title: Male FOM, Rep 5

description: Library name: Sample 9

source_name: liver

growth_protocol: Mice were ordered from Jackson labs and arrived at MUSC at 7 weeks of age. They were maintained in co-housed cages on normal chow in controlled temperature and humidity for 1 week to acclimate, then were placed on a high-fat diet for 20 weeks beginning at 8 weeks old.

extract_protocol:
Liver lysates were prepared by homogenization in the bullet blender and RNA was isolated using the RNeasy Qiagen kit with the optional DNaseI on-column digestion step
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Mice were treated daily during the last four weeks of the diet with formoterol (1 mg/kg) or vehicle (DMSO) via i.p. injection.

value: liver

value: 28 week old

value: Bulk Tissue


title: 4-Rel_1_CD34_negative_CD38_negative

status: Public on Jan 15 2026

type: SRA

city: Toronto

first: Mathieu

last: Lupien

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

description: Library name: 4-Rel_1_CD34_negative_CD38_negative

library_source: genomic

data_processing:
The data is processed using bowtie2 and called peaks using MACS2.
Assembly: hg38
Supplementary files format and content: narrowPeak

molecule: genomic DNA

organism: Homo sapiens

source_name: Acute Myeloid Leukemia

extract_protocol:
Nuclei were isolated using digitnnin-containing buffer from viable frozen peripheral blood cells from AML patients and then incubated with Illumina Transposase for 30min at 37 C.
Libraries were amplified using per-sample determined PCR cycles

tag: tissue

value: Acute Myeloid Leukemia

tag: cell line

tag: cell type


title: cell-free DNA from healthy control sample 60.2 at T3

type: other

city: Renton

first: Dantong

last: Zhu

address: 401 Terry Ave N

country: USA

institute: Institute for Systems Biology

description: PBMC DNA from healthy control mice

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MouseMethylation array using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScan and standard recommend Illumina scanner setting

data_processing: SeSame package in R environment (v. 4.4.2)

label: Cy3 and Cy5

molecule: other

organism: Mus musculus

source_name: PBMC

label_protocol: Standard Illumina Protocol

extract_protocol: Red blood cells were removed with RBC lysis buffer (155 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA, pH 7.3), and then the remaining cells were digested overnight at 65°C with proteinase K (20 mg/mL) in TESR buffer (10 mM Tris-HCl, 25 mM EDTA, 0.5% SDS, 20 µg/mL RNase). DNA was washed and isolated using SPRI beads and eluted in 10 mM Tris-HCl pH8.

value: PBMC

tag: treatment

value: control


title: WT_RNAP_II_CT00

city: Dallas

first: Noheon

last: Park

state: Texas

address: 5323 Harry Hines BLVD, NA4.124

department: Neuroscience

institute: UT Southwestern Medical Center

description: Library name: Sample1

data_processing:
Illumina bcl2fastq version 2.17 for base calling and demultiplexing.
For ChIPseq, the adaptor and the reads with < 30bp were trimmed by CutAdapt v.1.18. Then, the data were mapped by BWA v0.7.16a-r1185-dirty with default options and the uniquely mapped reads were chosen by SAMtools v1.9. The PCR duplicates were removed by awk commands, and the final reads were extended to the MACS2 prediction sizes.
For mRNAseq, the adaptor, poly T sequences, and < 30bp reads of the raw data were trimmed by CutAdapt v.1.18 and mapped by STAR v2.5.3a. The uniquely mapped reads were chosen by SAMtools v1.9.
For PROseq, the adaptor sequences and < 16bp reads were removed by CutAdapt v.1.18 and the reverse complement (RC) sequences were made from FASTX-Toolkit. The RC was mapped by BWA v0.7.16a-r1185-dirty aln and the uniquely mapped reads were determined by SAMtools v1.9.
The normalized BigWig files are from BEDTools v2.27.1. The raw counts of the NGS data are retrieved from FeatureCounts v1.6.4.
Assembly: M14 from GENCODE
Supplementary files format and content: ChIP-seq BigWig files were made from Uniquely mapped duplicate-removed bed files. PRO-seq and mRNA-seq BigWig files were made from uniquely mapped STAR Bam files
Supplementary files format and content: Excel  file includes raw counts and RPKM values for the mRNA-seq results

source_name: Liver

growth_protocol: At 6 weeks old, the animals were housed in the two light chambers with a 2hr shifted light:dark (LD)=12hrs:12hrs condition and fed ad libitum.

extract_protocol:
For ChIP-seq, , the fresh whole liver lobes were homogenized in 4 ml PBS containing 1% formaldehyde and kept for 8 min at room temperature (RT). For dual crosslinking, the fresh whole liver lobes were homogenized in 4 ml PBS containing 2mM EGS for 20 min at RT. After quencing and cell lysis, chromatin was sonicated by Covaris S2 with the options of 30 sec on/off, intensity 5, cycles/burst 200, duty 20% at 4°C. For PRO-seq, the largest mouse liver lobe was homogenized and the dissociated cells were filtered by 100mm mesh and centrifuged. The precipitated cells were re-suspended and lysed.  The extracted nucleus was re-suspended with the storage buffer and frozen till the next step. After the nuclear run-on, the RNA was extracted by Trizol LS (ThermoFisher). For mRNA-seq, the frozen liver samples were homogenized with Trizol (ThermoFisher) and RNA was extracted according to the manufacturer's instructions.
For ChIP-seq, the DNA fragments ranging from 125 to 175bp were size selected by AMPure magnetic beads (Beckman). Then, the DNA is adenylated, ligated to NEXTflex DNA barcode adaptors (PerkinElmer) and amplified (Enzymatics). For PRO-seq, the libraries were made with TruSeq small RNA Library primers nad the amplified libraries were size-separated by 8% PAGE gels and the DNA ranging from 140 bp to 200 bp was cut out and eluted by the crush/soak methods. For mRNA-seq, the mRNA was extracted from 10 mg of total RNA (RIN values > 8) pooled from three mice by NEXTflex Poly (A) Beads (PerkinElmer), fragmented by heat, reversely transcribed, ligated and amplified with NEXTflex DNA barcode adaptors (PerkinElmer). For all libraries, the size and quality of the libraries were validated by TapeStation (Agilent) and the amounts were measured by Qubit (ThermoFisher)

treatment_protocol: After 4 weeks of the entrainment(10 weeks old), a light/dark chamber was released to constant darkness (DD) condition 24hrs earlier than the other. The liver samples (N=3) were collected after 36 hours of DD condition beginning with the first point (CT00) and subsequent every 4hrs collections for each light chamber till CT44.

value: Liver

tag: strain

tag: collectiontime

tag: genotype

value: WT

tag: age

tag: chip antibody

value: anti Pan Pol II (SantaCruz, Cat#SC899)


title: cell-free DNA from healthy control sample 60.3 at BL

description: PBMC DNA from healthy control mice


title: 3-Rel_1_CD34_negative_CD38_positive

description: Library name: 3-Rel_1_CD34_negative_CD38_positive


title: cell-free DNA from healthy control sample 60.2 at T2

description: PBMC DNA from healthy control mice


title: Male FOM, Rep 3

city: Charleston

first: Jessica

middle: H

last: Hartman

state: South Carolina

address: 70 President St., Drug Discovery Bldg/Rm DD220

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

description: Library name: Sample 7

library_source: transcriptomic

data_processing:
Novogene performed data analysis in the Novogene platform
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Alignments were performed with HISAT2 v2.0.5 by Novogene
Differentially expressed genes were determined with the R package DESeq2
Assembly: mm39
Supplementary files format and content: spreadsheet containing gene counts

molecule: polyA RNA


title: WT, Control, 3

city: Hartsdale

first: michelle

last: ehrlich

state: New York

address: 88 Mercer Ave.

institute: Mount Sinai Hospital

description:
Library name: WT_Control_3
GQ03_S47_L007

data_processing:
RNA reads were aligned to the Mus Musculus Ensembl Reference genome (GRCm38.77) using STAR aligner software (Version 2.5.2b).
Gene count filtering, normalization, and differential expression analysis were performed in R using the Limma package.
Assembly: Mus Musculus Ensembl Reference genome (GRCm38.77)
Supplementary files format and content: tab delimited .txt file with raw counts for each gene/sample

molecule: total RNA

source_name: Hippocampus and cortex

extract_protocol:
Cells were lysed with Qiazol, and RNA was extracted using the miRNeasy Micro Qiagen Kit.
RNA samples were sequenced using the Illumina NovaSeq PE150 platform by Novogene. RNA quality of each sample was assessed by Novogene and cDNA libraries (150bp, paired end reads) were sequenced using an ultra-low input protocol.

treatment_protocol: Primary microglia cells from cortex and hippocampal regions of WT, Trem2 KO, and Tyrobp KO mice were isolated and plated overnight, and stimulated with control DMEM media, or LPS, or A11/OC mix, or OC-only preparation for 24h, then lysed and prepared for bulk RNA-seq.

value: Hippocampus and cortex

value: Primary microglia

value: Baseline

tag: batch


title: WT, Control, 1

description:
Library name: WT_Control_1
GQ01_S46_L007


title: TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 100ng/ml, input

city: Boston

first: Peter

middle: G

last: Kim

state: MA

address: 360 Longwood Ave, LC8202

department: Medical Oncology

institute: Dana Farber Cancer Institute

description: Library name: T_input_dox100

data_processing:
Trimmed reads were aligned to the mm10 or hu19 genome via bowtie2.3.5 (Langmead et al., Nature Methods. 2012) using --very-sensitive -X700 --no-mixed --no-discordant. Duplicates were marked using MarkDuplicates in Picard/2.19.0 (Broad Institute) or MACS2 (Zhang et al. Genome Biology 2008). Peaks were called using Macs2/2.1.1 using -f BAMPE -B --nomodel --broad --keep-dup 1 --extsize 200 -p 1e-2. For transcription factors, --broad parameter was omitted. ENCODE blacklist regions were excluded from analysis (Amemiya et al. Sci Reports 2019). BigWig files were generated via bedGraphToBigWig (Kent et al. Bioinformatics. 2010).
Assembly: Mouse mm10 or Human hg19
Supplementary files format and content: bigWig

source_name: blood

extract_protocol:
Briefly, cells were double cross-linked with disuccinimidyl glutarate (Thermo) and formaldehyde for 30 minutes at room temperature and quenched with 2.5M glycine. Cross-linked cells were treated with LB1 buffer (50mM HEPES-KOH, pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100 in distilled water) x 10 minutes at 4C, LB2 buffer (10mM Tris-HCl, pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA in distilled water) x 10 minutes at 4C, then sonicated in LB3 buffer (10mM Tris-HCL, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% Na-Lauroylsarcosine, 1% Triton X-100, in distilled water) using Covaris, E220. Following antibody incubation overnight, immunoprecipitation (IP) was performed using Protein-A or Protein-G Dynabeads (Thermo) or Strepavidin magnetic beads (Thermo 88817) for 1 hour. Beads were collected via a magnet and washed six times with RIPA buffer (50mM Hepes-KOH, pH 7.5, 500mM LiCl, 1mM EDTA, 0.7% Na-deoxycholate, 1% NP-40 in distilled water), twice with buffer 500 (0.5g deoxycholic acid, 1mM EDTA, 5mM Tris-HCl, pH 8.1, 1% Triton X-100, and 0.02% NaN3 in distilled water), and twice with LiCl buffer (2.5 g deoxycholic acid, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 10 mM Tris-HCl pH 8.1, 0.02% NaN3 in distilled water). Beads were washed briefly with TE buffer and DNA was eluted in ChIP elution buffer (50mM Tris-HCl, pH 8.0, 10mM EDTA, 1% SDS in distilled water) and de-crosslinked at 65C for 2 hours. DNA was purified by column purification (DNA Clean and Concentration, Zymo Research).
Library preparation was done according to manufacturer’s instructions (ThruPlex DNA-Seq Kit, Takara or NEBNext® Ultra, NEB).

treatment_protocol: WT or Tet2 KO BMDMs were incubated in a defined media containing DMEM without glucose or glutamine (Thermo A1443001), supplemented with ITS-X (Thermo), 20ng/ml M-CSF, HEPES (10mM), supplemented with 0.65mM glutamine (Sigma 49419), 5.5mM glucose, 0.5mM acetate (Sigma S2889), and 100uM palmitate (Sigma P0500) for 24 hours, washed with PBS twice, then incubated in the specified nutrient 24 hours prior to harvest. WT or TET2 KO human U937 cells with a doxycycline-inducible OGT tagged with a TurboID proximity labeling system were treated with doxycycline 0.1ng/ml, 1ng/ml or 100ng/ml for 18 hours prior to harvest with 300 nM biotin supplementation in biotin-free RPMI supplemented with 10% FCS and 5% glutamine and penicillin-streptomycin (PSG; Invitrogen). All cell cultures were performed at 37°C and 5% CO2.

value: blood

value: TET2 KO

value: doxycycline 100ng/ml, 18hrs

value: input


title: Male FOM, Rep 4

description: Library name: Sample 8


title: 970777-119B

description: Library name: 970777-119B


title: cell-free DNA from healthy control sample 60.1 at T4

description: PBMC DNA from healthy control mice


title: 6-Rel_2_CD34_positive_CD38_positive

description: Library name: 6-Rel_2_CD34_positive_CD38_positive


title: TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 1ng/ml, input

description: Library name: T_input_dox1

value: doxycycline 1ng/ml, 18hrs


title: Male FOM, Rep 2

description: Library name: Sample 6

value: liver


title: TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 0.1ng/ml, input

description: Library name: T_input_dox0.1

value: doxycycline 0.1ng/ml, 18hrs


title: 1-Rel_1_CD34_posittive_CD38_negative

description: Library name: 1-Rel_1_CD34_posittive_CD38_negative


title: 955423-130A

description: Library name: 955423-130A


title: cell-free DNA from healthy control sample 60.2 at BL

description: PBMC DNA from healthy control mice


title: Male FOM, Rep 1

description: Library name: Sample 5

value: 28 week old

value: Bulk Tissue


title: 2-Rel_1_CD34_positive_CD38_positive

description: Library name: 2-Rel_1_CD34_positive_CD38_positive

value: Acute Myeloid Leukemia


title: HeLa Cell CAGE

city: Cambridge

first: Jimmy

last: Ly

state: Massachusetts

address: 455 main street

department: Biology

institute: Whitehead Institute

description: Library name: HeLa Cell CAGE

data_processing:
Reads were mapped using STAR. 5' ends of reads were extracted and reads per position was quantified. TPM was calculated per position and a minimum of TPM = 1 and 5 read counts were required for each transcription start site.
Assembly: hg38
Supplementary files format and content: HeLa cell transcription start sites, with TPM, raw counts, and distance from the annotated start codon.

source_name: HeLa cell

growth_protocol: Cells were maintained in DMEM supplemented with 10% heat-inactivated fetal bovine serum, 2 mM L-glutamine, and 100 U/mL penicillin–streptomycin at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
Cells were lysed in 400 μL TRI reagent (Invitrogen, AM9738). Chloroform (120 μL) was added, and samples were mixed vigorously followed by centrifugation at 21,000 × g for 15 min at 4°C. The upper aqueous phase was transferred to a new tube, extracted again with an equal volume of chloroform, and centrifuged at 21,000 × g for 1 min at 4°C. For RACE, the RNA was precipitated by supplementing the aqueous phase with 300 mM NaCl and 30 μg GlycoBlue (AM9516), followed by addition of an equal volume of isopropanol and incubation at −20°C overnight. For CAGE, the RNA was precipitated with LiCl (2.5 M final) at −20°C overnight. RNA was pelleted by centrifugation at 21,000 × g for 30 min at 4°C, washed once with 70% ethanol, and resuspended in RNase-free water. RNA concentration was determined using a Nanodrop.
Library preparation was outsourced to DNAFORM for their standard CAGE-Seq pipeline.

value: HeLa cell


title: Male DMSO Control, Rep 4

description: Library name: Sample 4


title: cell-free DNA from healthy control sample 60.1 at T2

description: PBMC DNA from healthy control mice

value: PBMC

value: control


title: 928897-9B

description: Library name: 928897-9B


title: Male DMSO Control, Rep 3

description: Library name: Sample 3


title: cell-free DNA from healthy control sample 60.1 at T3

description: PBMC DNA from healthy control mice


title: WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 1ng/ml, input

description: Library name: W_input_dox1

value: WT


title: 928480_10A_S7

description: Library name: 928480_10A_S7


title: WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 0.1ng/ml, input

description: Library name: W_input_dox0.1


title: TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 100ng/ml, IP: Strepavidin

description: Library name: T_TO_dox100

value: Pierce™ Streptavidin Magnetic Beads Thermo 88817


title: Male DMSO Control, Rep 2

description: Library name: Sample 2


title: 925723_13A_S9

description: Library name: 925723_13A_S9


title: cell-free DNA from healthy control sample 60.1 at BL

description: PBMC DNA from healthy control mice


title: 924176-14B

description: Library name: 924176-14B


title: cell-free DNA from healthy control sample 58.4 at T4

description: PBMC DNA from healthy control mice


title: WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 100ng/ml, input

description: Library name: W_input_dox100


title: TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 1ng/ml, IP: Strepavidin

description: Library name: T_TO_dox1


title: 906010-17B

description: Library name: 906010-17B


title: TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 0.1ng/ml, IP: Strepavidin

description: Library name: T_TO_dox0.1


title: WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 100ng/ml, IP: Strepavidin

description: Library name: W_TO_dox100


title: cell-free DNA from healthy control sample 58.4 at BL

description: PBMC DNA from healthy control mice


title: ovary, FNZ, replicate 5

city: Nantong

first: Xiuling

last: Zhao

address: NO.16 WenFeng Road,  Chongchuan District

country: China

institute: Nantong University

description: Library name: mouse_ovary_fnz_03

data_processing:
Raw sequencing data (bcl files) were demultiplexed and converted to FASTQ format using Illumina's bcl2fastq software (v2.20). Differential gene expression analysis was performed on the raw count matrix using DESeq2 (v1.38.3) in R, which included data normalization and statistical testing.
Assembly: GRCm39
Supplementary files format and content: File fnz_vs_con.deseq2.annot is a tab-delimited text file containing the raw gene counts for all samples. The first column lists gene identifiers, and subsequent columns represent individual samples, with values being integer read counts.

source_name: Ovary

growth_protocol: Animals were maintained under standardized conditions: ambient temperature of 22-24°C, 40-60% relative humidity, and a 12-hour light/dark cycle with adlibitum access to food and water.

extract_protocol:
Total RNA was extracted from tissue samples using the TRIzol method. RNA concentration and purity were measured with a Nanodrop 2000 spectrophotometer (OD260/280 ≥ 1.8, OD260/230 ≥ 1.0). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (RIN value). A minimum of 1 μg total RNA with a concentration ≥35 ng/μL was used for library construction.
Libraries were prepared using the Illumina TruSeq™ RNA Sample Prep Kit. The workflow included: 1. Poly(A)+ mRNA enrichment using Oligo(dT) magnetic beads; 2. mRNA fragmentation to ~300 bp fragments using fragmentation buffer; 3. First- and second-strand cDNA synthesis using random hexamer primers; 4. End repair, 'A' base addition, and adapter ligation; 5. PCR enrichment for 15 cycles; 6. Size selection (target insert ~300 bp) via 2% agarose gel electrophoresis; 7. Quantification using the TBS380 (Picogreen) method and equimolar pooling for sequencing. Paired-end sequencing (2×150 bp) was performed on the Illumina NovaSeq 6000 platform.

treatment_protocol: FNZ was dissolved in a vehicle solution containing 50% polyethylene glycol 400 and 50% physiological saline. FNZ was administered through daily intraperitoneal injections at doses of 30 mg/kg for 7 days. Three ovaries from ICR mice were dissected for group.

value: Ovary

value: tissue

value: injection FNZ


title: cell-free DNA from healthy control sample 58.4 at T3

description: PBMC DNA from healthy control mice


title: 90752-126A

description: Library name: 90752-126A


title: 904019-12B

description: Library name: 904019-12B


title: ovary, control, replicate 4

description: Library name: mouse_ovary_control_03

value: injection solvent


title: cell-free DNA from healthy control sample 58.2 at T4

description: PBMC DNA from healthy control mice


title: WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 1ng/ml, IP: Strepavidin

description: Library name: W_TO_dox1

value: blood


title: Male DMSO Control, Rep 1

description: Library name: Sample 1


title: ovary, control, replicate 3

description: Library name: mouse_ovary_control_02


title: cell-free DNA from healthy control sample 58.2 at BL

description: PBMC DNA from healthy control mice


title: ovary, FNZ, replicate 3

description: Library name: mouse_ovary_fnz_02


title: cell-free DNA from healthy control sample 58.2 at T3

description: PBMC DNA from healthy control mice


title: 90327-92B

description: Library name: 90327-92B


title: TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 100ng/ml, IP: H3K27ac

description: Library name: T_H3K27ac_dox100

value: TET2 KO

value: doxycycline 100ng/ml, 18hrs

value: abcam ab4729


title: cell-free DNA from healthy control sample 57.2 at T5

description: PBMC DNA from healthy control mice


title: TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 0.1ng/ml, IP: H3K27ac

description: Library name: T_H3K27ac_dox0.1

value: doxycycline 0.1ng/ml, 18hrs


title: WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 0.1ng/ml, IP: Strepavidin

description: Library name: W_TO_dox0.1


title: ovary, control, replicate 2

description: Library name: mouse_ovary_control_01


title: 901824-11A

description: Library name: 901824-11A


title: ovary, FNZ, replicate 2

description: Library name: mouse_ovary_fnz_01


title: TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 1ng/ml, IP: H3K27ac

description: Library name: T_H3K27ac_dox1

value: doxycycline 1ng/ml, 18hrs


title: ChIP-Seq_H3K27ac_rpiaCBE_rep2

city: Jerusalem

first: Yehudit

last: Bergman

address: Ein Karem

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University Of Jerusalem

description: Library name: rpiaCBE2_H3K27ac

data_processing:
Quality control and adapter trimming of raw FASTQ files were performed using Trim Galore (v0.6.10)
Cleaned reads were aligned to the mm10 reference genome using Bowtie2 (v2.5.2)
Samtools (v1.19.2) merge was then used with default parameters to combine data from the two biological replicates
The merged BAM files were converted to BigWig format for visualization using bamCoverage, normalized to counts per million (CPM)
Assembly: mm10
Supplementary files format and content: bigwig file normalized to counts per million (CPM)

source_name: Bone marrow

extract_protocol:
Approximately 1.8–5.3 × 10⁶ CD19⁺ pre-B cells were enriched from WT-Rag1⁻/⁻.hIgM and mutant-Rag1⁻/⁻.hIgM mice using anti-CD19 magnetic beads (Miltenyi Biotec) and MACS column separation (Miltenyi Biotec). Cells were cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with 0.1 M glycine. Cells were washed twice with cold phosphate-buffered saline (PBS) and lysed with lysis buffer [0.5% SDS, 10 mM EDTA, 50 mM Tris-HCl (pH 8), and protease inhibitor]. DNA was sonicated in an ultrasonic bath (Diagenode, Bioruptor) to an average length of 300–500 bp. Sonicated chromatin was centrifuged at 16,000 rpm for 15 min, and the supernatants were immunoprecipitated overnight with anti-H3K27ac (Active Motif, #39133) antibodies. Protein G beads (Cell Signaling Technology, #9006) were added to immunoprecipitated samples and incubated for 2.5 h at 4 °C. Beads were sequentially washed for 5 min each in low-salt RIPA [20 mM Tris-HCl (pH 8), 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS], high-salt RIPA [20 mM Tris-HCl (pH 8), 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS], LiCl buffer [10 mM Tris (pH 8.0), 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% Na-deoxycholate], and Tris-EDTA buffer. Beads were eluted in TE (pH 8.0) with 0.1% SDS and 150 mM NaCl for 1 h at 65 °C, followed by RNase treatment for 30 min at 37 °C. Proteinase K was added and incubated at 50 °C for 2 h. Reverse cross-linking was performed by adding NaCl to a final concentration of 200 mM and incubating for at least 6 h at 65 °C. DNA was purified by phenol–chloroform extraction, and libraries were prepared from the immunoprecipitated DNA.
Libraries were prepared from the immunoprecipitated DNA using the KAPA Hyper Prep Kit according to the manufacturer’s protocol and sequenced on an Illumina NovaSeq 6000, generating 122-bp single-end reads

value: Bone marrow

value: small pre-B

value: rpiaCBE


title: cell-free DNA from healthy control sample 57.2 at T3

description: PBMC DNA from healthy control mice

value: PBMC


title: ChIP-Seq_H3K27ac_rpiaCBE_rep1

description: Library name: rpiaCBE1_H3K27ac


title: cell-free DNA from healthy control sample 57.2 at T2

description: PBMC DNA from healthy control mice

value: control


title: ChIP-Seq_H3K27ac_rsCBE_rep2

description: Library name: rsCBE2_H3K27ac

value: rsCBE


title: 899174-132B

description: Library name: 899174-132B

value: Acute Myeloid Leukemia


title: 903022-115A

description: Library name: 903022-115A


title: 898122_7A_S4

description: Library name: 898122_7A_S4


title: 897598-96A

description: Library name: 897598-96A


title: cell-free DNA from healthy control sample 57.1 at T3

description: PBMC DNA from healthy control mice


title: ChIP-Seq_H3K27ac_rsCBE_rep1

description: Library name: rsCBE1_H3K27ac


title: TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 100ng/ml, IP: H3K4me3

description: Library name: T_H3K4me3_dox100

value: abcam ab8580


title: ChIP-Seq_H3K27ac_WT_rep2

description: Library name: WT2_H3K27ac

value: WT


title: 897327-6A

description: Library name: 897327-6A


title: 900421_8A_S5

description: Library name: 900421_8A_S5


title: 892-79A

description: Library name: 892-79A


title: cell-free DNA from healthy control sample 52.2 at BL

description: PBMC DNA from healthy control mice


title: ChIP-Seq_H3K27ac_WT_rep1

description: Library name: WT1_H3K27ac


title: WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 100ng/ml, IP: H3K4me3

description: Library name: W_H3K4me3_dox100


title: WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 100ng/ml, IP: H3K27ac

description: Library name: W_H3K27ac_dox100


title: 4C-Seq_dEκ_VP_rsCBE_571bp_rep2

description: Library name: rsCBE2_571bp_dEκ_VP

data_processing:
4C-Seq data were analysed using the pipe4C pipeline
Assembly: mm10
Supplementary files format and content: wig file
Library strategy: 4C-Seq

growth_protocol: 445.3 cells were cultured at 37 °C in RPMI 1640 medium containing 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, and 50 μM 2-mercaptoethanol.

extract_protocol:
In brief, 5–10 × 10⁶ Rag1⁻/⁻ 445.3-WT, ΔrsCBE-571 bp 445.3, ΔrsCBE-18 bp 445.3, and ΔSIS 445.3 cells were crosslinked with 1% formaldehyde following stimulation with kinase inhibitors. Primary digestion was performed using NlaIII (NEB, R0125S), followed by dilution and ligation. Cross-links were then reversed by proteinase K treatment, and templates were trimmed with Csp6I (NEB, R0639S) before re-ligation.
Inverted PCR was carried out from multiple viewpoints using the Expand Long Template PCR System (Roche, #11681842001) with indexed Illumina sequencing adapters, and products were purified using the Qiaquick PCR Purification Kit (Qiagen, #28104). Libraries were sequenced on an Illumina NovaSeq 6000 with 122–160 bp single-end reads.

treatment_protocol: Cells were treated with STI571 for 20 hours and subsequently processed for 4C sequencing.

value: pro-B


title: cell-free DNA from healthy control sample 57.1 at BL

description: PBMC DNA from healthy control mice


title: TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 1ng/ml, IP: H3K4me3

description: Library name: T_H3K4me3_dox1


title: 4C-Seq_dEκ_VP_rsCBE_571bp_rep1

description: Library name: rsCBE1_571bp_dEκ_VP


title: cell-free DNA from NMN treated sample 82.4 at T4

description: PBMC DNA from treated mice

value: NMN


title: WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 1ng/ml, IP: H3K27ac

description: Library name: W_H3K27ac_dox1

value: blood


title: 882435_3B_S2

description: Library name: 882435_3B_S2


title: 4C-Seq_dEκ_VP_WT_rep2

description: Library name: WT2_dEκ_VP


title: cell-free DNA from healthy control sample 57.1 at T4

description: PBMC DNA from healthy control mice


title: cell-free DNA from NMN treated sample 82.4 at T3

description: PBMC DNA from treated mice


title: cell-free DNA from healthy control sample 57.1 at T2

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 57.2 at T4

description: PBMC DNA from healthy control mice


title: WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 1ng/ml, IP: H3K4me3

description: Library name: W_H3K4me3_dox1


title: 881969_1A_S1

description: Library name: 881969_1A_S1


title: WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 0.1ng/ml, IP: H3K4me3

description: Library name: W_H3K4me3_dox0.1


title: WT U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 0.1ng/ml, IP: H3K27ac

description: Library name: W_H3K27ac_dox0.1


title: 4C-Seq_dEκ_VP_WT_rep1

description: Library name: WT1_dEκ_VP


title: 883587-4A

description: Library name: 883587-4A


title: 880454-125A

description: Library name: 880454-125A


title: cell-free DNA from NMN treated sample 82.4 at T2

description: PBMC DNA from treated mice


title: 878972-124A

description: Library name: 878972-124A


title: cell-free DNA from NMN treated sample 82.4 at BL

description: PBMC DNA from treated mice


title: 875546-94A

description: Library name: 875546-94A


title: 4C-Seq_rsEκ_VP_rsCBE_571bp_rep1

description: Library name: rsCBE1_571bp_rsEκ_VP


title: 4C-Seq_rsEκ_VP_rsCBE_571bp_rep2

description: Library name: rsCBE2_571bp_rsEκ_VP


title: 4C-Seq_rsEκ_VP_WT_rep1

description: Library name: WT1_rsEκ_VP


title: cell-free DNA from NMN treated sample 82.3 at T3

description: PBMC DNA from treated mice


title: LF1 cells, quiescent scRNA-seq 2

city: Belmont

first: Azucena

last: Rocha

address: 42 Alma Avenue

department: MCB

institute: Brown University

description:
Library name: Quiescent2
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: counts tables were generated using Seurat, csv files

source_name: cell culture

growth_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C and ~3% O2

extract_protocol:
Cells were trypsinized and washed with PBS and resuspended in PBS +BSA per 10X protocol recommendation.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 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.

treatment_protocol: Contact inhibition was induced by allowing cells to reach 100%confluency for 3 days then media was changed to Serum withdrawal with DMEM supplemented with 0.01% FBS for 2 days

value: cell culture

value: human lung fibroblasts

value: contact inhibition + serum withdrawal


title: 4C-Seq_rsEκ_VP_WT_rep2

description: Library name: WT2_rsEκ_VP


title: TET2KO U937 cells expressing doxycycline-inducible TurboID OGT, 18hr induction dox 0.1ng/ml, IP: H3K4me3

description: Library name: T_H3K4me3_dox0.1

value: TET2 KO

value: doxycycline 0.1ng/ml, 18hrs


title: 866494-84B

description: Library name: 866494-84B


title: 874808-86B

description: Library name: 874808-86B


title: LF1 cells, quiescent scRNA-seq 1

description:
Library name: Quiescent1
10x Genomics


title: cell-free DNA from NMN treated sample 82.3 at BL

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 82.3 at T4

description: PBMC DNA from treated mice


title: 839984-120B

description: Library name: 839984-120B


title: HCT116, miR-7974-OE cells, replicate 2

city: Taoyuan

first: Yi-Tung

last: Chen

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

data_processing:
Partek® Flow® Genomic Analysis Software
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek® Flow® Genomic Analysis Software
Trimmed sequence reads were mapped to hg38 using Partek® Flow® Genomic Analysis Software
Read count extraction and normalization were performed using Partek® Flow® Genomic Analysis Software
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq stranded-mRNA Library Prep Kit following manufacturer's protocols.

value: Colorectal cancer cell line

value: miR-7974 overexpression


title: 857886-131A

description: Library name: 857886-131A


title: HCT116, miR-7974-OE cells, replicate 1


title: 4C-Seq_RC_VP_rsCBE_571bp_rep1

description: Library name: rsCBE1_571bp_RC_VP

value: Bone marrow


title: 4C-Seq_RC_VP_rsCBE_571bp_rep2

description: Library name: rsCBE2_571bp_RC_VP


title: cell-free DNA from NMN treated sample 82.2 at T2

description: PBMC DNA from treated mice

value: PBMC


title: HCT116, Ctrl cells, replicate 1

value: Control vector


title: 802259_20A_S2

description: Library name: 802259_20A_S2


title: HCT116, Ctrl cells, replicate 2


title: 814239-19B

description: Library name: 814239-19B


title: 4C-Seq_RC_VP_WT_rep1

description: Library name: WT1_RC_VP


title: 4C-Seq_RC_VP_WT_rep2

description: Library name: WT2_RC_VP


title: cell-free DNA from NMN treated sample 82.1 at T4

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 82.2 at BL

description: PBMC DNA from treated mice


title: 4C-Seq_rsCBE_VP_SIS_rep1

description: Library name: SIS1_rsCBE_VP

value: SIS


title: 4C-Seq_rsCBE_VP_SIS_rep2

description: Library name: SIS2_rsCBE_VP


title: 7625-68B

description: Library name: 7625-68B

value: Acute Myeloid Leukemia


title: 4C-Seq_rsCBE_VP_rsCBE_18bp_rep2

description: Library name: rsCBE2_18bp_rsCBE_VP


title: Granulosa cells cultured with NEFA rep3

type: RNA

city: Dummerstorf

first: Vijay simha

last: Baddela

address: Wilhelm-Stahl-Allee 2

department: Reproductive biology

country: Germany

institute: Leibniz institute for farm animal biology

hyb_protocol: The RNA was hybridized overnight (45°C) in the GeneChipR Hybridization Oven (Affymetrix) to the Affymetrix Bovine Gene 1.0 ST arrays. Washing and staining were performed according to the Affymetrix standard protocol.

scan_protocol: The scanning of the microarray was done with the GeneChip Scanner 3000 HR (Affymetrix) and image processing was done with the software AGCC (Affymetrix).

data_processing: Data analysis was performed with the TAC 4.0 software (Affymetrix) and RMA method was used for normalization.

label: Biotin

organism: Bos taurus

source_name: NEFA treatment

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol (GeneChip® Expression 3’Amplification One-Cycle Target Labeling and Control Reagents).

growth_protocol: Granulosa cells were cultured serum-free in alpha-MEM supplemented with FSH, IGF-1 and androstenedione.

extract_protocol: Total RNA was prepared using RNeasy mini kit (Qiagen, Hilden, Germany).

treatment_protocol: Spent media were replaced with fresh media containing BSA or NEFA on day 2 and on day 4 and cell were analyzed on day 6

value: Primary granulosa cells


title: cell-free DNA from NMN treated sample 82.1 at T2

description: PBMC DNA from treated mice


title: Granulosa cells cultured with NEFA rep4


title: Granulosa cells cultured with NEFA rep2


title: cell-free DNA from NMN treated sample 82.2 at T3

description: PBMC DNA from treated mice


title: 7205-109A

description: Library name: 7205-109A


title: 616072-31A

description: Library name: 616072-31A


title: cell-free DNA from NMN treated sample 82.1 at T3

description: PBMC DNA from treated mice


title: Granulosa cells cultured with NEFA rep1


title: 4C-Seq_rsCBE_VP_rsCBE_571bp_rep2

description: Library name: rsCBE2_571bp_rsCBE_VP


title: Granulosa cells cultured with BSA rep3

source_name: BSA treatment


title: 307250-123B

description: Library name: 307250-123B


title: Granulosa cells cultured with BSA rep4


title: 304799-91B

description: Library name: 304799-91B


title: cell-free DNA from NMN treated sample 78.4 at T3

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 78.4 at T2

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 78.4 at BL

description: PBMC DNA from treated mice


title: 298550-87B

description: Library name: 298550-87B


title: 4C-Seq_rsCBE_VP_rsCBE_571bp_rep1

description: Library name: rsCBE1_571bp_rsCBE_VP


title: Igk_repertoire_BM_rsCBE_rep5

description:
Library name: rsCBE_BM_Replicate_5
RS_BM_Replicate_5

library_source: other

data_processing:
Sequencing reads were processed to retain only read pairs (R1 and R2) with an average Phred quality score ≥30
both R1 and R2 were aligned independently to the C57BL/6 mouse kappa light chain V and J gene reference sequences from the IMGT9 database using IgBLAST
Assembly: mm10
Supplementary files format and content: TSV-formatted repertoire table including V/J gene assignments and clonotype counts for each sample.

extract_protocol:
RNA was extracted from ex vivo FACS-purified pre-B cells using the NucleoSpin RNA Kit according to the manufacturer’s instructions.
Libraries were prepared using a protocol adapted from Rena Levin-Klein et al., 2017, and sequenced on a MiSeq platform, producing 151-bp paired-end reads.

value: small pre-B

value: rsCBE


title: 280129-65B

description: Library name: 280129-65B


title: cell-free DNA from NMN treated sample 82.1 at BL

description: PBMC DNA from treated mice

value: NMN


title: cell-free DNA from NMN treated sample 78.3 at T3

description: PBMC DNA from treated mice


title: Granulosa cells cultured with BSA rep2


title: 4C-Seq_rsCBE_VP_WT_rep1

description: Library name: WT1_rsCBE_VP

value: pro-B

value: WT


title: cell-free DNA from NMN treated sample 78.3 at BL

description: PBMC DNA from treated mice


title: 295346-61B

description: Library name: 295346-61B


title: 273098-26B

description: Library name: 273098-26B


title: Granulosa cells cultured with BSA rep1


title: ATAC-seq_small_pre-B_rpiaCBE_rep2

description: Library name: rpiaCBE2

extract_protocol:
ATAC-seq was performed on 50–100 × 10³ ex vivo FACS-purified small pre-B cells.
Libraries were amplified using the Nextera Illumina kit according to the manufacturer’s instructions (Active Motif, #53150) and sequenced on an Illumina NovaSeq 6000 platform, generating 61-bp paired-end reads.

value: rpiaCBE


title: Igk_repertoire_BM_rsCBE_rep3

description:
Library name: rsCBE_BM_Replicate_3
RS_BM_Replicate_3


title: cell-free DNA from NMN treated sample 78.2 at BL

description: PBMC DNA from treated mice


title: 4C-Seq_rsCBE_VP_WT_rep2

description: Library name: WT2_rsCBE_VP


title: ATAC-seq_small_pre-B_rsCBE_rep2

description: Library name: rsCBE2


title: 241516-129A

description: Library name: 241516-129A


title: 4C-Seq_rsCBE_VP_rsCBE_18bp_rep1

description: Library name: rsCBE1_18bp_rsCBE_VP


title: Igk_repertoire_BM_rsCBE_rep2

description:
Library name: rsCBE_BM_Replicate_2
RS_BM_Replicate_2


title: cell-free DNA from NMN treated sample 78.2 at T3

description: PBMC DNA from treated mice


title: ATAC-seq_small_pre-B_rsCBE_rep1

description: Library name: rsCBE1


title: cell-free DNA from NMN treated sample 78.2 at T2

description: PBMC DNA from treated mice


title: ATAC-seq_small_pre-B_rpiaCBE_rep1

description: Library name: rpiaCBE1


title: Igk_repertoire_BM_rsCBE_rep4

description:
Library name: rsCBE_BM_Replicate_4
RS_BM_Replicate_4


title: Igk_repertoire_BM_rsCBE_rep1

description:
Library name: rsCBE_BM_Replicate_1
RS_BM_Replicate_1


title: Igk_repertoire_BM_WT_rep4

description:
Library name: WT_BM_Replicate_4
WT_BM_Replicate_4


title: 236273-25A

description: Library name: 236273-25A


title: ATAC-seq_small_pre-B_WT_rep2

description: Library name: WT2


title: 255-117B

description: Library name: 255-117B


title: cell-free DNA from NMN treated sample 78.1 at T2

description: PBMC DNA from treated mice


title: 230362-136B

description: Library name: 230362-136B


title: cell-free DNA from NMN treated sample 78.1 at T3

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 78.1 at T4

description: PBMC DNA from treated mice


title: 6B_seq_WG_replicate2

first: Somdutta

last: Dhir

address: Robinson Way

department: CRUK-CI

country: United Kingdom

institute: University of Cambridge

description: Library name: Sample19

data_processing:
Fastq files from tagmentation-based duet evoC were processed through a modified version of biomodal’s duet analysis pipeline. 9nt scar sequences, AAGAGATAG and AAAAAACAA were trimmed from the 5`-ends of Reads 1 and 2. Read pairs that lacked either scar sequence were discarded. Adapters containing the full 19nt Tn5 ME sequence and 2 Uracils (ME2U) hairpin were trimmed from the 3`-ends of Reads 1 and 2. A further 9nt were trimmed from the 3`-ends of Read 1 and 2.The trimmed read pairs were then resolved using the bespoke resolution algorithm described in Füllgrabe et al. (2023). The resolved, single-end reads were aligned against a GRCm38 reference (gencode vM25) that contained additional sequences for pUC19, bacteriophage lambda and short spike-in oligonucleotides using bwa-mem2 (v2.2.1).
For Mosaic end CUT&Tag, raw fastq files were trimed with cutadapt version 1.18 to remove adaptors and bases with quality lower than 20 (-q 20) mapped with bwa-mem 0.7.17-r2188 to mm10 genome, and only the reads within the whitelist have been retained.
Bigwig files were created using bamCoverage with counts per milion normalisation (CPM) after extending the paired-end reads.
Assembly: mm10 and GRCm38(gencode vM25)
Supplementary files format and content: CG_quant reports , BigWigs

source_name: Embryonic stem cells

growth_protocol: E14TG2A mouse embryonic stem cells were cultured in serum/LIF conditions on gelatin-coated plates. Serum/LIF medium was prepared with high-glucose DMEM (Sigma, D6546-500mL) supplemented with 10% FBS (Gibco, 16141079), 1X GlutaMax-I (Gibco, 35050-038), 1X NEAA (Gibco, 11140-035), 0.1 mM β-mercaptoethanol (Sigma, M3148) and 1,000 U/mL LIF (PeproTech, murine LIF, 250-02-25UG).

extract_protocol:
Cells were harvested by Accutase dissociation and used in CUT&Tag (Kaya-Okur et al. 2020, PMID: 32913232) assays for different histone mark antibodies and a non-specific IgG control (H3K27ac, H3K4me1, H3K4me3, H3K27me3, total rabbit IgG). Genomic DNA was extracted from cells after CUT&Tag using proteinase K digestion and Zymo DNA clean and concentrator clean-up.
Genomic DNA isolated from each CUT&Tag cell sample replicate was subjected to end repair and 6-base-seq library construction (Fullgrabe and Gosal et al. 2023, PMIID: 36747096).

treatment_protocol: No treatment

value: Embryonic stem cells


title: Igk_repertoire_BM_WT_rep3

description:
Library name: WT_BM_Replicate_3
WT_BM_Replicate_3


title: Igk_repertoire_BM_WT_rep1

description:
Library name: WT_BM_Replicate_1
WT_BM_Replicate_1


title: 191224-97B

description: Library name: 191224-97B


title: sc_PBMC_Y6

city: Tarrytown

first: Kun

last: Xiong

state: NY

address: 777 Old Saw Mill River Road

department: Molecular Profiling and Data Science

institute: Regeneron Pharmaceuticals

description:
Library name: 1509026
s24

data_processing:
For bulk RNAseq, raw fastq were processed by ArrayStudio (11.7.4) to obtain counts of gene expression. For scRNA, Cell Ranger Single Cell Software Suite (6.1.1) were used to de-muliplexing, alignment, filtering, and UMI counting.
Assembly: GRCm38
Supplementary files format and content: txt file of raw counts for bulk RNAseq. H5ad of processed cells for scRNA

extract_protocol:
For bulk RNAseq, ribosomal RNA-depleted RNA-seq libraries were generated using QIAseq® FastSelect −rRNA HMR (QIAGEN) with the KAPA® RNA HyperPrep Kit (Roche Sequencing). For scRNA, single cells suspended in PBS with 0.04% BSA were loaded, 10K cells per lane, on a Chromium Controller (10X Genomics).
For bulk RNAseq, starting material was 100 ng of RNA dependent on availability per tissue type. RNA fragmentation was done at 85°C for 6 minutes. cDNA was ligated with 1.5 µM or 300 nM xGen Dual Index UMI Adapters (Integrated DNA Technologies) respective to RNA input. Ligated cDNA libraries were amplified using 14 PCR cycles, also respective to RNA input. Sequencing of the resulting libraries was done on NovaSeq 6000 (Illumina) using a 2x76, paired-end sequencing recipe. For scRNA, libraries were prepared using Chromium Next GEM Single Cell 3’ Kit, v3.1 (10X Genomics) with single-index barcoding, according to the manufacturer’s guidelines.

value: Young


title: 222966-118A

description: Library name: 222966-118A


title: sc_PBMC_Y5

description:
Library name: 1509025
s23


title: cell-free DNA from NMN treated sample 78.1 at BL

description: PBMC DNA from treated mice


title: ATAC-seq_small_pre-B_WT_rep1

description: Library name: WT1


title: 217106-63A

description: Library name: 217106-63A


title: 206506-62B

description: Library name: 206506-62B


title: 162148-127B

description: Library name: 162148-127B


title: cell-free DNA from NMN treated sample 77.3 at T3

description: PBMC DNA from treated mice


title: sc_PBMC_Y3

description:
Library name: 1509023
s21


title: Igk_repertoire_BM_WT_rep2

description:
Library name: WT_BM_Replicate_2
WT_BM_Replicate_2


title: 6B_seq_WG_replicate1

description: Library name: Sample18


title: cell-free DNA from NMN treated sample 77.4 at T2

description: PBMC DNA from treated mice


title: ChIP-Seq_CTCF_rsCBE_rep2

description: Library name: rsCBE2_CTCF

extract_protocol:
Approximately 3–6 × 10⁶ IL-7-cultured pre-B cells were cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with 0.1 M glycine. Cells were washed twice with cold phosphate-buffered saline (PBS) and lysed with lysis buffer [0.5% SDS, 10 mM EDTA, 50 mM Tris-HCl (pH 8), and protease inhibitor]. DNA was sonicated in an ultrasonic bath (Diagenode, Bioruptor) to an average length of 300–500 bp. Sonicated chromatin was centrifuged at 16,000 rpm for 15 min, and the supernatants were immunoprecipitated overnight with anti-CTCF (Cell Signaling Technology, #3418S) antibodies. Protein G beads (Cell Signaling Technology, #9006) were added to immunoprecipitated samples and incubated for 2.5 h at 4 °C. Beads were sequentially washed for 5 min each in low-salt RIPA [20 mM Tris-HCl (pH 8), 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS], high-salt RIPA [20 mM Tris-HCl (pH 8), 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS], LiCl buffer [10 mM Tris (pH 8.0), 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% Na-deoxycholate], and Tris-EDTA buffer. Beads were eluted in TE (pH 8.0) with 0.1% SDS and 150 mM NaCl for 1 h at 65 °C, followed by RNase treatment for 30 min at 37 °C. Proteinase K was added and incubated at 50 °C for 2 h. Reverse cross-linking was performed by adding NaCl to a final concentration of 200 mM and incubating for at least 6 h at 65 °C. DNA was purified by phenol–chloroform extraction, and libraries were prepared from the immunoprecipitated DNA.
Libraries were prepared from the immunoprecipitated DNA using the KAPA Hyper Prep Kit according to the manufacturer’s protocol and were sequenced on an Illumina NextSeq, generating 122-bp single-end reads.

value: pre-B


title: cell-free DNA from NMN treated sample 77.4 at T3

description: PBMC DNA from treated mice


title: ChIP-Seq_CTCF_WT_rep2

description: Library name: WT2_CTCF


title: cell-free DNA from NMN treated sample 77.4 at BL

description: PBMC DNA from treated mice


title: ChIP-Seq_CTCF_rsCBE_rep1

description: Library name: rsCBE1_CTCF


title: cell-free DNA from NMN treated sample 77.3 at T4

description: PBMC DNA from treated mice


title: sc_PBMC_Y2

description:
Library name: 1509022
s20


title: RNA-Seq_rsCBE_rep3

description: Library name: rsCBE3

data_processing:
Quality control of raw FASTQ files were performed using Trim Galore (v0.6.10)
Trimmed reads were aligned to the mm10 reference genome using STAR (v2.7.11)
Resulting BAM files were used for gene-level quantification with HTSeq
Raw read counts normalization and differential gene expression analysis were performed using the DESeq2 package
Assembly: mm10
Supplementary files format and content: csv file include raw counts for each sample

extract_protocol:
RNA was extracted from ex vivo FACS-purified pre-B cells using the NucleoSpin RNA Kit according to the manufacturer’s instructions. A total of 1 µg of DNase-treated RNA was used. Ribosomal RNA was depleted prior to library construction
RNA-seq libraries were prepared using the SMARTer Stranded Total RNA Sample Prep Kit – HI Mammalian (Takara) following the manufacturer’s recommendations.


title: sc_PBMC_Y4

description:
Library name: 1509024
s22


title: 167941-93A

description: Library name: 167941-93A

data_processing:
The data is processed using bowtie2 and called peaks using MACS2.
Assembly: hg38
Supplementary files format and content: narrowPeak

extract_protocol:
Nuclei were isolated using digitnnin-containing buffer from viable frozen peripheral blood cells from AML patients and then incubated with Illumina Transposase for 30min at 37 C.
Libraries were amplified using per-sample determined PCR cycles


title: 161652-89A

description: Library name: 161652-89A


title: 161528-66B

description: Library name: 161528-66B


title: RNA-Seq_WT_rep3

description: Library name: WT3


title: cell-free DNA from NMN treated sample 77.2 at T2

description: PBMC DNA from treated mice

data_processing: SeSame package in R environment (v. 4.4.2)

extract_protocol: Red blood cells were removed with RBC lysis buffer (155 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA, pH 7.3), and then the remaining cells were digested overnight at 65°C with proteinase K (20 mg/mL) in TESR buffer (10 mM Tris-HCl, 25 mM EDTA, 0.5% SDS, 20 µg/mL RNase). DNA was washed and isolated using SPRI beads and eluted in 10 mM Tris-HCl pH8.


title: cell-free DNA from NMN treated sample 77.3 at T2

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 77.2 at BL

description: PBMC DNA from treated mice


title: sc_PBMC_Y1

description:
Library name: 1509021
s19


title: 162102-122A

description: Library name: 162102-122A


title: Igk_repertoire_BM_WT_rep5

description:
Library name: WT_BM_Replicate_5
WT_BM_Replicate_5


title: 160028-45A

description: Library name: 160028-45A


title: cell-free DNA from NMN treated sample 77.2 at T4

description: PBMC DNA from treated mice


title: 162248-121B

description: Library name: 162248-121B


title: 160006-46B

description: Library name: 160006-46B


title: sc_PBMC_O3

description:
Library name: 1509029
s15

value: Old


title: sc_PBMC_O4

description:
Library name: 1509030
s16


title: ChIP-Seq_CTCF_WT_rep1

description: Library name: WT1_CTCF


title: cell-free DNA from NMN treated sample 77.3 at BL

description: PBMC DNA from treated mice


title: CD45.1+P14 cells, HTO

city: Melbourne

first: Ian

last: Parish

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Library name: TCF1-multi-TotalSeqA
HTO library: read1 file contains the cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

data_processing:
Cell Ranger ARC v.2.0.0 was used to count reads across sequencing lanes into a single set of raw_feature_bc_matrix.h5, filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz and atac_fragments.tsv.gz.tbi
Cell barcodes from Cell Ranger ARC output were used as a whitelist to quantify HTOs using CITE-seq-Count (v 1.4.5) and aggregate counts into a single set of barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz
Assembly: mm10
Supplementary files format and content: Cell Ranger ARC output files: raw_feature_bc_matrix.h5, filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz and atac_fragments.tsv.gz.tbi
Supplementary files format and content: CITE-seq-Count output files: read_count.barcodes.tsv.gz, read_count.features.tsv.gz, read_count.matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: Spleen

extract_protocol:
Sorted CRISPR-edited CD45.1+P14 cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10X Controller using the Chromium Single Cell Multiome ATAC + Gene Expression kit
The CITE-seq and hashing protocol described by Stoeckius et al was used to generate hashtag oligo libraries. (Stoeckius et al. 2017)

treatment_protocol: C57BL/6 mice received CRISPR-edited CD45.1+ P14 cells and were infected with LCMV Clone 13. 20 days later, the CD45.1 P14 cells were isolated from the spleens of the recipient mice, sorted and analysed.

value: Spleen

value: CD8 T Lymphocyte

value: LCMV Clone 13 infection

tag: library type

value: HTO

tag: hto

value: TotalSeq-A0301 anti-mouse Hashtag 1, TotalSeq-A0302 anti-mouse Hashtag 2, TotalSeq-A0303 anti-mouse Hashtag 3


title: sc_PBMC_O6

description:
Library name: 1509032
s18

value: PBMC


title: 160500-30B

description: Library name: 160500-30B

value: Acute Myeloid Leukemia


title: sc_PBMC_O5

description:
Library name: 1509031
s17


title: RNA-Seq_WT_rep2

description: Library name: WT2

value: Bone marrow

value: small pre-B


title: RNA-Seq_rsCBE_rep1

description: Library name: rsCBE1

value: rsCBE


title: RNA-Seq_WT_rep1

description: Library name: WT1


title: RNA-Seq_rsCBE_rep2

description: Library name: rsCBE2


title: 151590-43B

description: Library name: 151590-43B


title: sc_PBMC_O1

description:
Library name: 1509027
s13


title: cell-free DNA from NMN treated sample 77.1 at T3

description: PBMC DNA from treated mice

value: NMN


title: 151258-48B

description: Library name: 151258-48B


title: sc_PBMC_O2

description:
Library name: 1509028
s14


title: CD45.1+P14 cells, ATAC

description:
Library name: TCF1-multi-ATAC
ATAC library: read1 file contains the cell barcode and UMI; read2 file contains chromatin accessibility data

library_source: genomic single cell

data_processing:
Cell Ranger ARC v.2.0.0 was used to count reads across sequencing lanes into a single set of raw_feature_bc_matrix.h5, filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz and atac_fragments.tsv.gz.tbi
Cell barcodes from Cell Ranger ARC output were used as a whitelist to quantify HTOs using CITE-seq-Count (v 1.4.5) and aggregate counts into a single set of barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz
Assembly: mm10
Supplementary files format and content: Cell Ranger ARC output files: raw_feature_bc_matrix.h5, filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz and atac_fragments.tsv.gz.tbi
Supplementary files format and content: CITE-seq-Count output files: read_count.barcodes.tsv.gz, read_count.features.tsv.gz, read_count.matrix.mtx.gz

value: genomic


title: cell-free DNA from NMN treated sample 77.1 at T2

description: PBMC DNA from treated mice


title: CD45.1+P14 cells, GEX

description:
Library name: TCF1-multi-GEX
GEX (3' mRNA) library: read1 file contains the cell barcode and UMI; read2 file contains the transcript

value: mRNA


title: sc_LinBM_Y5

description:
Library name: 1510014
s11


title: sc_LinBM_Y6

description:
Library name: 1510015
s12


title: 150935-50A

description: Library name: 150935-50A


title: cell-free DNA from NMN treated sample 77.1 at BL

description: PBMC DNA from treated mice


title: sc_LinBM_Y4

description:
Library name: 1510013
s10


title: WT BMDMs input

description: Library name: W_input_BMDM

extract_protocol:
Briefly, cells were double cross-linked with disuccinimidyl glutarate (Thermo) and formaldehyde for 30 minutes at room temperature and quenched with 2.5M glycine. Cross-linked cells were treated with LB1 buffer (50mM HEPES-KOH, pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100 in distilled water) x 10 minutes at 4C, LB2 buffer (10mM Tris-HCl, pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA in distilled water) x 10 minutes at 4C, then sonicated in LB3 buffer (10mM Tris-HCL, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% Na-Lauroylsarcosine, 1% Triton X-100, in distilled water) using Covaris, E220. Following antibody incubation overnight, immunoprecipitation (IP) was performed using Protein-A or Protein-G Dynabeads (Thermo) or Strepavidin magnetic beads (Thermo 88817) for 1 hour. Beads were collected via a magnet and washed six times with RIPA buffer (50mM Hepes-KOH, pH 7.5, 500mM LiCl, 1mM EDTA, 0.7% Na-deoxycholate, 1% NP-40 in distilled water), twice with buffer 500 (0.5g deoxycholic acid, 1mM EDTA, 5mM Tris-HCl, pH 8.1, 1% Triton X-100, and 0.02% NaN3 in distilled water), and twice with LiCl buffer (2.5 g deoxycholic acid, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 10 mM Tris-HCl pH 8.1, 0.02% NaN3 in distilled water). Beads were washed briefly with TE buffer and DNA was eluted in ChIP elution buffer (50mM Tris-HCl, pH 8.0, 10mM EDTA, 1% SDS in distilled water) and de-crosslinked at 65C for 2 hours. DNA was purified by column purification (DNA Clean and Concentration, Zymo Research).
Library preparation was done according to manufacturer’s instructions (ThruPlex DNA-Seq Kit, Takara or NEBNext® Ultra, NEB).

value: blood

value: macrophages

value: WT

value: input


title: WT BMDMs treated with sucrose, 55mM, 24 hrs; IP: Ogt

description: Library name: W_Ogt_BMDM_sucrose_55mM

value: sucrose, 55mM, 24 hrs

value: Cell Signaling 24083


title: cell-free DNA from NMN treated sample 75.4 at T5

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 77.1 at T4

description: PBMC DNA from treated mice


title: 150749-51A

description: Library name: 150749-51A


title: sc_LinBM_Y3

description:
Library name: 1510012
s9

value: Young


title: 150825-49A

description: Library name: 150825-49A


title: cell-free DNA from NMN treated sample 75.4 at BL

description: PBMC DNA from treated mice


title: sc_LinBM_Y2

description:
Library name: 1510011
s8


title: 150587-55B

description: Library name: 150587-55B


title: WT BMDMs treated with glucose, 55mM, 24 hrs; IP: H3K4me3

description: Library name: W_H3K4me3_BMDM_glucose_55mM

value: glucose, 55mM, 24 hrs

value: abcam 8580


title: cell-free DNA from NMN treated sample 75.4 at T4

description: PBMC DNA from treated mice

value: PBMC


title: WT BMDMs treated with glucose, 55mM, 24 hrs; IP: Ogt

description: Library name: W_Ogt_BMDM_glucose_55mM


title: 150625-58A

description: Library name: 150625-58A

value: Acute Myeloid Leukemia


title: 150509-60A

description: Library name: 150509-60A


title: WT BMDMs treated with glucose, 55mM, 24 hrs; IP: H3K27me3

description: Library name: W_H3K27me3_BMDM_glucose_55mM

value: abcam 6002


title: sc_LinBM_O6

description:
Library name: 1510021
s6

value: Old


title: sc_LinBM_Y1

description:
Library name: 1510010
s7


title: cell-free DNA from NMN treated sample 75.3 at T5

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 75.3 at T4

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 75.3 at T3

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 75.4 at T3

description: PBMC DNA from treated mice


title: 141040-99A

description: Library name: 141040-99A


title: WT BMDMs treated with glucose, 55mM, 24 hrs; IP: GlcNAc

description: Library name: W_GlcNAc_BMDM_glucose_55mM

value: Cell Signaling 82332


title: 150028-101B

description: Library name: 150028-101B


title: Wt BMDMs treated with glucose, 12mM, 24 hrs; IP: Ogt

description: Library name: W_Ogt_BMDM_glucose_12mM

value: glucose, 12mM, 24 hrs


title: 140586-80B

description: Library name: 140586-80B


title: cell-free DNA from NMN treated sample 75.3 at T2

description: PBMC DNA from treated mice

value: NMN


title: WT BMDMs treated with glucose, 12mM, 24 hrs; IP: GlcNAc

description: Library name: W_GlcNAc_BMDM_glucose_12mM


title: 140425-64B

description: Library name: 140425-64B


title: WT BMDMs treated with glucose, 55mM, 24 hrs; IP: H3K4me1

description: Library name: W_H3K4me1_BMDM_glucose_55mM

value: abcam 8895


title: sc_LinBM_O4

description:
Library name: 1510019
s4


title: cell-free DNA from NMN treated sample 75.2 at T2

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 75.2 at T3

description: PBMC DNA from treated mice


title: 130889-104A

description: Library name: 130889-104A


title: WT BMDMs treated with galactose, 55mM, 24 hrs; IP: Ogt

description: Library name: W_Ogt_BMDM_galactose_55mM

value: blood

value: galactose, 55mM, 24 hrs


title: 130800-100A

description: Library name: 130800-100A


title: sc_LinBM_O2

description:
Library name: 1510017
s2


title: 130597-85B

description: Library name: 130597-85B


title: sc_LinBM_O1

description:
Library name: 1510016
s1


title: Tet2 KO BMDMs treated with glucose, 55mM, 24 hrs; IP: H3K27me3

description: Library name: T_H3K27me3_BMDM_glucose_55mM

value: macrophages

value: Tet2 KO


title: Tet2 KO BMDMs input

description: Library name: T_input_BMDM

value: input


title: cell-free DNA from NMN treated sample 75.3 at BL

description: PBMC DNA from treated mice


title: HSC_bulk_Old_9

description:
Library name: 1519090
HSC_bulk_Old_9

source_name: HSC

value: HSC


title: cell-free DNA from NMN treated sample 75.2 at BL

description: PBMC DNA from treated mice


title: Tet2 KO BMDMs treated with glucose, 55mM, 24 hrs; IP: Ogt

description: Library name: T_Ogt_BMDM_glucose_55mM

value: Cell Signaling 24083


title: sc_LinBM_O3

description:
Library name: 1510018
s3


title: 130473-77B

description: Library name: 130473-77B


title: 130361-135A

description: Library name: 130361-135A


title: cell-free DNA from NMN treated sample 75.1 at T5

description: PBMC DNA from treated mice


title: Tet2 KO BMDMs treated with glucose, 55mM, 24 hrs; IP: H3K4me3

description: Library name: T_H3K4me3_BMDM_glucose_55mM

value: glucose, 55mM, 24 hrs


title: HSC_bulk_Old_8

description:
Library name: 1519089
HSC_bulk_Old_8


title: HSC_bulk_Old_10

description:
Library name: 1519091
HSC_bulk_Old_10


title: Tet2 KO BMDMs treated with glucose, 55mM, 24 hrs; IP: H3K4me1

description: Library name: T_H3K4me1_BMDM_glucose_55mM


title: cell-free DNA from NMN treated sample 75.1 at T4

description: PBMC DNA from treated mice


title: 130347-128B

description: Library name: 130347-128B


title: HSC_bulk_Old_7

description:
Library name: 1519088
HSC_bulk_Old_7


title: 110382-90B

description: Library name: 110382-90B


title: sc_LinBM_O5

description:
Library name: 1510020
s5


title: cell-free DNA from NMN treated sample 73.4 at T2

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 75.1 at BL

description: PBMC DNA from treated mice


title: Tet2 KO BMDMs treated with glucose, 12mM, 24 hrs; IP: GlcNAc

description: Library name: T_GlcNAc_BMDM_glucose_12mM


title: HSC_bulk_Old_6

description:
Library name: 1519087
HSC_bulk_Old_6


title: 1039353-81B

description: Library name: 1039353-81B


title: HSC_bulk_Old_3

description:
Library name: 1519084
HSC_bulk_Old_3


title: HSC_bulk_Old_1

description:
Library name: 1519082
HSC_bulk_Old_1


title: HSC_bulk_Old_2

description:
Library name: 1519083
HSC_bulk_Old_2


title: cell-free DNA from NMN treated sample 75.1 at T2

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 73.4 at BL

description: PBMC DNA from treated mice


title: ovary, recurrent, patient23

city: Yeonsu-gu, Incheon

first: Johyeon

last: Nam

address: 265, Harmony-ro

department: Division of Life Sciences

country: South Korea

institute: Incheon National University

description: Library name: RNA_R_23

data_processing:
Low-quality adapter sequences were trimmed using TrimGalore.
The STAR 2-pass method was used to align the raw sequencing data to the human reference genome (GRCh38.p14) using the STAR aligner.
Read count was extracted using featureCounts.
Assembly: GRCh38.p14
Supplementary files format and content: Tab-deliminated text file includes normalized counts for each sample.

extract_protocol:
A total of 100 ng of total RNA was subjected to a sequencing library construction using the Agilent SureSelect RNA Direct kit as per the manufacturer's protocol.
The final purified product was quantified using KAPA Library Quantification kits for Illumina Sequencing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, #KK4854).

value: Ovary

tag: tissue type

value: recurrent ovarian cancer tissues

tag: subject id


title: Tet2 KO BMDMs treated with glucose, 55mM, 24 hrs; IP: GlcNAc

description: Library name: T_GlcNAc_BMDM_glucose_55mM

data_processing:
Trimmed reads were aligned to the mm10 or hu19 genome via bowtie2.3.5 (Langmead et al., Nature Methods. 2012) using --very-sensitive -X700 --no-mixed --no-discordant. Duplicates were marked using MarkDuplicates in Picard/2.19.0 (Broad Institute) or MACS2 (Zhang et al. Genome Biology 2008). Peaks were called using Macs2/2.1.1 using -f BAMPE -B --nomodel --broad --keep-dup 1 --extsize 200 -p 1e-2. For transcription factors, --broad parameter was omitted. ENCODE blacklist regions were excluded from analysis (Amemiya et al. Sci Reports 2019). BigWig files were generated via bedGraphToBigWig (Kent et al. Bioinformatics. 2010).
Assembly: Mouse mm10 or Human hg19
Supplementary files format and content: bigWig


title: HSC_bulk_Old_4

description:
Library name: 1519085
HSC_bulk_Old_4


title: Tet2 KO BMDMs treated with sucrose, 55mM, 24 hrs; IP: Ogt

description: Library name: T_Ogt_BMDM_sucrose_55mM

value: sucrose, 55mM, 24 hrs


title: HSC_bulk_Young_10

description:
Library name: 1519081
HSC_bulk_Young_10

value: Young


title: Tet2 KO BMDMs treated with galactose, 55mM, 24 hrs; IP: Ogt

description: Library name: T_Ogt_BMDM_galactose_55mM


title: ovary, recurrent, patient21

description: Library name: RNA_R_21


title: Tet2 KO BMDMs treated with glucose, 12mM, 24 hrs; IP: Ogt

description: Library name: T_Ogt_BMDM_glucose_12mM


title: cell-free DNA from NMN treated sample 73.3 at BL

description: PBMC DNA from treated mice

value: PBMC


title: ovary, recurrent, patient22

description: Library name: RNA_R_22


title: ovary, recurrent, patient24

description: Library name: RNA_R_24


title: HSC_bulk_Young_9

description:
Library name: 1519080
HSC_bulk_Young_9


title: cell-free DNA from NMN treated sample 75.1 at T3

description: PBMC DNA from treated mice


title: HSC_bulk_Young_8

description:
Library name: 1519079
HSC_bulk_Young_8


title: ovary, recurrent, patient19

description: Library name: RNA_R_19


title: 080243-107A

description: Library name: 080243-107A

value: Acute Myeloid Leukemia


title: HSC_bulk_Young_7

description:
Library name: 1519078
HSC_bulk_Young_7


title: cell-free DNA from NMN treated sample 73.3 at T3

description: PBMC DNA from treated mice


title: ovary, recurrent, patient18

description: Library name: RNA_R_18


title: E10.5 Wildtype female gonad, ScRNAseq

city: Baltimore

first: Allan

last: Spradling

address: 3520 San Martin Dr

institute: Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution for Science

description:
Library name: E10.5 Wildtype female gonad
Embryonic gonads were dissected from mouse embryos, and fetal sex was determined by Quinacrine and DAPI staining of tail samples to exclude male gonads. A total of 18 female gonads from three pregnant females were pooled and dissociated into single cells using 0.25% Trypsin at 37°C for 5–7 minutes with gentle trituration. Trypsin activity was quenched with 10% fetal bovine serum (FBS), and the cell suspension was passed through a 100 μm cell strainer to remove debris and aggregates. Following centrifugation, cells were resuspended in 0.04% BSA in PBS. Cell viability was assessed using trypan blue exclusion, and only samples with >90% viability were used for downstream processing. Approximately 20,000 cells were loaded onto the Chromium Controller (10x Genomics) for library preparation using the Chromium Single Cell 3’ Gene Expression v4 chemistry, according to the manufacturer's protocol. Libraries were sequenced, and data processing was performed using Cell Ranger version 8.0.1 (10x Genomics).

data_processing:
Raw data was processed using standard protocol: using cell ranger pipeline (v6.0.1 and v8.0.1) and then data was visualized and analyzed by using Seurat v5.1.0
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: E10.5 gonad

extract_protocol:
The embryonic gonad/ovary were dissected from fetuses of pregnant mouse and were dissociated into single cell using 0.25 %trypsin-EDTA
ScRNAseq

value: E10.5 gonad

value: Gondal cells

value: No treatment


title: HSC_bulk_Young_5

description:
Library name: 1519076
HSC_bulk_Young_5


title: cell-free DNA from NMN treated sample 73.2 at T2

description: PBMC DNA from treated mice

value: NMN


title: E15.5 Wildtype ovary, ScRNASeq

description:
Library name: E15.5 Wildtype ovary
Embryonic ovaries were dissected from mouse embryos. A total of 10 female gonads from two pregnant females were pooled and dissociated into single cells using 0.25% Trypsin at 37°C for 5–7 minutes with gentle trituration. Trypsin activity was quenched with 10% fetal bovine serum (FBS), and the cell suspension was passed through a 100 μm cell strainer to remove debris and aggregates. Following centrifugation, cells were resuspended in 0.04% BSA in PBS. Cell viability was assessed using trypan blue exclusion, and only samples with >90% viability were used for downstream processing. Approximately 20,000 cells were loaded onto the Chromium Controller (10x Genomics) for library preparation using the Chromium Single Cell 3’ Gene Expression v3 chemistry, according to the manufacturer's protocol. Libraries were sequenced, and data processing was performed using Cell Ranger version 6.0.1 (10x Genomics).

source_name: E15.5 Ovary

value: E15.5 Ovary

value: Ovarian cells


title: cell-free DNA from NMN treated sample 73.3 at T2

description: PBMC DNA from treated mice


title: HSC_bulk_Young_4

description:
Library name: 1519075
HSC_bulk_Young_4


title: cell-free DNA from NMN treated sample 73.2 at BL

description: PBMC DNA from treated mice


title: ovary, recurrent, patient16

description: Library name: RNA_R_16


title: HSC_bulk_Old_5

description:
Library name: 1519086
HSC_bulk_Old_5

value: Old


title: ME_CnT_H3K27ac_replicate1

description: Library name: Sample21

data_processing:
Fastq files from tagmentation-based duet evoC were processed through a modified version of biomodal’s duet analysis pipeline. 9nt scar sequences, AAGAGATAG and AAAAAACAA were trimmed from the 5`-ends of Reads 1 and 2. Read pairs that lacked either scar sequence were discarded. Adapters containing the full 19nt Tn5 ME sequence and 2 Uracils (ME2U) hairpin were trimmed from the 3`-ends of Reads 1 and 2. A further 9nt were trimmed from the 3`-ends of Read 1 and 2.The trimmed read pairs were then resolved using the bespoke resolution algorithm described in Füllgrabe et al. (2023). The resolved, single-end reads were aligned against a GRCm38 reference (gencode vM25) that contained additional sequences for pUC19, bacteriophage lambda and short spike-in oligonucleotides using bwa-mem2 (v2.2.1).
For Mosaic end CUT&Tag, raw fastq files were trimed with cutadapt version 1.18 to remove adaptors and bases with quality lower than 20 (-q 20) mapped with bwa-mem 0.7.17-r2188 to mm10 genome, and only the reads within the whitelist have been retained.
Bigwig files were created using bamCoverage with counts per milion normalisation (CPM) after extending the paired-end reads.
Assembly: mm10 and GRCm38(gencode vM25)
Supplementary files format and content: CG_quant reports , BigWigs
Library strategy: CUT&Tag

extract_protocol:
Cells were harvested by Accutase dissociation and used in CUT&Tag (Kaya-Okur et al. 2020, PMID: 32913232) assays for different histone mark antibodies (H3K27ac, H3K4me1, H3K4me3, H3K27me3). Genomic DNA was extracted from cells after CUT&Tag using proteinase K digestion and Zymo DNA clean and concentrator clean-up.
Genomic DNA isolated from each CUT&Tag cell sample replicate was subjected to end repair and 6-letter-seq library construction (Fullgrabe and Gosal et al. 2023, PMIID: 36747096).

value: Embryonic stem cells


title: cell-free DNA from NMN treated sample 73.1 at T2

description: PBMC DNA from treated mice


title: ME_CnT_H3K4Me3_replicate2

description: Library name: Sample19


title: ovary, recurrent, patient13

description: Library name: RNA_R_13


title: cell-free DNA from NMN treated sample 70.1 at T3

description: PBMC DNA from treated mice


title: LinBM_bulk_Old_11

description:
Library name: 1528198
LinBM_bulk_Old_11

source_name: bone marrow

value: bone marrow


title: ME_CnT_H3K27ac_replicate3

description: Library name: Sample23


title: ovary, recurrent, patient15

description: Library name: RNA_R_15


title: ovary, recurrent, patient11

description: Library name: RNA_R_11


title: cell-free DNA from NMN treated sample 73.1 at T3

description: PBMC DNA from treated mice


title: HSC_bulk_Young_3

description:
Library name: 1519074
HSC_bulk_Young_3

value: HSC


title: E11.5 Wildtype female gonad, ScRNAseq

description:
Library name: E11.5 Wildtype female gonad
Embryonic gonads were dissected from mouse embryos, and fetal sex was determined by Quinacrine and DAPI staining of tail samples to exclude male gonads. A total of 12 female gonads from three pregnant females were pooled and dissociated into single cells using 0.25% Trypsin at 37°C for 5–7 minutes with gentle trituration. Trypsin activity was quenched with 10% fetal bovine serum (FBS), and the cell suspension was passed through a 100 μm cell strainer to remove debris and aggregates. Following centrifugation, cells were resuspended in 0.04% BSA in PBS. Cell viability was assessed using trypan blue exclusion, and only samples with >90% viability were used for downstream processing. Approximately 10,000 cells were loaded onto the Chromium Controller (10x Genomics) for library preparation using the Chromium Single Cell 3’ Gene Expression v3 chemistry, according to the manufacturer's protocol. Libraries were sequenced, and data processing was performed using Cell Ranger version 6.0.1 (10x Genomics).

source_name: E11.5 gonad

value: E11.5 gonad

value: Gonadal cells


title: E12.5 Dazl homozygous mutant female gonad, ScRNAseq

description:
Library name: E12.5 Dazl homozygous mutant female gonad
Dazl+/- males and females were mated, and E12.5 fetuses were collected at 4 degree celcius. Tail DNA was extracted using the KAPA Express Extract Kit and genotyped using standard JAX protocols (strain 035880). Identified homozygous mutant fetuses were dissected and female gonads were collected. Finally six Dazl mutant female gonads were pooled from teo pregnant females and dissociated into single cells using 0.25% Trypsin at 37°C for 5–7 minutes with gentle trituration. Trypsin was neutralized with 10% FBS, and cells were filtered through a 100 μm strainer. After centrifugation and resuspension in 0.04% BSA, cell viability was assessed with trypan blue, and high-quality samples (>90% viability) were loaded (~10,000 cells) onto the 10X  (Genomics Chromium platform (v3 chemistry) per manufacturer’s instructions. Library sequencung and dataprocessing was performed using Cell Ranger version 6.0.1

source_name: E12.5 Ovary

value: E12.5 Ovary


title: LinBM_bulk_Old_10

description:
Library name: 1528197
LinBM_bulk_Old_10


title: ME_CnT_H3K27ac_replicate2

description: Library name: Sample22


title: cell-free DNA from NMN treated sample 73.2 at T5

description: PBMC DNA from treated mice

source_name: PBMC


title: E11.5 Dazl homozygous mutant female gonad, ScRNAseq

description:
Library name: E11.5 Dazl homozygous mutant female gonad
Dazl+/- males and females were mated, and E11.5 fetuses were collected at 4 degree celcius. Tail DNA was extracted using the KAPA Express Extract Kit and genotyped using standard JAX protocols (strain 035880). Identified homozygous mutant fetuses were dissected, and fetal sex was identified using Quinacrine and DAPI staining of tail samples to exclude males in E10.5/E11.5 gonad samples. Finally six Dazl mutant female gonads were pooled from three different females and dissociated into single cells using 0.25% Trypsin at 37°C for 5–7 minutes with gentle trituration. Trypsin was neutralized with 10% FBS, and cells were filtered through a 100 μm strainer. After centrifugation and resuspension in 0.04% BSA, cell viability was assessed with trypan blue, and high-quality samples (>90% viability) were loaded (~10,000 cells) onto the 10X  (Genomics Chromium platform (v3 chemistry) per manufacturer’s instructions. Library sequencung and dataprocessing was performed using Cell Ranger version 6.0.1

value: gonadal cells


title: ME_CnT_H3K4Me1_replicate2

description: Library name: Sample16


title: HSC_bulk_Young_6

description:
Library name: 1519077
HSC_bulk_Young_6

value: Young


title: ME_CnT_H3K4Me1_replicate1

description: Library name: Sample15


title: ovary, recurrent, patient20

description: Library name: RNA_R_20

value: Ovary

value: recurrent ovarian cancer tissues


title: ovary, recurrent, patient9

description: Library name: RNA_R_09


title: cell-free DNA from NMN treated sample 67.3 at T2

description: PBMC DNA from treated mice

value: PBMC


title: ovary, recurrent, patient17

description: Library name: RNA_R_17


title: LinBM_bulk_Old_8

description:
Library name: 1528195
LinBM_bulk_Old_8


title: ovary, recurrent, patient12

description: Library name: RNA_R_12


title: cell-free DNA from NMN treated sample 67.3 at BL

description: PBMC DNA from treated mice


title: LinBM_bulk_Old_7

description:
Library name: 1528194
LinBM_bulk_Old_7


title: ME_CnT_H3K27Me3_replicate2

description: Library name: Sample13


title: cell-free DNA from NMN treated sample 73.2 at T4

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 67.2 at T5

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 67.3 at T4

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 70.1 at T4

description: PBMC DNA from treated mice


title: ovary, recurrent, patient10

description: Library name: RNA_R_10


title: ovary, recurrent, patient14

description: Library name: RNA_R_14


title: HSC_bulk_Young_1

description:
Library name: 1519072
HSC_bulk_Young_1


title: ovary, recurrent, patient6

description: Library name: RNA_R_06


title: ME_CnT_H3K4Me3_replicate1

description: Library name: Sample18


title: cell-free DNA from NMN treated sample 67.2 at T4

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 67.2 at T3

description: PBMC DNA from treated mice


title: ME_CnT_H3K4Me3_replicate3

description: Library name: Sample20


title: HSC_bulk_Young_2

description:
Library name: 1519073
HSC_bulk_Young_2


title: LinBM_bulk_Old_4

description:
Library name: 1528190
LinBM_bulk_Old_4


title: cell-free DNA from NMN treated sample 67.3 at T3

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 73.2 at T3

description: PBMC DNA from treated mice


title: LinBM_bulk_Old_3

description:
Library name: 1528189
LinBM_bulk_Old_3


title: ovary, recurrent, patient4

description: Library name: RNA_R_04


title: cell-free DNA from NMN treated sample 67.2 at T2

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 67.2 at BL

description: PBMC DNA from treated mice


title: ovary, recurrent, patient8

description: Library name: RNA_R_08


title: ME_CnT_H3K4Me1_replicate3

description: Library name: Sample17


title: ovary, recurrent, patient7

description: Library name: RNA_R_07


title: LinBM_bulk_Old_1

description:
Library name: 1528187
LinBM_bulk_Old_1


title: LinBM_bulk_Old_2

description:
Library name: 1528188
LinBM_bulk_Old_2


title: LinBM_bulk_Old_6

description:
Library name: 1528192
LinBM_bulk_Old_6


title: ME_CnT_H3K27Me3_replicate3

description: Library name: Sample14


title: LinBM_bulk_Young_9

description:
Library name: 1528185
LinBM_bulk_Young_9


title: LinBM_bulk_Young_10

description:
Library name: 1528186
LinBM_bulk_Young_10


title: ME_CnT_H3K27Me3_replicate1

description: Library name: Sample12


title: LinBM_bulk_Old_9

description:
Library name: 1528196
LinBM_bulk_Old_9


title: LinBM_bulk_Young_8

description:
Library name: 1528184
LinBM_bulk_Young_8


title: ovary, primary, patient23

description: Library name: RNA_P_23

value: primary ovarian cancer tissues


title: Alb_Cre_Bmal1fxfx_NELF-E_CT44

description: Library name: Sample220

data_processing:
Illumina bcl2fastq version 2.17 for base calling and demultiplexing.
For ChIPseq, the adaptor and the reads with < 30bp were trimmed by CutAdapt v.1.18. Then, the data were mapped by BWA v0.7.16a-r1185-dirty with default options and the uniquely mapped reads were chosen by SAMtools v1.9. The PCR duplicates were removed by awk commands, and the final reads were extended to the MACS2 prediction sizes.
For mRNAseq, the adaptor, poly T sequences, and < 30bp reads of the raw data were trimmed by CutAdapt v.1.18 and mapped by STAR v2.5.3a. The uniquely mapped reads were chosen by SAMtools v1.9.
For PROseq, the adaptor sequences and < 16bp reads were removed by CutAdapt v.1.18 and the reverse complement (RC) sequences were made from FASTX-Toolkit. The RC was mapped by BWA v0.7.16a-r1185-dirty aln and the uniquely mapped reads were determined by SAMtools v1.9.
The normalized BigWig files are from BEDTools v2.27.1. The raw counts of the NGS data are retrieved from FeatureCounts v1.6.4.
Assembly: M14 from GENCODE
Supplementary files format and content: ChIP-seq BigWig files were made from Uniquely mapped duplicate-removed bed files. PRO-seq and mRNA-seq BigWig files were made from uniquely mapped STAR Bam files
Supplementary files format and content: Excel  file includes raw counts and RPKM values for the mRNA-seq results

source_name: Liver

extract_protocol:
For ChIP-seq, , the fresh whole liver lobes were homogenized in 4 ml PBS containing 1% formaldehyde and kept for 8 min at room temperature (RT). For dual crosslinking, the fresh whole liver lobes were homogenized in 4 ml PBS containing 2mM EGS for 20 min at RT. After quencing and cell lysis, chromatin was sonicated by Covaris S2 with the options of 30 sec on/off, intensity 5, cycles/burst 200, duty 20% at 4°C. For PRO-seq, the largest mouse liver lobe was homogenized and the dissociated cells were filtered by 100mm mesh and centrifuged. The precipitated cells were re-suspended and lysed.  The extracted nucleus was re-suspended with the storage buffer and frozen till the next step. After the nuclear run-on, the RNA was extracted by Trizol LS (ThermoFisher). For mRNA-seq, the frozen liver samples were homogenized with Trizol (ThermoFisher) and RNA was extracted according to the manufacturer's instructions.
For ChIP-seq, the DNA fragments ranging from 125 to 175bp were size selected by AMPure magnetic beads (Beckman). Then, the DNA is adenylated, ligated to NEXTflex DNA barcode adaptors (PerkinElmer) and amplified (Enzymatics). For PRO-seq, the libraries were made with TruSeq small RNA Library primers nad the amplified libraries were size-separated by 8% PAGE gels and the DNA ranging from 140 bp to 200 bp was cut out and eluted by the crush/soak methods. For mRNA-seq, the mRNA was extracted from 10 mg of total RNA (RIN values > 8) pooled from three mice by NEXTflex Poly (A) Beads (PerkinElmer), fragmented by heat, reversely transcribed, ligated and amplified with NEXTflex DNA barcode adaptors (PerkinElmer). For all libraries, the size and quality of the libraries were validated by TapeStation (Agilent) and the amounts were measured by Qubit (ThermoFisher)

value: Liver

value: anti NELF-E (Abcam Cat# ab170104)


title: Alb_Cre_Bmal1fxfx_NELF-E_CT40

description: Library name: Sample219


title: Alb_Cre_Bmal1fxfx_NELF-E_CT36

description: Library name: Sample218


title: Alb_Cre_Bmal1fxfx_NELF-E_CT28

description: Library name: Sample216


title: Alb_Cre_Bmal1fxfx_NELF-E_INPUT

description: Library name: Sample221

value: input mix(00-44)


title: ovary, recurrent, patient2

description: Library name: RNA_R_02


title: cell-free DNA from NMN treated sample 67.1 at T3

description: PBMC DNA from treated mice

value: NMN


title: LinBM_bulk_Old_5

description:
Library name: 1528191
LinBM_bulk_Old_5

value: Old


title: ovary, recurrent, patient3

description: Library name: RNA_R_03


title: ovary, primary, patient24

description: Library name: RNA_P_24


title: ovary, recurrent, patient5

description: Library name: RNA_R_05


title: cell-free DNA from NMN treated sample 67.1 at T4

description: PBMC DNA from treated mice


title: Alb_Cre_Bmal1fxfx_NELF-E_CT32

description: Library name: Sample217


title: cell-free DNA from NMN treated sample 67.1 at T2

description: PBMC DNA from treated mice


title: Alb_Cre_Bmal1fxfx_NELF-E_CT24

description: Library name: Sample215


title: ovary, recurrent, patient1

description: Library name: RNA_R_01


title: Alb_Cre_Bmal1fxfx_NELF-E_CT20

description: Library name: Sample214


title: ovary, primary, patient22

description: Library name: RNA_P_22


title: cell-free DNA from NMN treated sample 65.4 at T2

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 67.1 at BL

description: PBMC DNA from treated mice


title: ovary, primary, patient20

description: Library name: RNA_P_20


title: LinBM_bulk_Young_5

description:
Library name: 1528181
LinBM_bulk_Young_5


title: LinBM_bulk_Young_7

description:
Library name: 1528183
LinBM_bulk_Young_7


title: cell-free DNA from NMN treated sample 65.4 at T4

description: PBMC DNA from treated mice


title: Alb_Cre_Bmal1fxfx_NELF-E_CT16

description: Library name: Sample213


title: ovary, primary, patient21

description: Library name: RNA_P_21


title: ovary, primary, patient19

description: Library name: RNA_P_19


title: LinBM_bulk_Young_6

description:
Library name: 1528182
LinBM_bulk_Young_6


title: Alb_Cre_Bmal1fxfx_NELF-E_CT04

description: Library name: Sample210


title: LinBM_bulk_Young_2

description:
Library name: 1528178
LinBM_bulk_Young_2


title: cell-free DNA from NMN treated sample 65.3 at T3

description: PBMC DNA from treated mice


title: Alb_Cre_Bmal1fxfx_NELF-E_CT00

description: Library name: Sample209


title: cell-free DNA from NMN treated sample 65.3 at BL

description: PBMC DNA from treated mice


title: ovary, primary, patient17

description: Library name: RNA_P_17


title: cell-free DNA from NMN treated sample 65.4 at BL

description: PBMC DNA from treated mice


title: LinBM_bulk_Young_4

description:
Library name: 1528180
LinBM_bulk_Young_4


title: No_Cre_Bmal1fxfx_NELF-E_INPUT

description: Library name: Sample208


title: PBMC_bulk_Old_12

description:
Library name: 1528176
PBMC_bulk_Old_12


title: ovary, primary, patient16

description: Library name: RNA_P_16


title: LinBM_bulk_Young_1

description:
Library name: 1528177
LinBM_bulk_Young_1


title: No_Cre_Bmal1fxfx_NELF-E_CT44

description: Library name: Sample207


title: No_Cre_Bmal1fxfx_NELF-E_CT40

description: Library name: Sample206


title: PBMC_bulk_Old_11

description:
Library name: 1528175
PBMC_bulk_Old_11


title: cell-free DNA from NMN treated sample 65.2 at T3

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 65.2 at T5

description: PBMC DNA from treated mice


title: No_Cre_Bmal1fxfx_NELF-E_CT36

description: Library name: Sample205


title: cell-free DNA from NMN treated sample 65.4 at T3

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 65.2 at BL

description: PBMC DNA from treated mice


title: ovary, primary, patient12

description: Library name: RNA_P_12


title: cell-free DNA from NMN treated sample 65.2 at T2

description: PBMC DNA from treated mice


title: ovary, primary, patient15

description: Library name: RNA_P_15


title: No_Cre_Bmal1fxfx_NELF-E_CT32

description: Library name: Sample204


title: ovary, primary, patient14

description: Library name: RNA_P_14


title: PBMC_bulk_Old_9

description:
Library name: 1528173
PBMC_bulk_Old_9


title: ovary, primary, patient18

description: Library name: RNA_P_18


title: ovary, primary, patient11

description: Library name: RNA_P_11


title: ovary, primary, patient13

description: Library name: RNA_P_13


title: cell-free DNA from NMN treated sample 65.1 at T3

description: PBMC DNA from treated mice


title: No_Cre_Bmal1fxfx_NELF-E_CT28

description: Library name: Sample203


title: LinBM_bulk_Young_3

description:
Library name: 1528179
LinBM_bulk_Young_3


title: No_Cre_Bmal1fxfx_NELF-E_CT24

description: Library name: Sample202


title: PBMC_bulk_Old_10

description:
Library name: 1528174
PBMC_bulk_Old_10


title: cell-free DNA from NMN treated sample 65.1 at T5

description: PBMC DNA from treated mice


title: ovary, primary, patient9

description: Library name: RNA_P_09


title: ovary, primary, patient8

description: Library name: RNA_P_08


title: PBMC_bulk_Old_7

description:
Library name: 1528171
PBMC_bulk_Old_7


title: cell-free DNA from NMN treated sample 65.1 at BL

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 65.1 at T2

description: PBMC DNA from treated mice


title: ovary, primary, patient10

description: Library name: RNA_P_10


title: PBMC_bulk_Old_6

description:
Library name: 1528170
PBMC_bulk_Old_6


title: No_Cre_Bmal1fxfx_NELF-E_CT12

description: Library name: Sample199


title: PBMC_bulk_Old_5

description:
Library name: 1528169
PBMC_bulk_Old_5


title: ovary, primary, patient7

description: Library name: RNA_P_07


title: No_Cre_Bmal1fxfx_NELF-E_CT08

description: Library name: Sample198


title: No_Cre_Bmal1fxfx_NELF-E_CT20

description: Library name: Sample201


title: cell-free DNA from NMN treated sample 63.4 at T4

description: PBMC DNA from treated mice


title: PBMC_bulk_Old_8

description:
Library name: 1528172
PBMC_bulk_Old_8


title: No_Cre_Bmal1fxfx_NELF-E_CT16

description: Library name: Sample200


title: PBMC_bulk_Old_4

description:
Library name: 1528168
PBMC_bulk_Old_4


title: cell-free DNA from NMN treated sample 63.4 at T3

description: PBMC DNA from treated mice


title: ovary, primary, patient6

description: Library name: RNA_P_06


title: cell-free DNA from NMN treated sample 63.4 at BL

description: PBMC DNA from treated mice


title: PBMC_bulk_Old_3

description:
Library name: 1528167
PBMC_bulk_Old_3


title: cell-free DNA from NMN treated sample 63.4 at T2

description: PBMC DNA from treated mice


title: Cry12DKO_NELF-E_INPUT

description: Library name: Sample195


title: ovary, primary, patient5

description: Library name: RNA_P_05


title: No_Cre_Bmal1fxfx_NELF-E_CT04

description: Library name: Sample197


title: Cry12DKO_NELF-E_CT44

description: Library name: Sample194


title: ovary, primary, patient4

description: Library name: RNA_P_04


title: PBMC_bulk_Young_10

description:
Library name: 1528164
PBMC_bulk_Young_10


title: PBMC_bulk_Young_9

description:
Library name: 1528163
PBMC_bulk_Young_9


title: cell-free DNA from NMN treated sample 63.3 at BL

description: PBMC DNA from treated mice


title: Cry12DKO_NELF-E_CT40

description: Library name: Sample193


title: PBMC_bulk_Old_1

description:
Library name: 1528165
PBMC_bulk_Old_1


title: cell-free DNA from NMN treated sample 63.2 at T3

description: PBMC DNA from treated mice


title: Cry12DKO_NELF-E_CT36

description: Library name: Sample192


title: No_Cre_Bmal1fxfx_NELF-E_CT00

description: Library name: Sample196


title: ovary, primary, patient1

description: Library name: RNA_P_01


title: ovary, primary, patient3

description: Library name: RNA_P_03


title: PBMC_bulk_Young_8

description:
Library name: 1528162
PBMC_bulk_Young_8


title: LF1 Quiescence 4 Low Ox

description: Library name: TRNAQ4

data_processing:
counts tables were generated using HTSeq
Assembly: hg38
Supplementary files format and content: .txt files, counts tables

source_name: Cell Culture

growth_protocol: Cells were maintained in Ham’s F-10 nutrient mixture media (Gibco) supplemented with 15% fetal bovine serum (FBS) and antibiotics for LF1 cells and in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics for all other cell lines, in humidified atmosphere with 5% CO2 at 37C. High Ox cells were maintained at ~20% O2, Low Ox cells were maintained at ~3% O2

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries. For LF1 samples, Total RNA was extracted from early passage, SW-induced quiescent, early and late senescent cells. Cells were washed with PBS and harvested using Trizol reagent (Invitrogen), after which Total RNA was harvested using the Qiagen Rneasy kit.
Libraries were constructed by Azenta. For LF1 samples, NEBNext ultra II directional RNA library prep kit for Illumina along with the NEBNext Poly(A) mRNA magnetic bead isolation module was used to make isolated mRNA and cDNA libraries. Strand specific cDNA libraries were sent to Azenta for paired-end sequencing

treatment_protocol: Contact inhibition was induced by allowing cells to reach 100%confluency for 3 days. Serum withdrawal was induced with DMEM media supplimented with 0.01% FBS for 3 days and for LF1 cells, with Ham’s F-10 nutrient mixture media (Gibco) supplemented with 0.01% fetal bovine serum (FBS; Corning), and antibiotics for 5 days for LF1 cells. Replicatively senescent LF1 cells were attained by serial passaging until cell division ceased.  1 month after cells entered senescence, LF1 cells were harvested for the early replicative senescent cell state timepoint, and late replicative senescent cells were harvested 4 months after entry into senescence.

value: Cell Culture

value: Fibroblasts

value: Serum Withdrawal


title: Alb_Cre_Bmal1fxfx_NELF-E_CT08

description: Library name: Sample211


title: cell-free DNA from NMN treated sample 63.2 at T4

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 63.2 at T2

description: PBMC DNA from treated mice


title: cell-free DNA from NMN treated sample 63.2 at BL

description: PBMC DNA from treated mice


title: Cry12DKO_NELF-E_CT28

description: Library name: Sample190


title: LF1 Quiescence 2 Low Ox

description: Library name: TRNAQ2


title: ovary, primary, patient2

description: Library name: RNA_P_02


title: Cry12DKO_NELF-E_CT32

description: Library name: Sample191


title: LF1 Quiescence 3 Low Ox

description: Library name: TRNAQ3


title: PBMC_bulk_Young_5

description:
Library name: 1528159
PBMC_bulk_Young_5


title: PBMC_bulk_Young_6

description:
Library name: 1528160
PBMC_bulk_Young_6


title: cell-free DNA from NMN treated sample 63.1 at T5

description: PBMC DNA from treated mice


title: PBMC_bulk_Young_7

description:
Library name: 1528161
PBMC_bulk_Young_7


title: cell-free DNA from NMN treated sample 63.1 at T3

description: PBMC DNA from treated mice