fetal liver monocytes, sample 1, GFP- fraction

description:
Library name: Brain_FL_monocytes_GFPneg_sample1
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
Brain_FL_monocytes_GFPneg_sample1_IPJ22_raw_feature_bc_matrix.h5
MetadataBrain_FL_monocytes_GFPneg.GFPpos_IPJ22.23.24.25.csv

value: brain


title: Mouse brains after injection of adult human blood monocytes, donor 2

description:
Library name: hCSF1_brain_human_adult_monocytes_donor2
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
hCSF1_brain_human_adult_monocytes_donor2_MVP10_raw_feature_bc_matrix.h5
Metadata_hCSF1_brain_human.cord.monocytes.adult.monocytes.csv
Metadata_hCSF1_brain_human.cord.monocytes.adult.monocytes_Macrophage_subset.csv

value: hCSF1:Rag2-/-:gamma c-/-


title: Subdural leptomeninges of mice treated with PLX3397

description:
Library name: Subdura_PLX
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
Subdura_PLX_IPJ21_raw_feature_bc_matrix.h5
Metadata_Subdura_PLX.Ctrl_IPJ20.21.csv

value: 2 weeks PLX3397 chow followed by 7 weeks of repopulation on control chow


title: Brains of control mice

description:
Library name: Brain_Ctrl
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
Brain_Ctrl_IPJ18_raw_feature_bc_matrix.h5
Metadata_Brain_PLX.Ctrl_IPJ18.19.csv
Metadata_Brain_PLX.Ctrl_Macrophage_subset_IPJ18.19.csv


title: Neonate female mouse brains after adoptive transfer of monocytes, ADT

description:
Library name: Neonate_female_brain_GFP_monocytes_ADT
ADT: read1 contains cell barcode and UMI; read2 contains Antibody Derived Tag sequences
Neonate_female_brain_GFP_monocytes_IPJ13_raw_feature_bc_matrix.h5
Metadata_Brain_GFP_monocytes_IPJ11.12.13.csv
Metadata_Brain_GFP_monocytes_Macrophage_subset_IPJ11.12.13.csv

library_source: other

data_processing:
Raw data bcl files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
Assembly: mm10, GRCh38
Supplementary files format and content: Compressed .h5/tar.gz files containing UMI RNA/ADT/ATAC peak counts in Cellranger output format, ATAC fragment (.tsv.gz) files, and comma-delimited text files including metadata per cell
Library strategy: CITE-seq

molecule: protein

value: CD45+; mix GFP- and GFP+  1:1

value: adoptive transfer of monocytes from Cx3cr1 GFP/+ mice


title: Adult mouse brains after adoptive transfer of monocytes, ADT

description:
Library name: Adult_brain_GFP_monocytes_ADT
ADT: read1 contains cell barcode and UMI; read2 contains Antibody Derived Tag sequences
Adult_brain_GFP_monocytes_IPJ11_raw_feature_bc_matrix.h5
Metadata_Brain_GFP_monocytes_IPJ11.12.13.csv
Metadata_Brain_GFP_monocytes_Macrophage_subset_IPJ11.12.13.csv


title: Neonate male mouse brains after adoptive transfer of monocytes, ADT

description:
Library name: Neonate_male_brain_GFP_monocytes_ADT
ADT: read1 contains cell barcode and UMI; read2 contains Antibody Derived Tag sequences
Neonate_male_brain_GFP_monocytes_IPJ12_raw_feature_bc_matrix.h5
Metadata_Brain_GFP_monocytes_IPJ11.12.13.csv
Metadata_Brain_GFP_monocytes_Macrophage_subset_IPJ11.12.13.csv


title: total RNA, Female Fast24h WT Digitonin PP, biol rep 2

city: Bronx

first: Jeffrey

middle: E

last: Pessin

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

description: Library name: F24hPP2

data_processing:
Transcript-level counts were estimated by Kallisto v0.46.0
Outputs from Kallisto (v0.46.0) were imported into R using the Bioconductor package tximport (v1.20.0), and the expression levels of each gene were estimated.
Assembly: mm10
Supplementary files format and content: comma-separated text file including gene-level raw counts for each sample

extract_protocol:
Total RNA isolation from isolated hepatocytes and mouse liver was done with RNeasy mini kit (Qiagen, #74106) combined with TRIzol (Invitrogen, #15596026) according to the manufacture’s protocol.
RNA libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: All 12-week-old mice were fed Normal Chow: lab diet #5053

value: Liver

value: periportal hepatocyte

tag: Sex

value: Female

tag: diet

value: Normal Chow:lab diet #5053


title: Neonate female mouse brains after adoptive transfer of monocytes, cDNA

description:
Library name: Neonate_female_brain_GFP_monocytes_cDNA
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
Neonate_female_brain_GFP_monocytes_IPJ13_raw_feature_bc_matrix.h5
Metadata_Brain_GFP_monocytes_IPJ11.12.13.csv
Metadata_Brain_GFP_monocytes_Macrophage_subset_IPJ11.12.13.csv


title: total RNA, Female Fast24h WT Digitonin PP, biol rep 3

description: Library name: F24hPP3

value: WT


title: Brains of mice treated with PLX3397

description:
Library name: Brain_PLX
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
Brain_PLX_IPJ19_raw_feature_bc_matrix.h5
Metadata_Brain_PLX.Ctrl_IPJ18.19.csv
Metadata_Brain_PLX.Ctrl_Macrophage_subset_IPJ18.19.csv


title: toal RNA, Female Fast24h WT Digitonin PC, biol rep 2

description: Library name: F24hPC2

value: pericentral hepatocytes


title: Neonate male mouse brains after adoptive transfer of monocytes, cDNA

description:
Library name: Neonate_male_brain_GFP_monocytes_cDNA
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
Neonate_male_brain_GFP_monocytes_IPJ12_raw_feature_bc_matrix.h5
Metadata_Brain_GFP_monocytes_IPJ11.12.13.csv
Metadata_Brain_GFP_monocytes_Macrophage_subset_IPJ11.12.13.csv


title: total RNA, Female Fast24h WT Digitonin PP, biol rep 1

description: Library name: F24hPP1

value: periportal hepatocytes


title: total RNA, Female Fast24h WT Digitonin PC, biol rep 3

description: Library name: F24hPC3


title: Adult mouse bone marrow monocytes, GEX

description:
Library name: BM_monocytes_scRNAseq
3’ mRNA (v4 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
BM_monocytes_scRNAseq_JBA6_raw_feature_bc_matrix.h5
Metadata_FL.monocytes.BM.monocytes_scRNAseq_Monocyte.macrophage.subset.csv

value: bone marrow monocytes


title: Mouse fetal liver monocytes, GEX

description:
Library name: FL_monocytes_scRNAseq
3’ mRNA (v4 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
FL_monocytes_scRNAseq_JBA7_raw_feature_bc_matrix.h5
Metadata_FL.monocytes_scRNAseq_Monocyte.macrophage.subset.csv
Metadata_FL.monocytes.BM.monocytes_scRNAseq_Monocyte.macrophage.subset.csv

value: fetal liver monocytes


title: total RNA, Female Fed4h WT Digitonin PP, biol rep 2

description: Library name: F0hPP2


title: total RNA, Female Fed4h WT Digitonin PP, biol rep 3

description: Library name: F0hPP3


title: total RNA, Female Fed4h WT Digitonin PC, biol rep 3

description: Library name: F0hPC3


title: Dox_KO_164

city: Tainan

first: Hung-Chia

last: Hsieh

address: 70101 No.1-3, Daxue Rd., East Dist.

country: Taiwan

institute: National Cheng Kung University

data_processing:
Read pairs mapping from each sample were aligned to the reference genome by the HISAT2 software (v2.1.0) and the results were reported following the “fragments per kilobase of transcript per million mapped reads” method, known as FPKM, which quantile normalized all samples.
Genes with fragments per kilobase of transcript per million mapped reads (FPKM) values larger than four and that exhibited low variation across three biological replicates were considered reliable and were used in subsequent analyses
Assembly: mm39
Supplementary files format and content: tab-delimited Excel file includes FPKM values for each sample

source_name: Lung tumor

growth_protocol: The triple transgenic mice (Scgb1a1-rtTA/EGFRL858R/Usp24C1695A) were fed with doxycycline (0.5 g/l) for ten weeks to induce lung adenocarcinoma formation.

extract_protocol:
Total RNA was extracted and purified by a Quick-RNA MiniPrep Kit (Zymo Research, Irvine, CA, USA);  3 μg of isolated total RNA was qualified for sequencing libraries
RNA fragmentation and library preparation (KAPA Biosystems, Roche, Basel, Switzerland) were carried out by the NovaSeq 6000 System (Illumina, San Diego, CA, USA), through which the constructed libraries were analyzed by 150 bp paired-end high-throughput sequencing at Biotools Co., Ltd. (New Taipei City, Taiwan).

value: Lung tumor

value: 10 weeks doxycycline


title: Dox_KO_145


title: Dox_WT_1370


title: Dox_WT_1364


title: Dox_WT_1354


title: ND6, replicate1, scRNA-seq

city: Hangzhou

first: Cheng

last: Ai

state: Zhejiang

address: 866 Yuhangtang Road

institute: Institute of Genetics, Zhejiang University School of Medicine

description: 10X Genomics

data_processing:
fter quality control, raw sequencing reads were aligned to the mouse reference genome mm10 and processed to a matrix representing the UMI’s per cell barcode per gene using CellRanger (v3.0.2, 10x Genomics)
Assembly: mm10
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: retina

extract_protocol:
Retina was dissected from the eyeball and digested with Tyrisin and papain to sing cell solution
Libraries for scRNA-seq were generated using the Chromium Single Cell 3′ library and Gel Bead & Multiplex Kit from 10x Genomics.

value: retina

value: male

tag: age

value: 7 months


title: Adult mouse brains after adoptive transfer of monocytes, cDNA

description:
Library name: Adult_brain_GFP_monocytes_cDNA
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
Adult_brain_GFP_monocytes_IPJ11_raw_feature_bc_matrix.h5
Metadata_Brain_GFP_monocytes_IPJ11.12.13.csv
Metadata_Brain_GFP_monocytes_Macrophage_subset_IPJ11.12.13.csv

value: brain


title: total RNA, Female Fast24h WT Digitonin PC, biol rep 1

description: Library name: F24hPC1


title: HEK293T DNA methylation derived from IF1_KO UCP4_OE_4

type: genomic

city: Research Triangle Park

first: Elizabeta

last: Gjoneska

state: North Carolina

address: 111 TW Alexander Dr., David P Rall Building A030

department: Neurobiology Laboratory

institute: National Institute of Environmental Health Sciences (NIEHS/NIH)

description: IF1-KO pcDNA3.1-UCP4(SLC25A27)-NE whole cell DNA

hyb_protocol: Differential methylation at the CpG dinucleotide level was conducted using Human Infinium Methylation EPIC 850K v1.0 BeadChip arrays (Illumina) following the Infinium methylation protocol.

data_processing:
R package ChAMP version 2.30.0
BMIQ normalized beta values

label: Cy3 and Cy36

label_protocol: Samples were bisulfite-converted using an EZ DNA Methylation kit (Zymo Research) following the manufacturer’s protocol

growth_protocol: HEK293T cells were routinely maintained in DMEM high glucose (25 mM), FBS 10% (v/v), sodium pyruvate 1 mM, uridine 100 μg/mL, 1% (v/v) HEPES, pH 7.1-7.6 (10 mM), pen/strep 0.16% (v/v), and hygromycin 150 μg/mL in a humified incubator with 5% CO2 at 37 °C (standard conditions). Subculture was performed by diluting 90% confluent T-25 (Corning) flasks into 5 mL fresh medium in a 1:6 to 1:10 ratio. Medium was replaced every other day.

extract_protocol: Medium was removed and cells were gently washed once with ice-cold PBS. DNA was isolated using DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer's instruction. DNA was quantified using Nanodrop, and for quality control, samples were re-assessed using Qubit 3.0.

treatment_protocol: Cells from three independently growing flasks were split into 6-well plates. 2×105 cells were plated and incubated under standard conditions for 6 h. For treatment with DMSO (1:1000), telmisartan 2 μM, and annatto 10 μM, cells were treated for 3 days. Cells were split and counted, and  2×105 cells were plated and incubated in each treatment group medium for an additional 3 days (6 cumulative days). Cells were split and counted, and  1.25×105 cells were plated and incubated in each treatment group medium for an additional 4 days (10 cumulative days).  For genotype comparison (IF1-KO vs. IF1-KO PEMT-OE), cells were allowed to grow for 4 days.

value: DN-POLG, IF1-KO, UCP4-OE

value: No treatment


title: E11.5, NCAPH2, Sample 2

city: Rochester

first: Laurie

last: Steiner

address: 601 Elmwood Ave

department: Pediatrics

institute: University of Rochester

data_processing:
Bowtie2 alignment to mm10 genome
Picard duplicate removal
bamCoverage RPKM normalization
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: erythroblast

growth_protocol: For timed pregnancies, females were monitored for vaginal plugs. The presence of a vaginal plug marked embryonic day 0.5 (E11.5). Embryos were dissected from pregnant females at E11.5.

extract_protocol:
CUT&RUN was performed using the EpiCypher CUTANA ChIC/CUT&RUN Kit
Libraries were generated using the NEBNext Ultra II DNA Library Prep kit (NEB). Size selection was optimized for small fragments (end prep for 20C for 30 minutes followed by 50C for 60 minutes, ligation AMPure XP cleanup at 1.75X, annealing temperature of 65C for library amplification, and library AMPure XP cleanup using 1st round negative selection at 0.8X followed by a 2nd round positive selection at 1.2X).

tag: developmental stage

value: erythroblast

value: NCAPH2 +/+

tag: antibody


title: E11.5, NCAPH2, Sample 3


title: Nrl(+/f);Cag-CreERT(+)_rep2

description: RNA isolated from control retinas at p63

value: Nrl(+/f);Cag-CreERT(+)


title: E11.5, NCAPH2, Sample 1


title: WT, replicate1, scRNA-seq

description: 10X Genomics


title: HEK293T DNA methylation derived from IF1_KO UCP4_OE_2

scan_protocol: Differential methylation at the CpG dinucleotide level was conducted using Human Infinium Methylation EPIC 850K v1.0 BeadChip arrays (Illumina) following the Infinium methylation protocol.

label: Cy3 and Cy34


title: KO, NCAPH2, H4K20me1, E11.5, Rep 4

value: NCAPH2 FL/FL EpoR Cre


title: Neg, WT, NCAPH2, IgG, E11.5

value: IgG


title: E11.5, H4K20me1, Sample 3


title: HEK293T DNA methylation derived from IF1_KO UCP4_OE_1

label: Cy3 and Cy33


title: E11.5, H4K20me1, Sample 2


title: KO, NCAPH2, H4K20me1, E11.5, Rep 3


title: total RNA, Female Fed4h WT Digitonin PC, biol rep 1

description: Library name: F0hPC1

value: Liver

value: pericentral hepatocytes

value: WT

value: Female

value: Normal Chow:lab diet #5053


title: HEK293T DNA methylation derived from IF1_KO empty_4

description: IF1-KO pcDNA3.1 whole cell DNA

label: Cy3 and Cy32

value: DN-POLG, IF1-KO


title: total RNA, Female Fed4h WT Digitonin PP, biol rep 1

description: Library name: F0hPP1

value: periportal hepatocytes


title: KO, NCAPH2, H4K20me1, E11.5, Rep 2


title: KO, NCAPH2, H4K20me1, E11.5, Rep 1


title: HEK293T DNA methylation derived from IF1_KO empty_3

description: IF1-KO pcDNA3.1 whole cell DNA

label: Cy3 and Cy31


title: HEK293T DNA methylation derived from IF1_KO empty_2

description: IF1-KO pcDNA3.1 whole cell DNA

label: Cy3 and Cy30


title: Dox_KO_134

value: Lung tumor

value: 10 weeks doxycycline


title: toal RNA, Female Fed4h WT Digitonin PC, biol rep 2

description: Library name: F0hPC2


title: Het, NCAPH2, H4K20me1, E11.5, Rep 3

value: NCAPH2 FL/+ EpoR Cre


title: HEK293T DNA methylation derived from IF1_KO UCP4_OE_3

label: Cy3 and Cy35

value: DN-POLG, IF1-KO, UCP4-OE


title: HEK293T DNA methylation derived from IF1_KO DNP_4

description: IF1-KO treated with 2,4-DNP 25 μM whole cell DNA

label: Cy3 and Cy28

value: 2,4-DNP 25 μM for 3 days


title: E11.5, H4K20me1, Sample 1

value: erythroblast


title: Het, NCAPH2, H4K20me1, E11.5, Rep 2


title: Het, NCAPH2, H4K20me1, E11.5, Rep 1


title: HEK293T DNA methylation derived from IF1_KO DNP_1

label: Cy3 and Cy25


title: HEK293T DNA methylation derived from IF1_KO DMSO_4

description: IF1-KO treated with DMSO whole cell DNA

label: Cy3 and Cy24

value: DMSO (1:1000) for 3 days


title: HEK293T DNA methylation derived from IF1_KO DNP_3

label: Cy3 and Cy27


title: WT, NCAPH2, H4K20me1, E11.5, Rep 3

value: NCAPH2 +/+


title: HEK293T DNA methylation derived from IF1_KO DMSO_3

description: IF1-KO treated with DMSO whole cell DNA

label: Cy3 and Cy23


title: HEK293T DNA methylation derived from IF1_KO DMSO_2

description: IF1-KO treated with DMSO whole cell DNA

label: Cy3 and Cy22


title: HEK293T DNA methylation derived from IF1_KO DNP_2

label: Cy3 and Cy26


title: WT, NCAPH2, H4K20me1, E11.5, Rep 2


title: NTC_replicate_3

data_processing:
Illumina adapter sequences were trimmed using CutAdapt
STAR (v2.7.3a) was used to align reads to the genome (GRCm38/mm10)
HTSeq (0.12.4) was used to count reads per gene
Differential gene expression was calculated with DESeq2 (v1.42.0) with a log fold-change threshold of 1 and and adjusted p-value threshold of 0.05
Assembly: mm10
Supplementary files format and content: .count files are tab delimited text files which include counts for each gene
Supplementary files format and content: DESeq2_AcuteNr2e2KOvsControl is an excel spreadsheet with the output of differential expression analysis from DESeq2- including average counts per gene for each condition, log2 fold-change values, and p-values.

extract_protocol:
6-months post-injection the retinas of injected mice were dissociated with papain and single cell suspensions were FAC sorted based on mCherry expression from the AAV. Approximately 100,000 cells were sorted per sample, each of which consisted of two injected retinas from a single animal. Total RNA was isolated in Trizol according to manufacturer's instructions
RNA integrity was determined using a Bioanalyzer. Total RNA was transcribed into cDNA using the SMARTer Ultra Low RNA kit for Illumina Sequencing per manufacturer's instructions.

treatment_protocol: 4-week old Rosa26-Cas9 mice were subretinally injected with AAV harboring guide RNA targeting either Nr2e3 or non-targeting control. Approximately 2x109 viral genomes were injected into each eye in a 0.25µl volume. The AAV was generated from a backbone (Addgene #91947) modified by replacing the CBh promoter with a human GRK1  promoter sequence in order to restrict mCherry expression to photoreceptors and packaged with a 7m8 coat.

value: retina

value: male

value: FACs-purified photoreceptor

value: control guide RNA


title: Nr2e3_KO_replicate_3

value: female

value: anti Nr2e3 guide RNA


title: WT, NCAPH2, H4K20me1, E11.5, Rep 4


title: WT, NCAPH2, H4K20me1, E11.5, Rep 1


title: HEK293T DNA methylation derived from IF1_OE_4

description: IF1-OE whole cell DNA

label: Cy3 and Cy20

value: DN-POLG, IF1-KO, IF1-OE

value: No treatment


title: NTC_replicate_2


title: NTC_replicate_1


title: HEK293T DNA methylation derived from IF1_KO DMSO_1

description: IF1-KO treated with DMSO whole cell DNA

label: Cy3 and Cy21

value: DN-POLG, IF1-KO


title: HEK293T DNA methylation derived from IF1_OE_2

description: IF1-OE whole cell DNA

label: Cy3 and Cy18


title: HEK293T DNA methylation derived from IF1_KO empty_1

description: IF1-KO pcDNA3.1 whole cell DNA

label: Cy3 and Cy29


title: HEK293T DNA methylation derived from IF1_OE_3

description: IF1-OE whole cell DNA

label: Cy3 and Cy19


title: HEK293T DNA methylation derived from IF1_OE_1

description: IF1-OE whole cell DNA

label: Cy3 and Cy17


title: HEK293T DNA methylation derived from IF1_KO_G6PDi_4

description: IF1-KO treated with G6PDi 50 μM whole cell DNA

label: Cy3 and Cy16

value: G6PDi 50 μM for 3 days


title: 2_month_female_islet_cells_repeat_2

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
After sequencing, the reads were filtered and aligned to the reference transcriptome using the DROPEST pipeline (https://github.com/hms-dbmi/dropEst). The mapped reads were quantified into UMI-filtered counts per gene and barcodes that corresponded to cells were retrieved using previously established methods (Southard-Smith et al., 2020).
Barcodes are limited to the filtered files submitted in the accompanying manuscript (Brown et al., 2024)
NextSeq: Technical read: Read 2 -UMI/Cell barcodes are positioned as in (Klein et al., 2015). Biological read: read1 -transcript
Assembly: Mouse: GRCm38.25
Supplementary files format and content: Delimited tables with cells and genes defined as columns and rows

source_name: endocrine islets, 2-months-old, 5 females

extract_protocol:
Islets were obtained as previously described (Huang et al., 2018a). Mouse cells were encapsulated using the inDrop platform (1CellBio) as described in (Simmones et al., 2022).
Libraries were prepped as previously described in (Southard-Smith et al., 2020)
RNA-Seq was performed on the NextSeq500 with a 2 x 75 paired-end kit using custom read lengths (for single index).

value: all islet cells

value: Myt1-cCre; Ngn3nCre; Ai18


title: Nr2e3_KO_replicate_1


title: 2_month_female_islet_cells_repeat_1

source_name: endocrine islets, 2-months-old, 4 females

value: Myt1-cCre; Ngn3nCre; Ai17


title: HEK293T DNA methylation derived from IF1_KO_G6PDi_3

label: Cy3 and Cy15


title: HEK293T DNA methylation derived from IF1_KO_G6PDi_1

label: Cy3 and Cy13


title: 2_month_male_islet_cells_repeat_1

source_name: endocrine islets, 2-months-old, 4male

value: Myt1-cCre; Ngn3nCre; Ai15


title: 2_month_male_islet_cells_repeat_2

source_name: endocrine islets, 2-months-old, 3 male

value: Myt1-cCre; Ngn3nCre; Ai16


title: HEK293T DNA methylation derived from IF1_KO_3

description: IF1-KO whole cell DNA

label: Cy3 and Cy11


title: 2_month_male_islet_cells

source_name: endocrine islets, 2-months-old, 4 male

value: Myt1-cCre; Ngn3nCre; Ai13


title: 2_month_female_islet_cells

value: Myt1-cCre; Ngn3nCre; Ai14


title: HEK293T DNA methylation derived from IF1_KO_4

description: IF1-KO whole cell DNA

label: Cy3 and Cy12


title: HEK293T DNA methylation derived from IF1_KO_1

description: IF1-KO whole cell DNA

label: Cy3 and Cy9


title: P2_islet_cells_repeat_3

source_name: endocrine islets, postnatal day-2, 4 mice of mixed sex

value: postnatal day-2

value: pooled male and female

value: Myt1-cCre; Ngn3nCre; Ai12


title: P2_islet_cells_repeat_1

value: Myt1-cCre; Ngn3nCre; Ai10


title: HEK293T DNA methylation derived from IF1_KO_2

description: IF1-KO whole cell DNA

label: Cy3 and Cy10


title: HEK293T DNA methylation derived from WT_3

description: WT whole cell DNA control

label: Cy3 and Cy7

value: DN-POLG, IF1-WT


title: P2_islet_cells_repeat_2

source_name: endocrine islets, postnatal day-2, 5 mice of mixed sex

value: Myt1-cCre; Ngn3nCre; Ai11


title: HEK293T DNA methylation derived from WT_2

description: WT whole cell DNA control

label: Cy3 and Cy6


title: C2C12, doxycycline, oligomycin + oleic acid, rep4

city: Dallas

first: Mangyu

last: Choe

state: Texas

address: 6000 Harry Hines Blvd

institute: University of Texas Southwestern

data_processing:
Analysis was performed using a combination of programs including STAR, HTseq, Cufflink and Novogene's wrapped scripts. Alignments were parsed using HISAT2 and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software.
Assembly: Mus Musculus (GRCm39/mm39)
Supplementary files format and content: gene_fpkm.xls (excel file format) contains normalized gene expression level.

source_name: muscle

growth_protocol: Cells were grown in DMEM + 10% FBS (with 1 mM pyruvate) at 37 0C and 5% CO2. Doxycycline or same volume of water was added 24 hr after seeding to induce protein expression. After 24 hr, various fatty acids or/and oligomycin were treated in the presence/absence of doxycycline. Cells were harvested after 16 hr of treatment using RNA lysis buffer from Biorad Aurum total RNA extraction kit.

extract_protocol:
Total RNA was extracted using Biorad Aurum total RNA Mini kit (7326820). Libraries were prepared using the NEBNext Ultra II RNA Library prep kit from Illumina (E7775). The construction of sequencing libraries was performed by Novogene Corporation Inc.
Libraries were prepared using the NEBNext Ultra II RNA Library prep kit from Illumina (E7775) according to the manufacturer's instructions.

value: muscle

value: myoblast

value: doxycycline, oligomycin + oleic acid,


title: HEK293T DNA methylation derived from WT_4

description: WT whole cell DNA control

label: Cy3 and Cy8

value: No treatment


title: P2_islet_cells

value: all islet cells

value: Myt1-cCre; Ngn3nCre; Ai9


title: Nr2e3_KO_replicate_2

value: retina

value: female

value: FACs-purified photoreceptor

value: anti Nr2e3 guide RNA


title: C2C12, doxycycline, oligomycin + oleic acid, rep2


title: C2C12, doxycycline, oligomycin + oleic acid, rep3


title: HEK293T DNA methylation derived from WT_1

description: WT whole cell DNA control

label: Cy3 and Cy5


title: DNA methylation derived from IF1_KO PEMT_OE_4

description: IF1-KO pcDNA3.1+/C-(K)-PEMT-DYK whole cell DNA

hyb_protocol: Differential methylation at the CpG dinucleotide level was conducted using Human Infinium Methylation EPIC 850K v2.0 BeadChip arrays (Illumina) following the Infinium methylation protocol.

label: cy3 and cy20

label_protocol: Samples were bisulfite-converted using an EZ DNA Methylation kit (Zymo Research) following the manufacturer’s protocol.

treatment_protocol: Cells from three independently growing flasks were split into 6-well plates. 2×105 cells were plated and incubated under standard conditions for 6 h. For treatment with DMSO (1:1000), telmisartan 2 μM, and annatto 10 μM, cells were treated for 3 days. Cells were split and counted, and  2×105 cells were plated and incubated in treatment medium for additional 3 days (6 cumulative days). Cells were split and counted, and  1.25×105 cells were plated and incubated in treatment medium for additional 4 days (10 cumulative days).  For genotype comparison (IF1-KO vs. IF1-KO PEMT-OE), cells were allowed to grow for 4 days.

value: DN-POLG, IF1-KO, PEMT-OE


title: DNA methylation derived from IF1_KO PEMT_OE_3

scan_protocol: Differential methylation at the CpG dinucleotide level was conducted using Human Infinium Methylation EPIC 850K v2.0 BeadChip arrays (Illumina) following the Infinium methylation protocol.

label: cy3 and cy19


title: C2C12, doxycycline, oleic acid, rep4

value: doxycycline, oleic acid,


title: C2C12, doxycycline, oligomycin + oleic acid, rep1


title: DNA methylation derived from IF1_KO PEMT_OE_2

label: cy3 and cy18


title: HEK293T DNA methylation derived from IF1_KO_G6PDi_2

label: Cy3 and Cy14

value: DN-POLG, IF1-KO

value: G6PDi 50 μM for 3 days


title: C2C12, doxycycline, oleic acid, rep3


title: DNA methylation derived from IF1_KO_4

description: IF1-KO whole cell DNA

label: cy3 and cy16


title: DNA methylation derived from IF1_KO PEMT_OE_1

label: cy3 and cy17


title: C2C12, doxycycline, oleic acid, rep1


title: DNA methylation derived from IF1_KO_3

description: IF1-KO whole cell DNA

label: cy3 and cy15


title: C2C12, doxycycline, BSA, rep4

value: doxycycline, BSA,


title: DNA methylation derived from IF1_KO_2

description: IF1-KO whole cell DNA

label: cy3 and cy14


title: C2C12, doxycycline, BSA, rep3


title: DNA methylation derived from IF1_KO_1

description: IF1-KO whole cell DNA

label: cy3 and cy13

value: Annatto 10 μM for 10 days


title: C2C12, doxycycline, BSA, rep2


title: DNA methylation derived from ANTO_3

description: WT treated with annatto 10 μM whole cell DNA

label: cy3 and cy12

value: DN-POLG, IF1-WT


title: C2C12, doxycycline, BSA, rep1

value: muscle


title: DNA methylation derived from ANTO_2

label: cy3 and cy11


title: C2C12, oligomycin + oleic acid, rep4

value: myoblast

value: oligomycin + oleic acid,


title: DNA methylation derived from TMS_3

description: WT treated with telmisartan 2 μM whole cell DNA

label: cy3 and cy9

value: Telmisartan 2 μM for 10 days


title: C2C12, oligomycin + oleic acid, rep3


title: DNA methylation derived from ANTO_1

label: cy3 and cy10


title: C2C12, oligomycin + oleic acid, rep2


title: C2C12, oligomycin + oleic acid, rep1


title: DNA methylation derived from TMS_1

label: cy3 and cy7


title: C2C12, oleic acid, rep4

value: oleic acid,


title: DNA methylation derived from TMS_2

label: cy3 and cy8


title: C2C12, oleic acid, rep3


title: DNA methylation derived from WT_2

description: WT treated with DMSO whole cell DNA

label: cy3 and cy6

value: DMSO (1:1000) for 10 days


title: DNA methylation derived from WT_1

description: WT treated with DMSO whole cell DNA

label: cy3 and cy5


title: ATAC_postBCG_R2

description: Library name: H4_ATAC

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the cell ranger software.
Paired-end ATAC-seq reads were quality trimmed using Trimmomatic.
After preprocessing and quality filtering, peaks were called on alignments with MACS2 using the BAMPE option.
For differential accessibility analyses the consensus peak set was generated using the R package DiffBind. The consensus peakset was generated per celltype.
Assembly: hg38
Supplementary files format and content: h5ad anndata files for RNA and .tsv  fragment files for ATAC

source_name: PBMC enriched for CD34+ cells

extract_protocol:
Cells were sorted into FACS buffer  using a BD Aria II.
The library was performed according to the manufacturers inscrutions (single cell 3' protocol 10x genomics)

treatment_protocol: Patients pre or post BCG adminsitration in the bladder, after 5 consequentive weekly doses

value: PBMC enriched for CD34+ cells

value: Post-BCG Treatment


title: C2C12, oleic acid, rep1


title: C2C12, doxycycline, oleic acid, rep2


title: C2C12, oleic acid, rep2


title: C2C12, BSA, rep4

value: BSA,


title: ATAC_postBCG_R1

description: Library name: H2_ATAC


title: ATAC_preBCG_R1

description: Library name: H1_ATAC

value: Pre-BCG Treatment


title: ATAC_preBCG_R2

description: Library name: H3_ATAC


title: C2C12, BSA, rep3


title: C2C12, BSA, rep2


title: RNA_postBCG_R2

description: Library name: H4_RNA


title: RNA_postBCG_R1

description: Library name: H2_RNA


title: 60-minute heat stress-2

city: Baltimore

first: Seth

last: Margolis

state: MD

address: 725 N. Wolfe St.

department: Department of Biological Chemistry

institute: The Johns Hopkins University School of Medicine

description:
100bp single-end
60m2-RNA_S6

data_processing:
Using reference transcriptome from m29 GRCm39 reads were indexed using Kallisto
Reads were quantified using Kallisto
Comparative analysis of the datasets in R studio using Sleuth with extra bootstrapping analysis
Performed likelihood ratio test (LRT) to determine if the batch or batch+condition best fit the dataset
Performed the Wald-Test (WT) to determine the significant differences between conditions
Assembly: M28 GRCm39 Feb 23, 2022
Supplementary files format and content: excel sheet containing all samples
Supplementary files format and content: transcripts per million by gene name

source_name: cortical brain

growth_protocol: Primary mouse neurons were isolated from e14.5 C57Bl/6 mice in the cortical region and maintained in incubators at 37°C/5% CO2  in culture media (DMEM with 4.5 g/L D-glucose, glutamine, and sodium pyruvate, 10% FBS, and 100 U/mL and 100 μg/mL penicillin-streptomycin, respectively). Cells rested for 2 hours at 37°C prior to start of experimentation.

extract_protocol:
extraction of RNA using Direct-zol RNA microprep kit
Followed protocol of Zymo-Seq RiboFree Total RNA kit (cat # R3000, R3003)

treatment_protocol: Cells were placed in incubators at 42°C/5% CO2 for 15 or 60 minutes.  Controls were maintained at 37°C for 60 minutes.

value: cortical brain

value: neuron

value: heat stress


title: IF1-KO cells, UCP4 plasmid,, seq run NOVO0502, rep3

description:
Library name: KO_UCP4.B1_3
NOVASeq0502, batch 2

data_processing:
STAR Alignment to Hg38 genome
Reads with mapping quality less than 20 were filtered & raw counts generated with featureCounts
Assembly: Hg38
Supplementary files format and content: Counts.Raw.txt
Supplementary files format and content: Counts.Norm.Deseq2.txt

growth_protocol: HEK293T cells were routinely maintained in DMEM high glucose (25 mM), FBS 10% (v/v), sodium pyruvate 1 mM, uridine 100 μg/mL, 1% (v/v) HEPES, pH 7.1-7.6 (10 mM), pen/strep 0.16% (v/v), and hygromycin 150 μg/mL in a humified incubator with 5% CO2 at 37 °C. Subculture was performed by diluting 90% confluent T-25 (Corning) flasks into 5 mL fresh medium in a 1:6 to 1:10 ratio. Medium was replaced every other 2 days.

extract_protocol:
Medium was removed and cells were gently washed once with ice-cold PBS. RNA was isolated using RNeasy® Mini Kit with on-column DNase digestion (Qiagen) according to the manufacturer's instruction. RNA was quantified using Nanodrop, and for quality control, samples were re-assessed using Qubit 3.0. RNA integrity was confirmed using Agilent RNA 6000 Nano Kit in 2100 Bioanalyzer (Agilent).
Libraries were prepared using TruSeq Stranded mRNA kit (Illumina) according to the manufacturer’s instruction.

treatment_protocol: Cells from three independently growing flasks for each genotype or treatment were split into 6-well plates. 1.25×105 cells were plated and incubated under standard conditions for 4 days.

value: DN-POLG, IF1-KO, UCP4-OE

tag: batch

value: NOVASeq0502 seq_run2


title: 60-minute heat stress

description:
100bp single-end
60m-RNA_S3


title: 15-minute heat stress

description:
100bp single-end
15m-RNA_S2


title: IF1-KO cells, UCP4 plasmid,, seq run NOVO0502, rep2

description:
Library name: KO_UCP4.B1_2
NOVASeq0502, batch 2


title: IF1-KO cells, UCP4 plasmid,, seq run NOVO0502, rep1

description:
Library name: KO_UCP4.B1_1
NOVASeq0502, batch 2


title: control

description:
100bp single-end
CTR-RNA_S1


title: IF1-KO cells, seq run NOVO0502, rep3

description:
Library name: IF1.KO_3
NOVASeq0502, batch 2

value: DN-POLG, IF1-KO


title: input_wKD_rep4, dme ovary, ChIP-seq

city: Moscow

first: Anastasiya

last: Kobelyatskaya

address: Vavilov str, 32

country: Russia

institute: Engelhardt Institute of Molecular Biology, RAS

description: MGI Tech DNBSEQ 400

data_processing:
FastQC and Trimmomatic were used for the quality control and trimming of reads. Bowtie2 aligner was used to map the reads to the reference genome (BDGP assembly R6/dm6). bamCoverage (deepTools) was used to obtain bigwig files (normalized ChIP signals - CPM).
Assembly: dme6
Supplementary files format and content: bigWig (lib size normalized CPM)

organism: Drosophila melanogaster

source_name: ovary

extract_protocol:
ChIP on Drosophila ovaries was performed according to a published procedure (PMID: 29358235).
ChIP on Drosophila ovaries was performed according to a published procedure (PMID: 29358235). Chromatin was immunoprecipitated with the following antibodies: anti-trimethyl-histone H3 Lys9 (Millipore); anti-dimethyl-histone H3 Lys4 (Millipore). The libraries for ChIPseq were prepared using MGIEasy FS DNA Library Prep Set (MGI) and sequencing was done on MGI Tech DNBSEQ 400 platform (MGI).

value: ovary

value: germline knockdown white_sh (#30033, VDRC)

tag: chip antibody


title: input_wKD_rep2, dme ovary, ChIP-seq

description: MGI Tech DNBSEQ 400


title: IF1-KO cells, seq run NOVO0502, rep2

description:
Library name: IF1.KO_2
NOVASeq0502, batch 2


title: IF1-KO cells, seq run NOVO0502, rep1

description:
Library name: IF1.KO_1
NOVASeq0502, batch 2


title: IF1-KO rescue cells + GFP, seq run NOVO0082, rep3

description:
Library name: ATP_cDNAgfp_Chandel_3
NOVASeq 0082, batch 1

value: DN-POLG, IF1-KO, IF1-OE

value: NOVASeq 0082 seq_run1


title: input_Ars2KD_rep3, dme ovary, ChIP-seq

description: MGI Tech DNBSEQ 400

value: germline knockdown Ars2_sh1 (#106344, VDRC)


title: LSK ATAC PBS Rep 1

description: Library name: LSK ATAC PBS Replicate 1

data_processing:
Samples were processed using a nextflow-based pipeline available at https://github.com/michaelbale/jlabflow.
Paired ends were Trimmed with CutAdapt
Mapped using Bowtie2
Assembly: MM10
Supplementary files format and content: .bw

source_name: Sorted LSK

extract_protocol:
Illumina Nextera ATACseq Kit
Omni-ATAC library contrustion protoocl

value: Sorted LSK

value: WT

value: PBS


title: IF1-KO rescue cells + GFP, seq run NOVO0082, rep2

description:
Library name: ATP_cDNAgfp_Chandel_2
NOVASeq 0082, batch 1


title: IF1-KO rescue cells + GFP, seq run NOVO0082, rep1

description:
Library name: ATP_cDNAgfp_Chandel_1
NOVASeq 0082, batch 1


title: input_Ars2KD_rep2, dme ovary, ChIP-seq

description: MGI Tech DNBSEQ 400


title: IF1-KO cells + GFP, seq run NOVO0082, rep3

description:
Library name: ATP_EVgfp_Chandel_3
NOVASeq 0082, batch 1


title: H3K9me3_wKD_rep2, dme ovary, ChIP-seq

description: MGI Tech DNBSEQ 400


title: C2C12, BSA, rep1

value: muscle

value: myoblast


title: RNA_preBCG_R1

description: Library name: H1_RNA

value: PBMC enriched for CD34+ cells

value: Pre-BCG Treatment


title: 15-minute heat stress-2

description:
100bp single-end
15m2-RNA_S5

value: cortical brain

value: neuron


title: control-2

description:
100bp single-end
CTR2-RNA_S4


title: input_Ars2KD_rep1, dme ovary, ChIP-seq

description: MGI Tech DNBSEQ 400


title: IF1-KO cells + GFP, seq run NOVO0082, rep2

description:
Library name: ATP_EVgfp_Chandel_2
NOVASeq 0082, batch 1


title: RNA_preBCG_R2

description: Library name: H3_RNA


title: H3K9me3_Ars2KD_rep2, dme ovary, ChIP-seq

description: MGI Tech DNBSEQ 400


title: IF1-KO cells, seq run NOVO0082, rep3

description:
Library name: IF1.KO_NOV0082_3
NOVASeq 0082, batch 1


title: H3K9me3_Ars2KD_rep1, dme ovary, ChIP-seq

description: MGI Tech DNBSEQ 400


title: IF1-KO cells, seq run NOVO0082, rep2

description:
Library name: IF1.KO_NOV0082_2
NOVASeq 0082, batch 1


title: IF1-KO cells, seq run NOVO0082, rep1

description:
Library name: IF1.KO_NOV0082_1
NOVASeq 0082, batch 1


title: H3K4me2_wKD_rep4, dme ovary, ChIP-seq

description: MGI Tech DNBSEQ 400


title: H3K4me2_wKD_rep2, dme ovary, ChIP-seq

description: MGI Tech DNBSEQ 400


title: WT cells, seq run NOVO0082, rep3

description:
Library name: WT_3
NOVASeq 0082, batch 1

value: DN-POLG, IF1-WT


title: input_wKD_rep1, dme ovary, ChIP-seq

description: MGI Tech DNBSEQ 400


title: H3K4me2_wKD_rep1, dme ovary, ChIP-seq

description: MGI Tech DNBSEQ 400


title: WT cells, seq run NOVO0082, rep2

description:
Library name: WT_2
NOVASeq 0082, batch 1


title: H3K4me2_Ars2KD_rep3, dme ovary, ChIP-seq

description: MGI Tech DNBSEQ 400


title: H3K4me2_Ars2KD_rep2, dme ovary, ChIP-seq

description: MGI Tech DNBSEQ 400


title: H3K9me3_wKD_rep1, dme ovary, ChIP-seq

description: MGI Tech DNBSEQ 400


title: PIE_Post_2_ATAC

description: Library name: PIE_Post_2_ATAC

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the cell ranger software.
Paired-end ATAC-seq reads were quality trimmed using Trimmomatic.
After preprocessing and quality filtering, peaks were called on alignments with MACS2 using the BAMPE option.
For differential accessibility analyses the consensus peak set was generated using the R package DiffBind. The consensus peakset was generated per celltype.
Assembly: hg38
Supplementary files format and content: h5ad anndata files for RNA and .tsv fragment files for ATAC

value: Post-BCG Treatment


title: PIE_Post_2_RNA

description: Library name: PIE_Post_2_RNA


title: PIE_Post_1_ATAC

description: Library name: PIE_Post_1_ATAC


title: PIE_Post_1_RNA

description: Library name: PIE_Post_1_RNA


title: C2C12 Cells, Day 2, frozen, native, IgG

city: Klosterneuburg

first: Kenneth

middle: David

last: Kuhn

address: Am Campus

country: Austria

institute: Institute of Science and Technology Austria

description: Library name: Day2_Frozen_Native_IgG

data_processing:
Reads were first cleaned by Trim Galore using automated adapter sequence detection. Reads were then mapped using Bowtie2 and then filtered for a MAPQ score of greater than 20. Peaks were called using MACS2 with the IgG sample used as a negative control for each condition (MFOLD bounds 5-50; 300 basepair band width; peak detection with q value and minimum FDR 0.05). Treatments and negative controls were not pooled for individual peak files (those with replicate names) and were pooled for all "comp" peak files. All peak files included are Broad Peak files generated by MACS2.
Assembly: mm10
Supplementary files format and content: Peak files are .bed format with the following columns (in order): Chrom. Start, End, Name, Score, Strand, ThickStart, ThickEnd, ItemRGB, BlockCount, BlockSizes, BlockStarts
Library strategy: CUT&Run

growth_protocol: C2C12 cells were maintained in DMEM with 20% FBS and split every 48 hours, never being allowed to exceed 70% confluency. Cells were either in the growth stage (cycling) or grown to confluency, switched to DMEM plus 2% horse serum, and collected 48 hours thereafter (day 2).

extract_protocol:
CUT&RUN was performed according to the manufacturer's instructions using the Cell Signaling Technology CUT&RUN kit (#86652), except that cells were incubated with the primary antibody at room temperature for thirty minutes instead of at 4 C for a longer duration to reduce cell death.
Libraries were constructed according to the manufacturer's instructions using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645L) using the NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (E7600S) as primers

treatment_protocol: Cycling cells were resuspended upon collection in 10% DMSO in FBS and frozen at -80C prior to performing CUT&RUN. Day 2 cells were subjected to other conditions to test the lability of PSME3 at the DNA. These cells were either frozen as cycling cells were, or collected fresh the day of the assay. In addition to this, cells were either used in their native state or were treated for five minutes at room temperature with 0.1% formaldehyde, followed immediately by quenching by bringing the solution to 12.5 mM glycine. When both crosslinking and freezing were performed, crosslinking was performed prior to freezing.

value: Myoblast

value: Frozen, native

value: IgG


title: C2C12 Cells, Day 2, frozen, native, PSME3

description: Library name: Day2_Frozen_Native_PSME3


title: C2C12 Cells, Day 2, frozen, native, H3K4me3

description: Library name: Day2_Frozen_Native_H3K4me3


title: Npas4l-HA OE

city: Beijing

first: Yabing

last: Song

state: Beijing

address: Chaoyang District

department: Institute of Microbiology

institute: Chinese Academy of Sciences

data_processing:
Illumina Casava2.1.7 software used for basecalling.
The quality of raw sequencing data was analyzed using FastQC version 0.11.4 and processed by Trim Galore version 0.6.0 to remove adapters and low-quality reads.
Clean reads were aligned to the GRCz11 reference genome using the bowtie2 version 2.4.5.
The aligned BAM files were then sorted and deduplicated using the samtools version 1.15.1 and Picard version 2.1.0 to mitigate PCR artifacts
The MACS2 version 2.2.7.1 was employed with parameters “-p 0.05” to call peaks, and the deepTools version 3.5.0 and ggcoverage version 1.4.0 were used to generate the heatmap and track plot separately
Assembly: GRCz11
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

organism: Danio rerio

source_name: heart

extract_protocol:
The ventricles (30 adult ventricles per sample) were gently chopped, transferred, and digested in digestion buffer for 15 min at 4℃ with constant gentle agitation using a rotator. The digestion was then neutralized with 10% FBS (fetal bovine serum) and the disassociated cells were filtered through a 100 μm-strainer to remove large clumps and pelleted at 500 × g for 10 min at 4℃. The pellet which mainly contained platelets and erythrocytes was re-suspended in Hank’s balance salt solution (HBSS). Then, around 2000,000 cells per sample were fixed in 0.2% formaldehyde for 2 min and neutralized by adding glycine to a final concentration 25 mM. The fixed cells were pelleted at 800 × g for 5 min at 4℃, washed twice with PBS and loaded for CUT&TAG reaction. In brief, the cells were incubated with primary antibody overnight. Next day, the cells were washed twice and incubated with second antibody with Tn5 transposase. The cells were lysed and antibody binding DNA fragments were extracted.
The extracted DNA fragments were ligated with double index primers and amplified to generate sequencing library. The library was extracted and qualified using Qubit and Fragment Analyzer.

value: heart

value: isolated primary cells

value: platelets

value: Mouse anti-HA Tag (Santa Cruz, #sc-7392)


title: PIE_Post_ATAC

description: Library name: PIE_Post_ATAC


title: control


title: IF1-KO cells + GFP, seq run NOVO0082, rep1

description:
Library name: ATP_EVgfp_Chandel_1
NOVASeq 0082, batch 1

value: DN-POLG, IF1-KO

value: NOVASeq 0082 seq_run1


title: C2C12 Cells, Day 2, frozen, crosslinked, IgG

description: Library name: Day2_Frozen_Crosslinked_IgG

value: Frozen, crosslinked


title: PIE_Post_RNA

description: Library name: PIE_Post_RNA


title: clofv087b/+ 7dpa

description: 10x Genomics

data_processing:
Illumina Casava2.1.7 software used for basecalling.
Cell Ranger (v3.0.2) pipeline (10x Genomics) was utilized to demultiplex the cellular barcodes and align reads to the GRCz11 zebrafish reference genome.
The output filtered gene expression matrices were loaded and analyzed using the Seurat package (v3.1.4)
Potential doublet cells were detected and filtered using the R package DoubletFinder (v2.0.2)
Low-quality cells were removed from the datasets based on the following criteria: (1) the number of detected genes <=200 or >=4,000, the percentage of mitochondrial genes >=25 for non-cardiomyocytes; (2) the number of detected genes <=200 or >=4,000 for CMs, the mitochondrial content was not filtered due to the nature of CMs containing high mitochondrial density
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
For each sample, 15 adult ventricles were collected and placed in ice-cold perfusion buffer (130 mM NaCl, 5 mM KCl, 0.5 mM NaH2PO4, 10 mM HEPES, 10 mM Glucose, 10 mM 2,3-butanedionemonoxime, 10 mM taurine, 5 mM MgCl2, adjusting pH to 7.8 with NaOH). The ventricles were gently torn up, transferred, and digested in the digestion buffer (10 mg/ml protease, 30 μg/ml DNase I in perfusion buffer) for 3 h at 4℃ with constant gentle agitation by using a rotator. The digestion was then neutralized with 10% FBS (fetal bone serum) and the disassociated cells were filtered through a 100 μm-strainer to remove large clumps and pelleted at 500 x g for 10 min at 4℃. The pellet was re-suspended in Hank’s balance salt solution (HBSS). The disassociated cells were stained with Hochest 33342 (1:300 diluted in HBSS),  gone through a 70 μm-strainer, and loaded on a Beckman Coulter MoFlo XDP system to remove cell debris and sort for single cells. The sorted single cells were pelleted at 1000 x g for 5 min at 4℃. The pellet was resuspended in HBSS. Cell viability and concentration were measured on a Countstar Rigel system (ALIT Life Science). Samples with more than 85% cell viability were qualified for single-cell loading. Around 12,000 cells per sample were loaded into 10x Genomics Chromium chip.
Single-cell RNA-seq libraries were generated using Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics, 1000269) according to the manufacturer’s instructions.

value: cardiac cells

value: 7 days post heart amputation


title: PBMC_Pre_ATAC

description: Library name: PBMC_Pre_ATAC

source_name: Bulk PBMC

value: Bulk PBMC

value: Pre-BCG Treatment


title: C2C12 Cells, Day 2, frozen, crosslinked, PSME3

description: Library name: Day2_Frozen_Crosslinked_PSME3


title: clofv087b/+ 3dpa

description: 10x Genomics

value: 3 days post heart amputation


title: PBMC_Pre_RNA

description: Library name: PBMC_Pre_RNA


title: C2C12 Cells, Day 2, frozen, crosslinked, H3K4me3

description: Library name: Day2_Frozen_Crosslinked_H3K4me3


title: clofv087b/+ sham

description: 10x Genomics

value: untreated


title: C2C12 Cells, Day 2, fresh, native, IgG

description: Library name: Day2_Fresh_Native_IgG

value: Fresh, native


title: WT cells, seq run NOVO0082, rep1

description:
Library name: WT_1
NOVASeq 0082, batch 1

value: DN-POLG, IF1-WT


title: H1975 MUC1sgRNA_2

city: Boston

first: Atrayee

last: Bhattacharya

state: Massachusetts

address: 450 Brookline Avenue

department: Medical Oncology

institute: DFCI

description: Library name: Sample 10

data_processing:
Sequencing reads from each replicate were aligned to the human genome (GRCh38) using bwa-mem to generate sorted and deduplicated BAM files. Accessible chromatin regions were identified for each replicate using MACS3 in paired-end mode with an FDR threshold of 0.01
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: were cultured in RPMI1640 medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS; GEMINI Bio-Products, West Sacramento, CA, USA).

extract_protocol:
Nuclear lysis buffer was used to isoltae nuclei
50,000 cells were subjected to tagmentation reactions with 2.5 μL Tn5 Transposase (Illumina), purified with Qiagen MinElute PCR Purification Kit (Qiagen) and PCR amplified for 8–9 cycles. Quality of ATAC-seq libraries was confirmed with Bioanalyzer prior to sequencing.

value: Non Small Cell Lung Cancer

value: MUC1 guide RNA


title: H1975 CsgRNA_2

description: Library name: Sample 8

value: Control guide RNA


title: H1975 MUC1sgRNA_1

description: Library name: Sample 9


title: H3K4me2_Ars2KD_rep1, dme ovary, ChIP-seq

description: MGI Tech DNBSEQ 400

value: ovary

value: germline knockdown Ars2_sh1 (#106344, VDRC)


title: WT 7dpa

description: 10x Genomics

value: heart

value: isolated primary cells

value: wild type


title: PBMC_Post_ATAC

description: Library name: PBMC_Post_ATAC

value: Post-BCG Treatment


title: C2C12 Cells, Day 2, fresh, native, PSME3

description: Library name: Day2_Fresh_Native_PSME3

value: Myoblast


title: H1975 CsgRNA_1

description: Library name: Sample 7


title: WT 3dpa

description: 10x Genomics

value: cardiac cells


title: C2C12 Cells, Day 2, fresh, native, H3K4me3

description: Library name: Day2_Fresh_Native_H3K4me3


title: WT sham

description: 10x Genomics


title: PBMC_Post_RNA

description: Library name: PBMC_Post_RNA

value: Bulk PBMC


title: H1975 RT_3

description: Library name: Sample 6


title: PBMC_Pool_Pre_ATAC

description: Library name: PBMC_Pool_Pre_ATAC

value: Pre-BCG Treatment


title: H1975 RT_2

description: Library name: Sample 5


title: C2C12 Cells, Day 2, fresh, crosslinked, PSME3

description: Library name: Day2_Fresh_Crosslinked_PSME3

value: Fresh, crosslinked


title: C2C12 Cells, Day 2, fresh, crosslinked, IgG

description: Library name: Day2_Fresh_Crosslinked_IgG

value: IgG


title: Npas4l OE rep2

data_processing:
Illumina Casava2.1.7 software used for basecalling.
The quality of raw sequencing data was analyzed using FastQC version 0.11.4 and processed by Trim Galore version 0.6.0 to remove adapters and low-quality reads.
Clean reads were aligned to the GRCz11 reference genome using the hisat2 version 2.1.0.
Significantly differential expression was detected using the DESeq2 version 1.22.1 package. Genes with a p-value < 0.05 and a log2 fold change value >= 0.485 (fold change >1.4) were considered to represent significantly differentially expressed genes (DEGs).
The pathway analysis of DEGs was performed using the Metascape webtool (www.metascape.org)
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include raw counts for each sample

extract_protocol:
For each sample, 15 adult ventricles were collected and placed in ice-cold perfusion buffer (130 mM NaCl, 5 mM KCl, 0.5 mM NaH2PO4, 10 mM HEPES, 10 mM Glucose, 10 mM 2,3-butanedionemonoxime, 10 mM taurine, 5 mM MgCl2, adjusting pH to 7.8 with NaOH). The ventricles were gently torn up, transferred, and digested in the digestion buffer (10 mg/ml protease, 30 μg/ml DNase I in perfusion buffer) for 3 h at 4℃ with constant gentle agitation by using a rotator. The digestion was then neutralized with 10% FBS (fetal bone serum) and the disassociated cells were filtered through a 100 μm-strainer to remove large clumps and pelleted at 500 x g for 10 min at 4℃. The pellet was re-suspended in Hank’s balance salt solution (HBSS). The disassociated cells were  gone through a 70 μm-strainer, and loaded on a Beckman Coulter MoFlo XDP system to sort for eGFP+ or DsRed+ cells. Either 6,000 eGFP+ or DsRed+ cells were sorted into lysis buffer (0.5% Triton X-100, 1 U/μl RNase inhibitor, 2.5 μM Oligo dT primer, 2.5 mM dNTP) on a Beckman Coulter MoFlo XDP system. After vortex and incubation for 3 min at 72℃, total mRNA was reverse-transcribed to cDNA using SuperScript II Reverse Transcriptase (Invitrogen, 18064014). cDNA was then amplified using KAPA HiFi HotStart ReadyMix (Huaruikang, kk2602) and purified using VAHTS DNA Clean Beads (Vazyme, N411).
1 ng cDNA per sample was used to generate library using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to the manufacturer’s instructions. In brief, 1 ng cDNA was fragmented using TruePrep Tagment Enzyme and then ligated with specific indexes. After amplification using TruePrep Amplify Enzyme, the cDNA library was purified using VAHTS DNA Clean Beads.

value: platelets

value: 7 days post 4-HT treatment


title: H1975 RT_1

description: Library name: Sample 4

value: Non Small Cell Lung Cancer


title: PBMC_Pool_Pre_RNA

description: Library name: PBMC_Pool_Pre_RNA


title: PBMC_Pie_Pre_ATAC

description: Library name: PBMC_Pie_Pre_ATAC

value: PBMC enriched for CD34+ cells


title: Npas4l OE rep1


title: H1975 WT_3

description: Library name: Sample3


title: control rep1


title: control rep2


title: C2C12 Cells, Cycling, IgG, replicate 3

description: Library name: Cycling_IgG_r3

value: Frozen, native


title: H1975 WT_2

description: Library name: Sample2


title: P5 Tumor, snRNAseq

city: Daejeon

first: Jeong Ho

last: Lee

address: 291 Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

description:
Library name: 2470-Tu
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Fresh frozen human brain tissue was minced, followed by addition of lysis buffer consisting of phosphate-buffered saline (PBS) containing 0.2% Triton X-100, 1X protease inhibitor cocktail (Roche), 1 mM DTT, 0.2 U/μl RNasin® ribonuclease inhibitor (Promega), and 2% BSA. After mechanical digestion, samples were incubated for 5 minutes on ice and centrifuged for 5 minutes at 500 x g at 4 °C. The resulting pellet, containing cell nuclei, was resuspended in PBS containing 1 mM EDTA, 0.2 U/μl RNasin®, and 2% BSA, and then filtered through a 20-μm pluriStrainer Mini (pluriSelect). DAPI was added and DAPI+ nuclei were collected by FACS in PBS containing 1 U/μl RNasin® and 5% BSA. The nuclei solution was concentrated by centrifugation for 15 minutes at 1000 x g at 4 °C and resuspended in PBS containing 0.2 U/μl RNasin® and 1% BSA, after which nuclei were counted.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Tumor

value: brain cells

value: 71 years old

value: female


title: clofv087b/+ rep3

value: heart

value: isolated primary cells

value: 1 days post heart amputation


title: P4 Tumor, snRNAseq

description:
Library name: 2459-Tu
10x Genomics

value: 76 years old

value: male


title: clofv087b/+ rep2


title: C2C12 Cells, Cycling, IgG, replicate 1

description: Library name: Cycling_IgG_r1

value: Myoblast


title: C2C12 Cells, Cycling, IgG, replicate 2

description: Library name: Cycling_IgG_r2


title: clofv087b/+ rep1