title: liver, old, SIRT6 tg, rep6

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: Library name: O31_TG_livDNA

data_processing:
Basecalling of PromethION sequencing output (POD5 files) was performed using Dorado v0.5.3, followed by conversion of unaligned BAM files to FASTQ, alignment to the GRCm38 mouse genome, and generation of aligned BAM files.
DNA methylation frequencies at CpG sites were estimated using Modkit, producing a bedMethyl-formatted table with counts of cytosines and 5-methylcytosines.
A bedMethyl-formatted table of each sample was converted to MethylKit-formatted table
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes methylation counts for each sample

source_name: liver

extract_protocol:
High molecular weight genomic DNA was extracted from liver tissue using the Monarch® HMW DNA Extraction Kit, involving tissue homogenization, proteinase K digestion, RNase A treatment, phase separation, NaCl precipitation, and isopropanol-based DNA retrieval using glass beads. The purified DNA was eluted, and concentration was measured via Nanodrop.
DNA was sheared using a Covaris g-TUBE, size-checked on TapeStation and Qubit, and processed using the Ligation Sequencing Kit V14 with adapter ligation and cleanup. Sequencing was carried out on the PromethION 24 platform using R10.4.1 flow cells, with each sample run for 72–112 hours, producing high-coverage long-read data

value: liver

value: SIRT6 tg


title: WT MRTX-1133 res 1

status: Public on Apr 13 2026

type: RNA

city: Columbus

first: Gian Luca

last: Rampioni Vinciguerra

state: OH

address: 460W 12th Avenue

department: Cancer Biology and Genetics

country: USA

institute: The Ohio State University

hyb_protocol: Following fragmentation, 2.3 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Transcriptome analysis was conducted on two different samples per condition and was performed with Clariom™ S Assay, Human (ThermoFisher Scientific, USA). The analysis for Clariom™ S Human Affymetrix panel of >21K genes was carried out by Transcriptome Analysis Console software (TAC v4 - Thermo Fisher Scientific) and it consists of three main steps: 1) data quality control; 2) normalization (signal space transformation robust multiple-array average); 3) differentially expression analysis employing the eBayes method from limma R package included in TAC software.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: WT MRTX-1133 resistant

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA (GeneChip WT PLUS Reagent Kit, 2013, Affymetrix).

growth_protocol: AsPC-1 cells were cultured in RPMI completed medium at 37 degrees and 5% CO2

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: WT MRTX-1133 resistant AsPC-1 cells were obtained with continuous administration of escalating doses of MRTX-1133 from 1nM to 50nM for 30 days. FRA2KO AsPC-1 cells were treated with MRTX-1133 50nM for 48hours.

tag: cell line

tag: genotype

value: WT

tag: treatment

value: MRTX-1133 res


title: WT unt 2

source_name: WT untreated

value: untreated


title: KO Day 4RB

type: SRA

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: abu dhabi

address: NYUAD Saadiyat Island

country: United Arab Emirates

institute: Biology

description:
Library name: SAMPLE 29
KO EBS Day R4B

library_source: transcriptomic

data_processing:
NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization was used to do Differential Expression transcriptional analysis. Through NASQAR, DEseq2 was used to perform pairwise differential expression comparisons between WT and KO mESCs and generate a Volcano plot, Distance heatmap and a PCA plot. GO analysis was also done on NASQAR to generate GO plots for Cellular Components and Molecular Functions. Heatmaps were generated in R (v4.3.0) using the pheatmap package to visualize the expression patterns of selected gene sets across wild-type (WT), β-actin knockout (KO), and nuclear-localized β-actin (NLS) mESCs at Day 0. Raw gene expression matrices from bulk RNA-seq were first imported using the readr package. Gene sets related to specific biological functions (e.g., stemness, lineage commitment, extracellular matrix) were defined manually, and the corresponding expression values were extracted from the full dataset using the dplyr package. Replicates for each condition (WT_1–3, KO_1–3, NLS_1–3) were retained as individual columns or averaged using rowMeans() to create representative condition-specific profiles when required. Expression values were transformed into a numeric matrix. The matrix was then scaled row-wise (z-score) to allow for comparison of relative expression across samples. Heatmaps were plotted using pheatmap with hierarchical clustering applied to genes (rows), while preserving the experimental condition order for samples (columns). A custom diverging color palette (navy–white–firebrick3) was used to depict low to high expression.
Assembly: mm10
Supplementary files format and content: raw counts

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: P60 culture dishes were coated with 3 mL of 0.1% gelatin solution and incubated at 37 °C for 15 min. Mouse embryonic stem cell (mESC) medium was pre-warmed to 37 °C. The gelatin solution was then replaced with 5 mL of mESC medium. A total of 5.0 × 10⁵ cells were seeded for each condition: wild type (WT), β-actin knockout (KO), and nuclear-localized β-actin (NLS). Cultures were maintained at 37 °C and 5% CO₂ for 2 days after seeding. Once cultures reached 70–90% confluency, cells were processed for RNA extraction.

extract_protocol:
RNA was extracted using RNAzol RT (Molecular Research Center, Catalog #R4533), a reagent designed for the isolation of total and small RNA from human, animal, plant, bacterial, and viral samples. Cells were washed with calcium- and magnesium-free DPBS and dissociated with TrypLE for 1 min. TrypLE was aspirated, then 1 mL of mESC medium was added, and cells were gently pipetted to detach them from the culture dish. The cell suspension was transferred to a 15-mL conical tube and pelleted by centrifugation at 500 × g for 3 min. The supernatant was removed, and 500 µL of RNAzol RT was added directly to the pellet. The pellet was fully resuspended by pipetting to ensure complete lysis and homogenization, and the lysate was transferred to a 1.5- mL microcentrifuge tube. A total of 0.2 mL of RNase-free water was added to each tube. Samples were capped, shaken vigorously for 15 s, and incubated for 15 min at room temperature. The mixture was centrifuged at 12,000 × g for 15 min at 4 °C, producing a pellet containing DNA, proteins, and polysaccharides, while RNA remained in the upper phase. The supernatant was carefully transferred to a new tube without disturbing the pellet. An equal volume of 100% isopropanol was added to the supernatant to precipitate RNA. Samples were incubated for 10 min at room temperature and then centrifuged at 12,000 × g for 10 min, forming a white RNA pellet. RNA pellets were washed twice with 75% ethanol (0.4–0.6 mL per mL of initial supernatant). Each wash was followed by centrifugation at 8,000 × g for 3 min at room temperature, after which the ethanol was removed by pipetting. The final RNA pellet was resuspended in 20 µL of RNase-free water without air-drying. Samples were vortexed at room temperature for 2 min to ensure complete solubilization.
45 NEB Ultra II RNA, PolyA selected

tag: tissue

value: Embryonic stem cells

tag: cell type

value: mESC


title: WT  Day 4RB

description:
Library name: SAMPLE 28
WT EBS Day R4B


title: AML 040 Relapse RNA seq

city: Charlottesville

first: Subhash

last: Prajapati

address: 1340 Jefferson Park Avenue

department: Biochemistry and Molecular Genetics

institute: University of Virginia

description: Library name: AML040_Rel

data_processing:
Reads were aligned to the hg19 human genome using STAR aligner (version 2.3.0e). Aligned results were annotated using RefSeq gene model and HTSeq union mode.
Read counts were normalized to Transcripts per million reads (TPM) with normal bone marrow controls included in expression analysis for normal variance estimation as described in PMID 41608320.
Assembly: GRCh37/hg19
Supplementary files format and content: Tab delimited file contains non-normalized raw read counts aligned to hg19

molecule: polyA RNA

source_name: Bone Marrow

extract_protocol:
High quality RNA was isolated using phenol-chloroform/Trizol with subsequent purification using Qiagen Rneasy kit.
TruSeq RNA-Seq by ploy(A) enrichment

value: Bone Marrow

tag: batch


title: liver, old, SIRT6 tg, rep7

description: Library name: O32_TG_livDNA

library_source: genomic

molecule: genomic DNA

tag: age


title: YZ408

city: Chongqing

first: Xinyu

last: Zhou

address: 1 Youyi Road, Yuzhong District

department: Department of Psychiatry

country: China

institute: The First Affiliated Hospital of Chongqing Medical University

data_processing:
Raw reads were first cleaned by removing reads containing the adapter by using Trimmomatic. FastQC (version0.10.1) was used to assess the quality of raw reads. Clean reads were then aligned to the human reference genome GRCh38 using HISAT2. FeatureCounts was used to count reads mapped to individual genes.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include rlogTransformed values for each Sample.

source_name: peripheral blood

extract_protocol:
For each enrolled participant, 2mL fasting venous blood samples were collected in PAXgene Blood RNA Tubes. Total RNA was extracted using the PAXgene Blood RNA Kit (QIAGEN) and isolated from peripheral blood using TRIzol® Reagent according to the manufacturer's protocol.
RNA purification, reverse transcription, library construction, and sequencing were done at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) (Illumina, San Diego, CA). A library of RNA-seq transcripts was made with 1μg of total RNA and the Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA). Messenger RNA was isolated using the polyA selection method with oligo (dT) beads and subsequently fragmented using a fragmentation buffer. The resulting double-stranded cDNA was synthesized using the SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). The synthesized cDNA was then subjected to end-repair, phosphorylation, and 'A' base addition as per Illumina's library construction protocol. The libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose, and then PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After measuring with Qubit 4.0, the Nova Seq 6000 sequencer was used to read the paired-end RNA-seq library (2 × 150bp read length).

value: peripheral blood

tag: disease state

value: Major depressive disorder (MDD)

value: Drug therapy


title: YZ406


title: liver, old, SIRT6 tg, rep4

description: Library name: O16_TG_livDNA


title: AML 040 Diagnosis RNA seq

description: Library name: AML040_Dx


title: KO  Day 4RA

description:
Library name: SAMPLE 26
KO EBS Day R4A


title: NLS  Day 4RA

description:
Library name: SAMPLE 27
NLS EBS Day R4A


title: liver, old, SIRT6 tg, rep5

description: Library name: O26_TG_livDNA


title: liver, old, SIRT6 tg, rep3

description: Library name: O12_TG_livDNA


title: AML 038 Relapse RNA seq

description: Library name: AML038_Rel


title: WT  Day 4RA

description:
Library name: SAMPLE 25
WT EBS Day R4A


title: liver, old, SIRT6 tg, rep2

description: Library name: O10_TG_livDNA


title: YZ376


title: NLS D0  R4A

description:
Library name: SAMPLE 24
NLS Cells R4A


title: YZ391


title: liver, young, SIRT6 tg, rep8

description: Library name: Y17_TG_livDNA

value: young (3-4 mo)


title: AML 032 Relapse RNA seq

description: Library name: AML032_Rel


title: YZ403

value: Without Drug therapy


title: liver, old, SIRT6 tg, rep1

description: Library name: O6_TG_livDNA


title: AML 032 Diagnosis RNA seq

description: Library name: AML032_Dx


title: YZ369


title: AML 028 Relapse RNA seq

description: Library name: AML028_Rel


title: YZ362


title: AML  028 Diagnosis RNA seq

description: Library name: AML028_Dx

source_name: PBMCs

value: PBMCs


title: YZ359


title: WT D0  R4A

description:
Library name: SAMPLE 22
WT  Day zero R4A


title: YZ353


title: NLS D0  R3A

description:
Library name: SAMPLE 21
NLS  Day zero R3A


title: liver, young, SIRT6 tg, rep7

description: Library name: Y15_TG_livDNA


title: liver, young, SIRT6 tg, rep6

description: Library name: Y13_TG_livDNA


title: KO D0  R3A

description:
Library name: SAMPLE 20
KO  Day zero R3A


title: KO D0  R4A

description:
Library name: SAMPLE 23
KO  Day zero R4A


title: liver, young, SIRT6 tg, rep5

description: Library name: Y11_TG_livDNA


title: YZ312


title: WT D0  R3A

description:
Library name: SAMPLE 19
WT  Day zero R3A


title: liver, young, SIRT6 tg, rep4

description: Library name: Y9_TG_livDNA


title: AML 026 Diagnosis RNA seq

description: Library name: AML026_Dx


title: AML 025 Relapse RNA seq

description: Library name: AML025_Rel


title: YZ268


title: AML 026 Relapse RNA seq

description: Library name: AML026_Rel


title: NLS D0  R2A

description:
Library name: SAMPLE 18
NLS  Day zero R2A


title: YZ188


title: liver, young, SIRT6 tg, rep2

description: Library name: Y5_TG_livDNA


title: KO D0  R2A

description:
Library name: SAMPLE 17
KO  Day zero R2A


title: liver, old, WT, rep8

description: Library name: O15_WT_livDNA


title: YZ166


title: YZ178


title: AML 024 Diagnosis RNA seq

description: Library name: AML024_Dx


title: AML 024 Relapse RNA seq

description: Library name: AML024_Rel


title: liver, young, SIRT6 tg, rep3

description: Library name: Y7_TG_livDNA


title: YZ164


title: AML 025 Diagnosis RNA seq

description: Library name: AML025_Dx


title: liver, old, WT, rep7

description: Library name: O14_WT_livDNA


title: KO D0  R1A

description:
Library name: SAMPLE 14
KO  Day zero R1A


title: liver, old, WT, rep6

description: Library name: O13_WT_livDNA


title: WT D0 R1A

description:
Library name: SAMPLE 13
WT Day zero R1A


title: NLS D0  R1A

description:
Library name: SAMPLE 15
NLS  Day zero R1A


title: AML 023 Diagnosis RNA seq

description: Library name: AML023_Dx


title: liver, old, WT, rep4

description: Library name: O9_WT_livDNA


title: liver, old, WT, rep5

description: Library name: O11_WT_livDNA


title: NLSD14-R4

description:
Library name: SAMPLE 12
Nuclear Localization signal Day 14-R4


title: AML 017 Relapse RNA seq

description: Library name: AML017_Rel


title: liver, old, WT, rep3

description: Library name: O7_WT_livDNA


title: YZ1083


title: AML 023 Relapse RNA seq

description: Library name: AML023_Rel


title: WT D0  R2A

description:
Library name: SAMPLE 16
WT  Day zero R2A


title: NLSD14-R3

description:
Library name: SAMPLE 11
Nuclear Localization signal Day 14-R3


title: YZ161


title: AML 017 Diagnosis RNA seq

description: Library name: AML017_Dx


title: liver, old, WT, rep2

description: Library name: O3_WT_livDNA


title: AML 015 Relapse RNA seq

description: Library name: AML015_Rel


title: YZ1045


title: YZ1092


title: NLSD14-R1

description:
Library name: SAMPLE 9
Nuclear Localization signal Day 14-R1


title: AML 015 Diagnosis RNA seq

description: Library name: AML015_Dx


title: AML 014 Relapse RNA seq

description: Library name: AML014_Rel


title: NLSD14-R2

description:
Library name: SAMPLE 10
Nuclear Localization signal Day 14-R2


title: liver, old, WT, rep1

description: Library name: O1_WT_livDNA


title: YZ1005


title: KOD14-R4

description:
Library name: SAMPLE 8
Knock Out Day14-R4


title: liver, young, WT, rep7

description: Library name: Y18_WT_livDNA


title: liver, young, WT, rep6

description: Library name: Y16_WT_livDNA


title: YZ1077


title: YZ1002


title: KOD14-R3

description:
Library name: SAMPLE 7
Knock Out Day14-R3


title: AML 014 Diagnosis RNA seq

description: Library name: AML014_Dx


title: AML 012 Relapse RNA seq

description: Library name: AML012_Rel


title: liver, young, WT, rep5

description: Library name: Y10_WT_livDNA


title: KOD14-R2

description:
Library name: SAMPLE 6
Knock Out Day14-R2


title: AML 012 Diagnosis RNA seq

description: Library name: AML012_Dx


title: C4-2 cells, CBX3_WT_1

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

description:
transfection infection
CBX3_EV_T60A_WT_gene_fpkm_expression.txt
CBX3_WT_1

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Library qualty assessement
illumina sequencing
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: treated group of overexpression of CBX3 by plasmids WT

growth_protocol: C4-2 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: prostate

value: prostate cancer cells

value: CBX3 overexpression (WT)


title: C4-2 cells, CBX3_WT_2

description:
transfection infection
CBX3_EV_T60A_WT_gene_fpkm_expression.txt
CBX3_WT_2


title: AML 038 Diagnosis RNA seq

description: Library name: AML038_Dx


title: KOD14-R1

description:
Library name: SAMPLE 5
Knock Out Day14-R1


title: AML 010 Relapse RNA seq

description: Library name: AML010_Rel


title: liver, young, WT, rep4

description: Library name: Y8_WT_livDNA

value: liver


title: WTD14-R4

description:
Library name: SAMPLE 4
Wild type Day14-R4


title: liver, young, WT, rep3

description: Library name: Y6_WT_livDNA


title: AML 010 Diagnosis RNA seq

description: Library name: AML010_Dx


title: liver, young, WT, rep1

description: Library name: Y2_WT_livDNA


title: C4-2 cells, CBX3_T60A_2

description:
transfection infection
CBX3_EV_T60A_WT_gene_fpkm_expression.txt
CBX3_T60A_2

source_name: treated group of overexpression of CBX3 by plasmids T60A

value: CBX3 overexpression (T60A)


title: C4-2 cells, CBX3_EV_2

description:
transfection infection
CBX3_EV_T60A_WT_gene_fpkm_expression.txt
CBX3_EV_2

source_name: control group of overexpression of CBX3 by plasmids

value: control for CBX3 overexpression


title: C4-2 cells, CBX3_EV_1

description:
transfection infection
CBX3_EV_T60A_WT_gene_fpkm_expression.txt
CBX3_EV_1


title: WTD14-R2

description:
Library name: SAMPLE 2
Wild type Day14-R2


title: WTD14-R3

description:
Library name: SAMPLE 3
Wild type Day14-R3


title: D7 CTRL Tendon

city: Dallas

first: Sneha

last: Korlakunta

state: TX

address: 6000 Harry Hines Blvd

department: Surgery

institute: UT Southwestern Medical Center

description:
Library name: Sample 5
10X Genomics

library_source: transcriptomic single cell

data_processing:
CellRanger pipeline (v8.0.1) was used for demultiplexing and counting as recommended by 10X Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq)
Assembly: GRCm39-2024-A
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Achilles tendon tissue

extract_protocol:
Cells from the excised tissue were isolated based on previously described methods. Briefly, tissue was digested using Collagenase I at 3 mg/mL (Thermo Fisher Scientific, 17100-017), Collagenase II at 2 mg/mL (Thermo Fisher Scientific, 17101-015), and Dispase at 3mg/mL (MilliporeSigma, D4693) per 1mL of DMEM (Thermo Fisher Scientific, 11960044) for 45 minutes at 37°C under constant agitation at 150 rpm. Digestions were then quenched with DMEM containing 10% FBS (Gibco, 10437028), filtered through 40um mesh and pelleted via centrifugation for 5min at 400xG at 4⁰C.Supernatant was removed and red blood cells were lysed by resuspending the pellets with 2ml of ACK Lysis Buffer (Gibco A10492-01) and incubating for 2 minutes at room temp. Cell viability was assessed with Trypan blue exclusion on a Countess III (Thermo Fisher Scientific) automated counter and only samples with >75% viability were processed for further sequencing.
Single Cell 3' v3

value: Achilles tendon tissue

value: 8-12 weeks

value: Burn/tenotomy


title: C4-2 cells, BI-2536_3

description:
drug inhibition
Vehicle_BI_gene_fpkm_expression.txt
BI-2536_3

source_name: treated group of inhibition of CBX3 by BRD4/PLK1 dual inhibitor (BI-2536)

tag: inhibition

value: CBX3 inhibition


title: D7 HFD Tendon

description:
Library name: Sample 6
10X Genomics

value: High-fat diet, burn/tenotomy


title: AML 006 Diagnosis RNA seq

description: Library name: AML006_Dx

value: Bone Marrow


title: C4-2 cells, CBX3_T60A_1

description:
transfection infection
CBX3_EV_T60A_WT_gene_fpkm_expression.txt
CBX3_T60A_1


title: WTD14-R1

description:
Library name: SAMPLE 1
Wild type Day14-R1

value: Embryonic stem cells

value: mESC


title: AML 003 Relapse RNA seq

description: Library name: AML003_Rel


title: D3 HFD Tendon

description:
Library name: Sample 4
10X Genomics


title: AML 003 Diagnosis RNA seq

description: Library name: AML003_Dx


title: snRNA-Seq, Liver, 2months, sample7

city: Wuhan

first: Jie

last: Cheng

state: Hubei

address: 13 Hangkong Road, Qiaokou District

department: School of Basic Medicine

institute: Huazhong University of Science and Technology

description:
Library name: Yn3
Male, 10x Genomics

data_processing:
The original FASTQ files were aligned to the mm10 reference genome using the cellranger count function in cellranger 7.0.1 (10x Genomics Cell Ranger v7.0.1).
Assembly: mm10 reference genome
Supplementary files format and content: three output files generated by cellranger

source_name: Liver

extract_protocol:
The mouse liver was placed in 1 mL lysis buffer (LB) and homogenized using a tissue homogenizer. The homogenate was then lysed on ice for 1-10 min. A 40 μm cell strainer was used to filter out debris, and the filtrate was centrifuged at 4 °C and 500 g for 5 min. After removing the supernatant, 300 μL of LB solution was added to the sediment, and the nucleus was resuspended by pipetting. The suspension was transferred to a new centrifuge tube, and 300 μL of resuspension buffer (RB) was added, followed by thorough mixing. Next, 600 μL of PB1 solution was slowly added to the bottom of the tube to form a layer. Similarly, 600 μL of PB2 solution was slowly added to the bottom of the tube to form another layer. The mixture was then centrifuged at 4 °C and 4,000 g for 20 min, with the nucleus located at the interface between PB1 and PB2. A volume of 150-300 μL of the nucleus layer was transferred to 1 mL of RB solution, mixed thoroughly, and filtered through a 40 μm cell strainer. The filtrate was centrifuged at 4 °C and 500 g for 5 min. After removing the supernatant, the nucleus sediment was resuspended in 100 μL of EB solution.
Cellular lysis and subsequent RNA barcoding were achieved through GEM-based reverse transcription. cDNA synthesis was conducted in a S1000TM Touch Thermal Cycler (Bio-Rad) using the following thermal profile: 45 min at 53 °C, 5 min at 85 °C, followed by 4 °C hold. Amplified cDNA products underwent quality control verification using the Agilent 4200 (service provided by CapitalBio Technology, Beijing). The constructed libraries were subsequently sequenced on an Illumina NovaSeq 6000 platform, employing a paired-end 150 bp (PE150) strategy, with a sequencing depth of at least 100,000 reads per cell. This sequencing process was carried out by CapitalBio Technology in Beijing.

value: Liver

value: All liver cell

value: WT


title: AML 006 Relapse RNA seq

description: Library name: AML006_Rel


title: D0 HFD Tendon

description:
Library name: Sample 2
10X Genomics


title: D3 CTRL Tendon

description:
Library name: Sample 3
10X Genomics


title: C4-2 cells, BI-2536_2

description:
drug inhibition
Vehicle_BI_gene_fpkm_expression.txt
BI-2536_2

value: prostate


title: snRNA-Seq, Liver, 2months, sample6

description:
Library name: Yn2
Male, 10x Genomics


title: AML 002 Relapse RNA seq

description: Library name: AML002_Rel


title: C4-2 cells, BI-2536_1

description:
drug inhibition
Vehicle_BI_gene_fpkm_expression.txt
BI-2536_1

value: prostate cancer cells


title: AML 002 Diagnosis RNA seq

description: Library name: AML002_Dx


title: snRNA-Seq, Liver, 2months, sample5

description:
Library name: Yn1
Male, 10x Genomics


title: snRNA-Seq, Liver, 18months, sample4

description:
Library name: On4
Male, 10x Genomics


title: D0 CTRL Tendon

description:
Library name: Sample 1
10X Genomics


title: C4-2 cells, Vehicle_3

description:
drug inhibition
Vehicle_BI_gene_fpkm_expression.txt
Vehicle_3

source_name: control group of inhibition of CBX3 by BRD4/PLK1 dual inhibitor (BI-2536)

value: control for CBX3 inhibition

value: Vehicle


title: Atf7ip KO

city: San Francisco

first: Jun Hyung

last: Sin

state: CA

address: 513 Parnassus Ave S-1076

department: Pediatrics

institute: University of California, San Francisco

description: Library name: KO_TIL

data_processing:
FASTQ files were converted into single-cell matrices using 10x Cell Ranger. Matrices were then log transformed into a Seurat object using the Seurat package in R. Initial exclusion criteria included features that were present in fewer than 200 cells and cells where fewer than 1000 features were detected. Samples were merged and integrated using 2000 variable features and dimensions 1:20. Cells with greater than 50% ribosomal RNA, greater than 10% mitochondrial RNA, and greater than 4000 features were excluded. Principal components analysis was performed using 30 principal components, and UMAPs were generated using dimensions 1:20. Cluster identities were assigned cell types and differential gene expression analysis was performed in Seurat.
Assembly: mm10
Supplementary files format and content: Barcodes, features, matrix files

source_name: Tumor

extract_protocol:
For scRNA-seq, TCRb+CD3+ T cells from three to four mice of each genotype were pooled and FACS sorted into 1.5 ml Eppendorf tubes containing 500 ul of DMEM with 2% FBS. Approximately 20,000 cells per 100 ul were sent to the UCSF Genomics Core for processing. Single cells were captured using the 10X Chromium microfluidics system (10x Genomics).
The cells were then barcoded complementary DNA libraries and sequenced on the NovaSeq (Illumina).

value: Tumor

value: KO


title: AML 001 Relapse RNA seq

description: Library name: AML001_Rel


title: C4-2 cells, Vehicle_1

description:
drug inhibition
Vehicle_BI_gene_fpkm_expression.txt
Vehicle_1


title: Atf7ip Het

description: Library name: Het_TIL

value: Wildtype


title: AML 001 Diagnosis RNA seq

description: Library name: AML001_Dx


title: snRNA-Seq, Liver, 18months, sample3

description:
Library name: On3
Male, 10x Genomics


title: C4-2 cells, Vehicle_2

description:
drug inhibition
Vehicle_BI_gene_fpkm_expression.txt
Vehicle_2


title: snRNA-Seq, Liver, 18months, sample2

description:
Library name: On2
Male, 10x Genomics


title: C4-2 cells, siCBX3_3

description:
transfection infection
siNC_siCBX3_gene_fpkm_expression.txt
siCBX3_3

source_name: treated group of knockdown of CBX3 by siRNA

value: CBX3 knockdown


title: Normal Bone Marrow Control 09 RNA seq

description: Library name: NBM_09


title: C4-2 cells, siCBX3_2

description:
transfection infection
siNC_siCBX3_gene_fpkm_expression.txt
siCBX3_2


title: snRNA-Seq, Liver, 18months, sample1

description:
Library name: On1
Male, 10x Genomics


title: Liver, 2months, sample7

description:
Library name: Y3
Male, 10x Genomics

data_processing:
The original FASTQ files were aligned to the mm10 reference genome using the cellranger count function in cellranger 7.0.1 (10x Genomics Cell Ranger v7.0.1). For samples O2 and Y2, the parameter --force-cells was explicitly set to 11,600 and 26,200, respectively, while default values were applied for other samples.
Assembly: mm10 reference genome
Supplementary files format and content: three output files generated by cellranger

extract_protocol:
scRNA-seq libraries were prepared using the 10x Genomics Chromium platform with the Single Cell 3' Library & Gel Bead Kit v3.1 (1000121) and Single Cell G Chip Kit (1000120). Cell suspensions containing 300-600 viable cells/μL (quantified by Count Star viability analysis) were processed using the Chromium Controller to create gel bead-in-emulsion (GEM) partitions following the recommended workflow. Briefly, single cells were resuspended in phosphate-buffered saline (PBS) supplemented with 0.04% bovine serum albumin (BSA), with approximately 12,000 cells loaded per microfluidic channel, yielding an anticipated recovery rate of ~10,000 cells per sample.
Cellular lysis and subsequent RNA barcoding were achieved through GEM-based reverse transcription. cDNA synthesis was conducted in a S1000TM Touch Thermal Cycler (Bio-Rad) using the following thermal profile: 45 min at 53 °C, 5 min at 85 °C, followed by 4 °C hold. Amplified cDNA products underwent quality control verification using the Agilent 4200 (service provided by CapitalBio Technology, Beijing). The constructed libraries were subsequently sequenced on an Illumina NovaSeq 6000 platform, employing a paired-end 150 bp (PE150) strategy, with a sequencing depth of at least 100,000 reads per cell. This sequencing process was carried out by CapitalBio Technology in Beijing.

value: Immune cell


title: biol rep2 T_3H_WT

city: HKSAR

first: Jialin

last: Peng

address: Kowloon Tong Kowloon, Hong Kong

institute: Hong Kong Baptist University

description:
Library name: Sample 17
Treat

data_processing:
Following adapter removal, RNA-seq reads were subjected to genomic alignment with STAR (v2.5.3a) against the Arabidopsis reference genome (Ensembl release 41; Aken et al., 2016). Alignment parameters followed the original publication (Dobin et al., 2013), utilizing default configurations. Gene expression levels were quantified from STAR-aligned reads from BAM files using RSEM v1.2.30 (Li and Dewey, 2011) with default settings.
Assembly: Following adapter removal, RNA-seq reads were subjected to genomic alignment with STAR (v2.5.3a) against the Arabidopsis reference genome (Ensembl release 41; Aken et al., 2016). Alignment parameters followed the original publication (Dobin et al., 2013), utilizing default configurations. Gene expression levels were quantified from STAR-aligned reads from BAM files using RSEM v1.2.30 (Li and Dewey, 2011) with default settings.
Supplementary files format and content: csv files include expression value for each sample

organism: Arabidopsis thaliana

source_name: Leaves

growth_protocol: Four-week-old short-day grown well plants

extract_protocol:
Arabidopsis tissue samples were subjected to total RNA extraction via the RNeasy Plant Mini Kit (QIAGEN), incorporating an on-column DNase I step for genomic DNA removal.
The RNA-Seq library construction and sequencing services were provided by Novogene Co., Ltd. (Beijing, China), with three biological replicates per sampleA total RNA preparation was cleaned of ribosomal RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During second-strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and the subjected to real-time PCR for quantification and a bioanalyzer for detection if fragment size distribution. Quantified libraries were pooled and sequenced on Illumina NovaSeq 6000 platforms using a PE150 read length, with over 12 G of raw data per sample were generated.

treatment_protocol: spray-inoculated with  Pst DC3000 avrRpm1

value: Leaves

value: Pst avrRpm1


title: C4-2 cells, siCBX3_1

description:
transfection infection
siNC_siCBX3_gene_fpkm_expression.txt
siCBX3_1


title: Liver, 2months, sample5

description:
Library name: Y1
Male, 10x Genomics


title: Normal Bone Marrow Control 08 RNA seq

description: Library name: NBM_08

value: Bone Marrow


title: Normal Bone Marrow Control 15 RNA seq

description: Library name: NBM_15


title: biol rep3  T_3H_B

description:
Library name: Sample 15
Treat

value: SIB1 knockout


title: C4-2 cells, sicontrol_3

description:
transfection infection
siNC_siCBX3_gene_fpkm_expression.txt
sicontrol_3

source_name: control group of knockdown of CBX3 by siRNA

value: control for CBX3 knockdown

value: sicontrol


title: Normal Bone Marrow Control 05 RNA seq

description: Library name: NBM_05


title: Liver, 2months, sample6

description:
Library name: Y2
Male, 10x Genomics

value: Liver


title: biol rep3 T_3H_WT

description:
Library name: Sample 18
Treat

value: WT


title: C4-2 cells, sicontrol_2

description:
transfection infection
siNC_siCBX3_gene_fpkm_expression.txt
sicontrol_2

value: prostate


title: Liver, 18months, sample4

description:
Library name: O4
Male, 10x Genomics


title: C4-2 cells, sicontrol_1

description:
transfection infection
siNC_siCBX3_gene_fpkm_expression.txt
sicontrol_1

value: prostate cancer cells


title: biol rep1 T_3H_B

description:
Library name: Sample 13
Treat


title: Normal Bone Marrow Control 04 RNA seq

description: Library name: NBM_04


title: biol rep2  T_3H_B

description:
Library name: Sample 14
Treat


title: biol rep1 T_3H_WT

description:
Library name: Sample 16
Treat


title: Liver, 18months, sample3

description:
Library name: O3
Male, 10x Genomics


title: Normal Bone Marrow Control 03 RNA seq

description: Library name: NBM_03


title: Normal Bone Marrow Control 02 RNA seq

description: Library name: NBM_02


title: biol rep3 T_3H_A

description:
Library name: Sample 12
Treat

value: SEC23A knockout


title: biol rep2 T_3H_A

description:
Library name: Sample 11
Treat


title: Liver, 18months, sample2

description:
Library name: O2
Male, 10x Genomics


title: NA_2

city: beijing

first: li

middle: yi

last: xiao

state: State...

address: road of xueyuan 38

institute: peking university

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.20.0).
Reference genome and gene annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA(v0.7.12) and clean reads were aligned to the reference genome using BWA mem.
All peak calling was performed with MACS2 (version 2.1.0) using ‘macs2 -q 0.05 -f AUTO --call-summits--nomodel --shift -100 --extsize 200 --keep-dup all’.
Peaks were adjusted to the same size (500 bp) centered peak summits and motif discoveries of these loci sequences were performed using findMotifsGenome.pl program in HOMER v4.9.1 checksoftware with ‘-len 8,10,12,14 -gc -size given -p 2 -S 25 -homer2 -dumpFasta’.
The position of peak summit around transcript start sites of genes can predict the interaction sites between protein and gene.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

source_name: HeLa

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Take out the cryovial and shake it in 37℃ water to quickly thaw it within 1-2min.Cells were centrifuged at 4 ℃ 500×g for 5 min. Cell activity was detected with LUNA-FL and counted.
ATAC libraries were generated with Chromatin Profile Kit for Illumina (N248, Novoprotein Scientific Inc.) according to the manufacturer’s recommendation.

treatment_protocol: Nicotinic acid treated for 24 hours

value: HeLa

value: Human cervical cancer cells

value: NA treated 24hours


title: biol rep1 T_3H_A

description:
Library name: Sample 10
Treat


title: Normal Bone Marrow Control 01 RNA seq

description: Library name: NBM_01


title: HTO_Thy_FTY

city: PARIS

first: Anne-laure

last: Le gac

address: 26 rue d'ulm

country: France

institute: Institut Curie

description:
Library name: HTO_Thy_FTY
10x Genomics

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger cellranger-7.1.0 and version 8.0.1)
Assembly: reference genome was mm10-2020-A for the scRNA-seq and vdj_GRCm38_alts_ensembl-3.1.0.gz-3.1.0 for sc V(D)J-seq.
Supplementary files format and content: fasta.gz
Library strategy: CITE-seq

molecule: other

source_name: Thymus

extract_protocol:
Cells were prepared as described in exprimental deign and were loaded onto the Chromium 5′ chip. Reverse transcription, library preparation and sequencing were performed according to manufacturer recommendations (10× Genomics).
Chromium GEM-X Single Cell 5' Reagent Kits v3 (10x genomics), according to manufacturer instructions, 5' VDJ scRNA-seq, Other : CITE-seq

value: Thymus

value: MAIT


title: NA_1


title: CON_3


title: NA_3


title: Liver, 18months, sample1

description:
Library name: O1
Male, 10x Genomics

value: Immune cell


title: ZFP281 Over Expression Early Lesion/Post-pregnant mouse 2

city: Bronx

first: Julio

middle: A

last: Aguirre-Ghiso

state: NY

address: 1301 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

description: Library name: OE-EL-2

data_processing:
The paired-end reads were aligned to the mouse reference genome (mm39) using STAR (v2.7.9a). Read counts and transcripts per million (TPM) were quantified with RSEM (v1.3.3) based on gene annotations from the Ensembl database (v105).
Assembly: mm39
Supplementary files format and content: csv file with raw counts and TPM for each sample.

source_name: Mammary Gland

growth_protocol: Whole mammary glands were minced with a sharp blade and then digested in 0.15% Collagenase 1 A, 2.5% bovine serum albumin at 37 °C with agitation for 30 min. Red blood cell lysis buffer was used for 2–5 min, and cells were filtered through a 40-μm filter. For mammosphere culture in virgin mice, 5 × 10^5 cells were cultured in mammosphere medium (DMEM-F12, B27 supplement, Epidermal Growth Factor). For organoids in post-pregnant mice, 5 x 10^5 cells were cultured in organoid medium (advanced DMEM, 5% FBS, Gemini, 10 ng/ml EGF; 20 ng/ml Fibroblast Growth Factor 2, 4 mg/ml Heparin, 5 mM ROCK inhibitor Y-27632, and 4% Matrigel).

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Plus Micro kit.
RNA samples were enriched for Poly-A mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA), and RNA-seq library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer’s recommendations.

value: Mammary Gland

value: Luminal + Basal

value: ZFP281 OE


title: ZFP281 Over Expression Early Lesion/Post-pregnant mouse 1

description: Library name: OE-EL-1


title: biol rep3 M_3H_WT

description:
Library name: Sample 9
Mock

value: Leaves

value: Pst avrRpm1


title: TCR_Thy_MR1fl

description:
Library name: TCR_Thy_MR1fl
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger cellranger-7.1.0 and version 8.0.1)
Assembly: reference genome was mm10-2020-A for the scRNA-seq and vdj_GRCm38_alts_ensembl-3.1.0.gz-3.1.0 for sc V(D)J-seq.
Supplementary files format and content: fasta.gz
Library strategy: TCR-Seq


title: ZFP281 Kncokout Early Lesion/Post-pregnant mouse 3

description: Library name: KO-EL-3

value: ZFP281 KO


title: ZFP281 Kncokout Early Lesion/Post-pregnant mouse 2

description: Library name: KO-EL-2


title: HTO_Thy_MR1fl

description:
Library name: HTO_Thy_MR1fl
10x Genomics


title: CON_2


title: CON_1


title: ZFP281 Kncokout Early Lesion/Post-pregnant mouse 1

description: Library name: KO-EL-1


title: biol rep1 M_3H_WT

description:
Library name: Sample 7
Mock


title: TRACER_rep1

city: Montreal

first: Marc

last: Fabian

state: Quebec

address: 3755 Côte Ste-Catherine Road

department: Department of Oncology

country: Canada

institute: McGill

description: Library name: F_TRACER_3_S24

data_processing:
TruSeq sequence adapters were trimmed from the eCLIP-seq reads with cutadapt (Version: 4.2. Options: version--match-read-wildcards, --error-rate 0.1 --overlap 3, --nextseq-trim 5, --minimum-length 40, --adapter AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) [PMID: 28715235].
The UMI barcode was extracted from the 3’ end of the reads and added to the read name using umi_tools (Version: 1.1.4. Options: extract --3prime –extract-method=string, --bc-pattern NNNNNNNNNNNN) [PMID: 28100584].
Qiaseq miRNA adapters were removed from the 3’ end of the reads with cutadapt (Version: 4.2. Options: --match-read-wildcards --times 1 --error-rate 0 --overlap 19, --adapter AACTGTAGGCACCATCAAT --minimum-length 5) [PMID: 28715235].
Reads were deduplicated by the UMI barcode using UMIcollapse (Version: 1.0.0) [PMID: 31871845].
Reads were aligned to the GRCh38 build of the human genome with STAR (Version: 2.7.11, Options: --alignEndsType EndToEnd, --limitOutSJcollapsed 5000000, --outFilterScoreMin 10, --outFilterMismatchNoverLmax 0.6, --outFilterMultimapNmax 5) [PMID: 23104886].
Reads mapping to rRNA and ENCODE blacklisted regions were removed [PMID: 33590861].
Cluster identification was performed on the aligned reads using CLIPper (Version: 2.0.1, Option: species GRCh38). The software build was run from an Apptainer environment (Obtained from: docker:brianyee/clipper:Osativa7_branch) [PMID: 19136955, and PMID: 24213538].
Assembly: GRCh38
Supplementary files format and content: CLIPper peaks as bed files

molecule: cytoplasmic RNA

growth_protocol: 10% FBS in DMEM

extract_protocol:
Trizol RNA extraction
qiagen miRNA-Seq protocol

treatment_protocol: doxycycline 3ug/mL for 24 hours


title: biol rep2 M_3H_WT

description:
Library name: Sample 8
Mock


title: biol rep3 M_3H_B

description:
Library name: Sample 6
Mock

value: SIB1 knockout


title: ZFP281 Wildtype Early Lesion/Post-pregnant mouse 3

description: Library name: WT-EL-3

value: ZFP281 WT


title: TRACER_rep2

description: Library name: F_TRACER_2_S25


title: Input RNA (no doxycycline)_Rep3

description: Library name: Sample_9_S17

data_processing:
Reads were aligned to the GRCh38 reference genome using STAR
raw counts were calculated with FeatureCounts 39 on the GRCh38 reference genome (release 110)
Differential expression of normalized data was carried out using DESeq2
Assembly: GRCh38 reference genome (release 110)
Supplementary files format and content: DESeq2 results (LFC, p-values, FDR etc) and raw counts in a CSV file.

extract_protocol:
Trizol extraction
RNA was depleted of ribosomal RNA prior to library generation and sequencing reactions were carried out by single-end 75 bp sequencing on a Nextseq500 platform

treatment_protocol: cultured in the presence/absence of doxyccyline (3ug/mL) for 24 hours.


title: biol rep2 M_3H_B

description:
Library name: Sample 5
Mock


title: RIP_Rep2

description: Library name: Sample_8_S16


title: Human intestinal enteroid, Wnt2b homozygous nonsense mutation, biol rep 1

city: Cincinnati

first: Abid Al

last: Reza

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Samples were sequenced with 150bp pair-end sequencing at a depth of 20M reads per sample by Novogene. Inc.
Trimmed sequence reads were mapped to Gencode Release 43 (GRCh38.p13) using kallisto (v0.46.1) pipeline to obtain raw transcript counts.
Clean data were generated from the raw data that was filtered by data-processing steps, including removal of adapter sequences, reads with more than 10% N, and low-quality sequences (the percentage of low-quality bases of quality value ≤ 5 is greater than 50% in a read)
Raw counts data was imported with Tximport and was converted to a DESeq2 dataset and normalized using DESeq2's variance stabilizing transformation to obtain normalized Log2 Counts-per-Million (CPM) values
Assembly: GRCh38.p13/hg38
Supplementary files format and content: comma-separated values files include log2 vst normalized CPM values for each Sample

source_name: Duodenum

extract_protocol:
Bulk RNA was extracted using an RNeasy Plus Micro Kit (Qiagen) according to manufacturer guidelines.
200 ng of RNA prepared into libraries following Illumina Stranded mRNA Prep protocol with all recommended reagents. Final library amplification step using 5 uL index anchors and 13 PCR cycles. Individual libraries were quantified using Qubit® dsDNA HS assay and run on the Agilent Fragment Analyzer for library bp size. Libraries were pooled using the percent range adjusted concentration of fragments 175-650 bp.
RNA-seq. Sequencing was run on Nova-SeqTM 6000 PE-100.

value: Duodenum

value: Patient Derived Enteroid

value: Wnt2b mutated

value: Untreated


title: Human intestinal enteroid, Wnt2b homozygous nonsense mutation, biol rep 3


title: biol rep1 M_3H_B

description:
Library name: Sample 4
Mock


title: ZFP281 Wildtype Early Lesion/Post-pregnant mouse 1

description: Library name: WT-EL-1


title: biol rep3 M_3H_A

description:
Library name: Sample 3
Mock

value: SEC23A knockout


title: ZFP281 Wildtype Early Lesion/Post-pregnant mouse 2

description: Library name: WT-EL-2


title: Input RNA (doxycycline)_Rep2

description: Library name: Sample_6_S15


title: Human intestinal enteroid, Control, biol rep 2

value: WT


title: Human intestinal enteroid, Wnt2b homozygous nonsense mutation, biol rep 2


title: ZFP281 Over Expression Virgin Mouse 2

description: Library name: OE-V-2


title: Input RNA (no doxycycline)_Rep2

description: Library name: Sample_5_S14


title: biol rep2 M_3H_A

description:
Library name: Sample 2
Mock


title: Human intestinal enteroid, Control, biol rep 1


title: ZFP281 Over Expression Virgin Mouse 1

description: Library name: OE-V-1


title: Human intestinal enteroid, Control, biol rep 3


title: biol rep1 M_3H_A

description:
Library name: Sample 1
Mock


title: ZFP281 Kncokout Virgin Mouse 2

description: Library name: KO-V-2


title: ZFP281 Kncokout Virgin Mouse 1

description: Library name: KO-V-1


title: RIP_Rep1

description: Library name: Sample_4_S13


title: Human intestinal organoid, Wnt2b homozygous nonsense mutation, biol rep 1

source_name: tHIO

value: tHIO

value: Stem cell derived Human Intestinal Organoid


title: HeLa cells, Uninfected, biol rep 3

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

description: Library name: Uninfected, replicate 3

data_processing:
Raw ATAC-seq reads were processed using the Nextflow atacseq pipeline v2.1.2 with the --aligner bwa option and the hg38 human genome assembly, which included alternative contigs and “sponge” sequences to reduce false positive peak calls [PMID: 26163063]. The pipeline performed read trimming, alignment, duplicate removal, quality filtering, and peak calling using MACS2. Gene annotation was based on the Gencode v37 GTF. A consensus peak set was quantified using the Rsubread v2.22.1 package [PMID: 24227677], and differential accessibility analysis was performed with edgeR v4.6.3 [PMID: 19910308]. Functional enrichment analysis was conducted using enrichR v3.4 [PMID: 23586463], and motif analysis was performed with HOMER findMotifs [PMID: 20513432]. Signal profiles and heatmaps were generated using deepTools v3.5.6 [PMID: 24799436]. All analyses were performed in R v4.5.1 and Bioconductor v3.21.
Assembly: hg38
Supplementary files format and content: bigWig, broadPeak

growth_protocol: Uninfected HeLa cells (CCL-2, ATCC) were maintained as described [PMID: 29734393]. Orientia tsutsugamushi strain Ikeda (NC_010793.1) was propagated in HeLa cells as described [PMID: 29734393]. Host cell-free bacteria were obtained for experimental purposes via mechanical lysis of highly infected HeLa cells as described [PMID: 39324805]. Synchronous infections were performed using a multiplicity of infection (MOI) of 5-10 as verified by immunofluorescence assay of coverslips infected in parallel and immunolabeled with antiserum specific for O. tsutsugamushi TSA56. Samples had to meet the criterion of having at least 80% of the cells infected to be analyzed further.

extract_protocol:
At 72 hours post infection, uninfected and infected HeLa cells were washed twice with pre-warmed media, washed once with PBS, and detached via trypsinization. All samples had at least 93% cell viability based on trypan blue exclusion. 50,000 cells per sample were centrifuged at 1000 x g for 5 min at 4C, washed with 100 uL of cold PBS, and resuspended in 100 uL cold ATAC-seq lysis buffer (ActiveMotif). Lysed samples were immediately centrifuged at 1000 x g for 10 min at 4C and the pellets were resuspended in 50 uL tagmentation master mix per sample (2X tagmentation buffer [ActiveMotif], 10X PBS, 1% digitonin, 10% Tween-20, and 5 uL loaded Tn5). The tagmentation reactions were mixed by thorough pipetting and incubated at 37C with shaking at 400 rpm for 30 min. Reactions were purified with a MinElute PCR Purification Kit (Qiagen) and eluted in 10mM Tris buffer, pH 8.
Tagmented DNA was sent to Novogene for library amplification and next-generation sequencing according to previously established protocols [PMID: 24097267, PMID: 28846090]. PCR amplification was performed with equimolar amounts of i5/i7 primers. PCR products were purified with AMPure beads and library quality was assessed with Qubit. Clustering of index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina). After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated.

value: HeLa

value: Immortalized cervical cancer cells

tag: time

value: 72 hours post infection


title: Input RNA (no doxycycline)_Rep1

description: Library name: Sample_1_S11


title: Human intestinal organoid, Wnt2b homozygous nonsense mutation, biol rep 2


title: PK-1_MeTA#17+Tet_exp1

city: Sendai

first: Shinichi

last: Fukushige

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Diabetes, Metabolism and Endocrinology

country: Japan

institute: Tohoku University Graduate School of Medicine

description: Gene expression in PK-1_MeTA#17 cell line with tetracycline

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9 pmol Cy3/ug cRNA) was fragmented at 60℃ for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A: HPDE_MeTA#1, MIA PaCa-2_MeTA#3, and PK-9_MeTA#15 cells and G4112F: PK-1_MeTA#17 cells) for 17 hours at 65℃ in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100% and 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Three cell lines derived from pancreatic cancer, MIA PaCa-2_MeTA#3, PK-1_MeTA#17, and PK-9_MeTA#15, were grown in RPMI1640 medium supplemented with 10% fetal bovine serum. A cell line derived from normal pancreatic ductal epithelial cell, HPDE_MeTA#1, was grown in HuMedia-KG2 (Kurabo, Osaka, Japan).

extract_protocol: The RNAs from HPDE_MeTA#1, MIA PaCa-2_MeTA#3, PK-1_MeTA#17, and PK-9_MeTA#15 cells with (4 days tetracycline treatment) or without tetracycline were prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: HPDE_MeTA#1, MIA PaCa-2_MeTA#3, PK-1_MeTA#17, and PK-9_MeTA#15  cells were treated with or without 1 μg/ml tetracycline for 4 days.

value: pancreatic cancer cell line

tag: tissue source

value: pancreas

tag: genotype/variation

value: with 1 μg/ml tetracycline for 4 days.


title: ZFP281 Wildtype Virgin Mouse 2

description: Library name: WT-V-2

value: Mammary Gland

value: Luminal + Basal


title: Human intestinal organoid, Control, biol rep 3

value: H1 GFP


title: RIP_Rep3

description: Library name: Sample_12_S19


title: Human intestinal organoid, Wnt2b homozygous nonsense mutation, biol rep 3


title: ZFP281 Wildtype Virgin Mouse 1

description: Library name: WT-V-1

value: ZFP281 WT


title: HeLa cells, Uninfected, biol rep 1

description: Library name: Uninfected, replicate 1


title: Human intestinal organoid, Control, biol rep 1


title: HeLa cells, Uninfected, biol rep 2

description: Library name: Uninfected, replicate 2


title: Human intestinal organoid, Control, biol rep 2


title: HeLa cells, Infected, biol rep 3

description: Library name: Infected, replicate 3

value: Infected, Orientia tsutsugamushi strain Ikeda


title: PK-1_MeTA#17-Tet_exp1

description: Gene expression in PK-1_MeTA#17 cell line without tetracycline

value: none (no tetracycline)


title: IEC_Ctrl_1

city: Hangzhou

first: Shiyuan

last: Xie

address: Shilongshan Street

institute: Westlake University

description:
Library name: 3_IEC_Ctrl
IE_STm_counts.txt

data_processing:
Low-quality reads and adaptor sequences were removed using Fastp (v0.23.4)
Clean reads were aligned to the mm10 genome by Bowtie2 (v2.5.3) with default parameters, and uniquely mapping reads were quantified using the featureCounts function in Subread (v2.0.6).
Bach effects in raw counts were corrected using the ComBat_seq function in sva (v3.50.0)
Differentially expressed genes (DEGs) were identified using DESeq2 (v1.42.0)
Assembly: mm10
Supplementary files format and content: txt file includes raw counts for each sample

source_name: Large intestine

extract_protocol:
Total RNA from γδIELs or intestinal epithelial tissues was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
For RNA sequencing of γδIEL subsets from BCL6RFP reporter mice, CD160+ BCL6RFP+ and CD160– BCL6RFP– γδΙELs were FACS-sorted and sent to BGI Genomics for cDNA library preparation. For sequencing of target-genes-knockout (KO) γδIELs, CD160+ CD122– CD8αα γδΙΕLs from Bcl6ΔCd8a or Tcf7ΔCd8a mice and total CD8αα γδIELs from Prdm1ΔCd8a mice were FACS-sorted and sent to Novogene for cDNA library preparation. For sequencing of the epithelial cell layer, the entire large intestinal epithelium from S. Tm. (SL3261)-infected or uninfected mice was isolated and sent to Novogene for cDNA library preparation.

value: Large intestine

value: Intestinal epithelial tissue

value: Uninfection


title: Input RNA (doxycycline)_Rep1

description: Library name: Sample_2_S12


title: CMZ401_R1_001

city: New York City

first: Alessandro

last: Vasciaveo

address: 1130 Saint Nicholas Ave., 910

department: Department of Systems Biology

institute: Columbia University

description: Sequencing file containing SB insertion sites on the genome

data_processing:
Common insertion sites (CIS), were identified using the Transposon Annotation Poisson Distribution Association Network Connectivity Environment (TAPDANCE) software (v3.1), which both maps insertion reads and computes statistically significant CIS. Reads were mapped using the UCSC indexed bowtie 1.2.3 compatible mm10 reference genome.
Assembly: mm10
Supplementary files format and content: the sb_data.tab contains all the insertion sites on the mouse genome that are collected and analyzed (library barcode, DNA sequence where the transposon is found inserted on the DNA, Quality of base calling columns)
Supplementary files format and content: Tabular data with association between barcode ID and SB adapters ID

source_name: prostate

extract_protocol:
Genomic DNA was extracted and digested with BfaI or NlaIII for sequencing from left or right side, respectively, making a total of 148 samples. Samples were subject to linker-mediated-PCR (LM-PCR)
Samples were prepared using the primers and barcodes described in Table Sxxx and sequenced using the Illumina HiSeq with 100bp read (Azenta, Burlington, MA, USA).

value: prostate

tag: castration status

value: intact


title: HaCaT, Lnc-DCi, biological rep2

city: ChongQing

first: Xue-ting

last: Hu

address: No. 10, Changjiang Branch Road, Yuzhong District

institute: Daping Hosptial，Army Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: HaCaT, Lnc-DCi

growth_protocol: MEPICF500 medium with 1.2 Mm Ca2+

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: Cells were treated with lentiviruses for lnc-DC knockdown or NC

value: HaCaT

value: keratinocytes

value: shlnc-DC

value: Lnc-DC knockdown


title: Input RNA (doxycycline)_Rep3

description: Library name: Sample_10_S18


title: CMZ356

data_processing:
RNA-seq profiles were generated by mapping mRNA reads to the mouse reference genome (version GRCm38 mm10), using kallisto v0.44.0. RNA-seq raw counts were normalized and variance stabilized using DESeq2 (v.1.36.0) package (Bioconductor) in R-studio 2023.03.0+385, R v.4.2.3 (R Foundation for Statistical Computing).
Assembly: mm10
Supplementary files format and content: Raw Read Counts

extract_protocol:
Briefly, snap-frozen tissues were homogenized in TRIzol (ThermoFisher Scientific, Waltham, MA, USA) with a Fisherbrand™ 150 Homogenizer (Fisher Scientific, Pittsburg, PA Catalog number 15-340-168) and RNA was extracted using the MagMAX-96 total RNA isolation kit (ThermoFisher Scientific, Waltham, MA, USA).
Total RNA was enriched for mRNA using poly-A pull-down; only samples having between 200 ng and 1 µg and with an RNA integrity number (RIN) > 8 were used. Libraries were made using an Illumina TruSeq RNA prep-kit v2 or TruSeq Stranded mRNA library prep kit and sequenced using an Illumina HiSeq2500/4000

value: NPp53SBT2(+)-NE-cross batch control


title: CMZ357

value: NPp53SBT2(+)-nonNE-cross batch control


title: IEC_Ctrl_2

description:
Library name: 4_IEC_Ctrl
IE_STm_counts.txt


title: HeLa cells, Infected, biol rep 2

description: Library name: Infected, replicate 2

value: HeLa

value: Immortalized cervical cancer cells

value: 72 hours post infection


title: HaCaT, Lnc-DCi, biological rep1


title: IEC_SL3261_2

description:
Library name: 2_IEC_SL3261
IE_STm_counts.txt

value: SL3261 S.Tm. infection


title: IEC_SL3261_1

description:
Library name: 1_IEC_SL3261
IE_STm_counts.txt


title: CMZ355


title: HaCaT, Control, biological rep2

source_name: HaCaT, Control

value: shNC

value: control


title: CD160p_gd_Tcf7_KO2

description:
Library name: 4_CD160gdIEL_Tcf7_KO2
Tcf7KO_gd_counts.txt

source_name: Small intestine

value: Small intestine

value: CD160+ CD122- CD8aa+ gdIEL

value: CD8-cre Tcf7-flox/flox

value: Steady state


title: Sample10-HRS

city: New York

first: Isabella

last: Kong

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

description: Library name: Sample 41

data_processing:
Raw data were mapped to the human genome GRCh37 using STAR version 2.3.0e.
Reads that mapped to any of 52,775 genes annotated in Ensembl were counted using HTSeq-counts v.0.6.1 after which genes without a counts per million reads (CPM) in at least 3 samples were excluded from downstream analysis.
Com-bat was used to correct for batch effects.
Count data were normalized using the trimmed mean of M-values (TMM) method and differential gene expression analysis was performed using the limma-voom pipeline.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

source_name: Tumour biopsy

growth_protocol: Cell lines were grown in RPMI+10% FBS + 1x gentamicin. Cells were cultured at 37C with 5% CO2.

extract_protocol:
RNA was extracted using the Arcturus PicoPure RNA Isolation kit (KIT0204, Life Technologies, Carlsbad, CA) with RNAse-Free DNase (79254, Qiagen, Venlo, Netherlands) to isolate high quality RNA from viable flow-sorted cells.
We applied the SMARTer Ultra Low Input RNA Kit (Clontech, Mountain View, CA) to 1-4 ng of input total mRNA.  Illumina-compatible libraries were constructed from cDNA using KAPA LTP Library Preparation Kit (KK8221, Woburn, MA).

value: Tumour biopsy

tag: patient

value: Primary tumour

value: Sorted HRS cells


title: CMZ354

value: prostate

value: intact


title: HeLa cells, Infected, biol rep 1

description: Library name: Infected, replicate 1

value: Infected, Orientia tsutsugamushi strain Ikeda


title: HaCaT, Control, biological rep1

value: HaCaT

value: keratinocytes


title: CD160p_gd_Tcf7_KO1

description:
Library name: 3_CD160gdIEL_Tcf7_KO1
Tcf7KO_gd_counts.txt


title: HepG2 cells, F_P_3

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp 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.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: human liver cancer cell

value: Flag-PPFIA1 overexpression

value: untreated

value: Day 1


title: CMZ353


title: L428_2

description: Library name: Sample 39

source_name: cHL cell line

value: cHL cell line

value: L428 cell line


title: CD160p_gd_Tcf7_WT2

description:
Library name: 2_CD160gdIEL_Tcf7_WT2
Tcf7KO_gd_counts.txt

value: Small intestine

value: CD160+ CD122- CD8aa+ gdIEL


title: CMZ352


title: HepG2 cells, F_P_2


title: CMZ350


title: HepG2 cells, F_P_1


title: CD160p_gd_Tcf7_WT1

description:
Library name: 1_CD160gdIEL_Tcf7_WT1
Tcf7KO_gd_counts.txt

value: Steady state


title: L428_1

description: Library name: Sample 38


title: total_gd_Prdm1_KO1

description:
Library name: 8_gdtotal_Prdm1_KO1
Prdm1KO_gd_counts.txt

value: CD8aa+ gdIELs

value: CD8-cre Prdm1-flox/flox


title: HepG2 cells, F_3

value: Flag overexpression


title: L1236

description: Library name: Sample 37

value: L1236 cell line


title: CMZ349

value: prostate

value: intact


title: CMZ348


title: Sample10-B

description: Library name: Sample 40

value: Tumour biopsy

value: Primary tumour

value: Sorted intratumoral B cells


title: HepG2 cells, F_2

value: human liver cancer cell


title: KMH2_1

description: Library name: Sample 35

value: KMH2 cell line


title: total_gd_Prdm1_WT2

description:
Library name: 7_gdtotal_Prdm1_WT2
Prdm1KO_gd_counts.txt


title: HepG2 cells, F_1

value: untreated

value: Day 1


title: HDLM2

description: Library name: Sample 34

value: cHL cell line

value: HDLM2 cell line


title: KMH2_2

description: Library name: Sample 36


title: total_gd_Prdm1_KO2

description:
Library name: 9_gdtotal_Prdm1_KO2
Prdm1KO_gd_counts.txt

value: Small intestine


title: total_gd_Prdm1_WT1

description:
Library name: 6_gdtotal_Prdm1_WT1
Prdm1KO_gd_counts.txt

value: Steady state


title: CD160p_gd_Bcl6_KO2

description:
Library name: 4-KO2-CD160p-gdIEL
Bcl6KO_gd_counts.txt

value: CD160+ CD122- CD8aa+ gdIEL

value: CD8-cre Bcl6-flox/flox


title: CMZ345


title: CMZ347


title: CMZ346


title: Sample5-HRS

description: Library name: Sample 33

value: Sorted HRS cells


title: human mito post exercise participant 12 [hmt-12-2]

city: Burwood

first: Jessica

last: Silver

address: 221 Burwood Highway

country: Australia

institute: Deakin University

description:
GENERATE FASTQ
silver_hmt raw.csv
2022-10-09_humanmito_normcounts.csv

data_processing:
A 2nM loading pool was prepared for gel-excised isolated mitochondria pool and contained 50% gel-excised miRNA region, 25% gel-excised 190 bp region and 25% Phi-X spike-in and was sequenced on a 2x51bp run (NovaSeq 6000 XP v1.5). Following sequencing, read1 was trimmed using fastp (fastp 0.20.0) and then mapped using blast (2.9.0+) with switch -task blastn and word length set to 19nt to miRbase human mature miRNAs (mature.fa download march 12 2018, miRbase v22.1). Raw read counts for each mature miRNA  generated using short perl script. Data normalisation and differential expression analysis was performed using DEseq2 v1.36 in rstudio v4.2.1
Assembly: miRbase v22.1
Supplementary files format and content: .csv file includes raw read counts for each miRNA for each sample
Supplementary files format and content: .csv file includes normalised read counts (DEseq2) for each miRNA for each sample

source_name: skeletal muscle (vastus lateralis)

extract_protocol:
Mitochondria were isolated from ~60mg skeletal muscle tissue with the MACS Mitochondria Isolation Kit (human) (cat# 130-094-532, Miltenyi Biotec). Following isolation, the mitochondrial fraction was resuspended in 50 μL ice-cold Storage Buffer (cat# 130-094-532, Miltenyi Biotec) and incubated with 312 μg RNase-A (cat# 19101, Qiagen) for 1 h at 37°C. Following incubation, RNase-A was degraded by the addition of 5 μL proteinase-K (stock concentration 600 mAU/mL) (cat# 19131, Qiagen) and inverting the tube briefly. The solution was centrifuged at 8,000g for 10-minutes at 4C. The supernatant was aspirated, and the mitochondria pellet was washed twice with 100 μL ice-cold Storage Buffer (cat#130-096-946, Miltenyi Biotec), and centrifuged at 13,000g for 2-minutes at 4C between washes. The mitochondria pellet was resuspended in 100 μL storage buffer (cat# 130-094-532, Miltenyi Boitec) and stored at -80°C until further analyses.  For RNA extraction from isolated mitochondria, frozen samples were suspended in 5x volumes of TriReagent (cat# R2061, Integrated Sciences), thawed on ice and then centrifuged at 16,000xg for 2 min at 4°C to pellet the mitochondria. The mitochondria pellet was first sheared 20x through a fine pipette tip. Total RNA was extracted from isolated mitochondrua using Zymo Direct-Zol Micro Prep kit (#R2061, Integrated Sciences) with on-column DNase-I digest (#E1010, Integrated Sciences) as per the manufacturer's protocol. RNA was eluted in 12ul NFW.
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set (cat# #E7560S, New England Biolabs.) with modifications as described by our group previously (Silver and Trewin, 2022, https://doi.org/10.1101/2022.04.27.489477). (3). Briefly, the 3’ and 5’ adapters and reverse transcription primer were diluted 0.3x, and 20 end-point PCR cycles were conducted. Following PCR amplification, the cDNA library was cleaned using the Monarch PCR & DNA Cleanup Kit (5 μg) (cat# T1030L, New England Biolabs.) using the 7:1 ratio of binding buffer:sample as per the manufacturer’s instructions. Uniquely indexed libraries were placed into an equimolar pool. Five aliquots of this pool were run in separate lands of a 6% Novex TBE-polyacrylamide gel (cat# EC6265BOX, Thermo Fisher Scientific), with 5 μL Quick-Load pBR322 DNA-MspI Molecular Marker (cat#E7560S, New England Biolabs.) run in a separate lane. Bands corresponding to the 143 and 190bp molecular markers were manually excised and extracted from the gel as per the manufacturer's protocol (cat#E7560S, New England Biolabs.).

tag: Sex

value: male

value: skeletal muscle (vastus lateralis)

value: acute endurance exercise


title: human mito 3hpost exercise participant 12 [hmt-12-3]


title: CMZ344

value: prostate

value: intact


title: CD160p_gd_Bcl6_KO1

description:
Library name: 3-KO1-CD160p-gdIEL
Bcl6KO_gd_counts.txt


title: Sample5-B

description: Library name: Sample 32

value: Tumour biopsy

value: Primary tumour

value: Sorted intratumoral B cells


title: Sample4-HRS

description: Library name: Sample 31


title: CMZ342


title: CD160p_gd_Bcl6_WT2

description:
Library name: 2-WT2-CD160p-gdIEL
Bcl6KO_gd_counts.txt


title: CMZ341


title: Sample4-B

description: Library name: Sample 30


title: human mito 3hpost exercise participant 11 [hmt-11-3]


title: CD160p_gd_Bcl6_WT1

description:
Library name: 1-WT1-CD160p-gdIEL
Bcl6KO_gd_counts.txt


title: human mito post exercise participant 11 [hmt-11-2]


title: RNA_Thy_FTY

description:
Library name: RNA_Thy_FTY
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger cellranger-7.1.0 and version 8.0.1)
Assembly: reference genome was mm10-2020-A for the scRNA-seq and vdj_GRCm38_alts_ensembl-3.1.0.gz-3.1.0 for sc V(D)J-seq.
Supplementary files format and content: fasta.gz

value: Thymus

value: MAIT


title: CMZ340


title: human mito 3hpost exercise participant 10 [hmt-10-3]


title: Sample3-B

description: Library name: Sample 28


title: human mito pre exercise participant 12 [hmt-12-1]

value: pre


title: Sample2-HRS

description: Library name: Sample 27


title: Sample3-HRS

description: Library name: Sample 29


title: human mito post exercise participant 10 [hmt-10-2]


title: RNA_Thy_MR1fl

description:
Library name: RNA_Thy_MR1fl
10x Genomics


title: CMZ337


title: CMZ338


title: Sample2-B

description: Library name: Sample 26


title: human mito pre exercise participant 10 [hmt-10-1]


title: Sample9-HRS

description: Library name: Sample 25


title: CMZ336


title: human mito 3hpost exercise participant 9 [hmt-09-3]


title: CMZ335


title: MVT1_Mki67-/-_KO2_1

city: Basel

first: Yongzhan

last: Zhang

address: Otto-Stern-Weg 7 HPL H17.2

country: Switzerland

institute: ETH Zurich

description: Library name: Sample 16

data_processing:
Sequencing reads were trimmed from the 3’ end until the final base had a quality score >30, utilizing Trimmomatic (v0.33). Quality assessment of RNA-seq data was performed using FastQC (v0.11.4). Trimmed reads were aligned to the appropriate reference genomes using STAR (v2.7.3a): the human genome (GRCh38) for LM2 samples and the mouse genome (GRCm39) for MVT1 samples. Gene-level expression counts were quantified with HTSeq (v2.0.5), using GENCODE gene annotations (release 44 for human, release M33 for mouse).
Aligned reads were counted using HTSeq.
Assembly: GRCh38, GRCm39
Supplementary files format and content: Tab-delimited text files includes raw counts for each sample

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) as per the manufacturer’s instructions.
Illumina Truseq mRNA

value: Breast cancer cells


title: MVT1_Mki67-/-_KO2_2

description: Library name: Sample 17


title: CMZ339


title: MVT1_Mki67-/-_KO1_3

description: Library name: Sample 14


title: Sample8-HRS

description: Library name: Sample 23


title: human mito 3hpost exercise participant 8 [hmt-08-3]


title: Sample9-B

description: Library name: Sample 24


title: human mito pre exercise participant 9 [hmt-09-1]


title: MVT1_Mki67-/-_KO2_3

description: Library name: Sample 18


title: MVT1_Mki67-/-_KO1_4

description: Library name: Sample 15


title: Sample8-B

description: Library name: Sample 22


title: CMZ333


title: human mito post exercise participant 8 [hmt-08-2]


title: CMZ334


title: MVT1_Mki67-/-_KO1_1

description: Library name: Sample 12


title: CMZ332


title: Sample7-B

description: Library name: Sample 20


title: MVT1_Mki67-/-_KO1_2

description: Library name: Sample 13


title: human mito post exercise participant 9 [hmt-09-2]


title: Sample7-HRS

description: Library name: Sample 21


title: human mito pre exercise participant 8 [hmt-08-1]


title: Sample6-HRS

description: Library name: Sample 19


title: human mito 3hpost exercise participant 7 [hmt-07-3]


title: MVT1_WT_2

description: Library name: Sample 10


title: human mito post exercise participant 7 [hmt-07-2]


title: MVT1_WT_3

description: Library name: Sample 11


title: MVT1_WT_1

description: Library name: Sample 9


title: CMZ330


title: human mito pre exercise participant 7 [hmt-07-1]


title: Sample16-HRS

description: Library name: Sample 17


title: Sample16-B

description: Library name: Sample 16


title: CMZ329


title: 8 weeks old OE mice_4_952

city: Kobe

first: Yusei

last: Hosokawa

state: Hyogo

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

department: 1Division of Diabetes and Endocrinology, Department of Internal Medicine

institute: Kobe University graduate school of medicine

description: Library name: 952

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to mm10 whole genome by using HISAT2 version 2.1.0 with parameter -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
FPKM were calculated by using StringTie version 2.1.3b, with parameter --rf -l -o -G -A -e
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Read Count, FPKM, TPM values for each Sample

source_name: epididymal white adipose tissue

growth_protocol: Mice were housed at 21°C-25°C on a 12-hr light/dark cycle in the animal facility at Kobe University Graduate School of Medicine.

extract_protocol:
Total RNA was extracted from tissues with RNeasy minikit (QIAGEN).
RNA libraries for RNA-Seq were Prepared using TruSeq stranded mRNA Library Prep. Kit Following manufacturers Protocols

treatment_protocol: Male A-LTA4HOE mice and their control mice at 4 weeks of age were randomized to individual diet groups and given free access to tap water and the HFD diet [60 kcal% fat (HFD22, CLEA Japan)] for 4 weeks or 16 weeks.

value: epididymal white adipose tissue

value: OE

value: 4 weeks HFD


title: Sample6-B

description: Library name: Sample 18


title: CMZ327


title: CMZ331


title: CMZ328


title: 8 weeks old OE mice_3_951

description: Library name: 951


title: human mito post exercise participant 6 [hmt-06-2]


title: 8 weeks old OE mice_2_938

description: Library name: 938


title: Sample15-HRS

description: Library name: Sample 15


title: human mito pre exercise participant 6 [hmt-06-1]


title: 8 weeks old OE mice_1_916

description: Library name: 916


title: Sample15-B

description: Library name: Sample 14


title: human mito 3hpost exercise participant 6 [hmt-06-3]


title: CMZ183


title: 8 weeks old Ctrl mice_4_936

description: Library name: 936

value: Control


title: CMZ184


title: human mito 3hpost exercise participant 5 [hmt-05-3]


title: Sample14-HRS

description: Library name: Sample 11

value: Sorted HRS cells


title: CMZ181


title: 8 weeks old Ctrl mice_3_935

description: Library name: 935

value: male


title: human mito 3hpost exercise participant 4 [hmt-04-3]

value: skeletal muscle (vastus lateralis)


title: 8 weeks old Ctrl mice_2_918

description: Library name: 918


title: CMZ111


title: CMZ182


title: Sample18-B

description: Library name: Sample 12


title: CMZ110


title: Sample17-HRS

description: Library name: Sample 9


title: human mito post exercise participant 5 [hmt-05-2]

value: acute endurance exercise


title: Sample14-B

description: Library name: Sample 10


title: CMZ109

value: prostate


title: 20 weeks old OE mice_3_583

description: Library name: 583

value: 16 weeks HFD


title: Sample17-B

description: Library name: Sample 8

value: Tumour biopsy


title: 8 weeks old Ctrl mice_1_915

description: Library name: 915


title: human mito 3hpost exercise participant 3 [hmt-03-3]


title: Sample13-HRS

description: Library name: Sample 7

value: Primary tumour


title: 20 weeks old OE mice_2_559

description: Library name: 559


title: CMZ108

value: intact


title: human mito post exercise participant 4 [hmt-04-2]


title: human mito 3hpost exercise participant 2 [hmt-02-3]


title: CMZ107


title: Sample13-B

description: Library name: Sample 6

value: Sorted intratumoral B cells


title: human mito pre exercise participant 4 [hmt-04-1]


title: Sample12-HRS

description: Library name: Sample 5


title: 20 weeks old OE mice_1_551

description: Library name: 551


title: CMZ105


title: 20 weeks old OE mice_4_607

description: Library name: 607


title: Sample11-HRS

description: Library name: Sample 3


title: human mito post exercise participant 1 [hmt-01-2]


title: 20 weeks old Ctrl mice_1_553

description: Library name: 553


title: human mito post exercise participant 2 [hmt-02-2]


title: human mito pre exercise participant 2 [hmt-02-1]


title: Sample19-HRS

description: Library name: Sample 1


title: 20 weeks old Ctrl mice_4_568

description: Library name: 568


title: Leucine3 NALM-6 high leucine 550 mg/L

status: Public on Apr 12 2026

city: Bonn

first: Jingjing

last: Pu

address: Auf dem Hügel 41, 2.0G

country: Germany

institute: Universitätsklinikum Bonn

description:
Library name: LD3_Nalm6-D26_S1_L001
Vazyme RNA Isolator, paired-end, BGI-2000

data_processing:
Paired-end RNA-seq data were generated on the BGI-2000 platform. Transcripts were quantified using Salmon.
Differential expression analysis was performed using DESeq2.
KEGG and GSEA pathway enrichment results were visualized using an open-source platform (SRplot, per manuscript reference).
Expression differences between high-leucine and control NALM-6 conditions were used to identify differentially expressed genes (DEGs) for downstream pathway analysis.
Processed output files include expression quantification tables and differential expression result tables for NALM-6 cells under normal versus high leucine culture conditions.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containing RNA-seq expression quantification results (e.g., gene- or transcript-level abundance/count values) for each sample and/or a merged expression matrix across samples.
Supplementary files format and content: Tab-delimited text file containing differential expression analysis results generated with DESeq2 (e.g., gene identifier, log2 fold change, p value, adjusted p value, and expression statistics) comparing high-leucine versus control NALM-6 cells.

growth_protocol: Human B-cell precursor acute lymphoblastic leukemia cell line NALM-6 was maintained in RPMI 1640 medium under standard cell culture conditions. Cells were cultured in medium containing a baseline physiological leucine concentration (50 mg/L, control) or high leucine supplementation (550 mg/L).

extract_protocol:
Total RNA was extracted from NALM-6 cells using Vazyme RNA Isolator (R401-01) according to the manufacturer’s instructions.
RNA-seq libraries were constructed from total RNA for paired-end sequencing on the BGI-2000 platform.

treatment_protocol: NALM-6 cells were exposed to two leucine conditions: control medium containing 50 mg/L leucine and treatment medium supplemented to 550 mg/L leucine (TargetMol, T4772). Cells were cultured under these conditions prior to RNA extraction for transcriptome sequencing.

value: not reported

value: high leucine (550 mg/L)

value: batch 1


title: human mito pre exercise participant 1 [hmt-01-1]

value: pre


title: Sample11-B

description: Library name: Sample 2


title: CMZ103


title: CMZ106


title: human mito post exercise participant 3 [hmt-03-2]


title: human mito 3hpost exercise participant 1 [hmt-01-3]


title: Leucine2 NALM-6 high leucine 550 mg/L

description:
Library name: LD2_Nalm6-D26_S1_L001
Vazyme RNA Isolator, paired-end, BGI-2000

value: B-cell precursor acute lymphoblastic leukemia cell


title: CMZ104


title: 20 weeks old Ctrl mice_2_560

description: Library name: 560

value: epididymal white adipose tissue


title: CMZ101


title: Leucine1 NALM-6 high leucine 550 mg/L

description:
Library name: LD1_Nalm6-D26_S1_L001
Vazyme RNA Isolator, paired-end, BGI-2000


title: Contor3 NALM-6 normal leucine 50 mg/L

description:
Library name: C3_Nalm6-D26_S1_L001
Vazyme RNA Isolator, paired-end, BGI-2000

value: normal leucine (50 mg/L)


title: Contor2 NALM-6 normal leucine 50 mg/L

description:
Library name: C2_Nalm6-D26_S1_L001
Vazyme RNA Isolator, paired-end, BGI-2000


title: 20 weeks old Ctrl mice_3_562

description: Library name: 562

value: Control


title: Contor1 NALM-6 normal leucine 50 mg/L

description:
Library name: C1_Nalm6-D26_S1_L001
Vazyme RNA Isolator, paired-end, BGI-2000


title: Sample12-B

description: Library name: Sample 4


title: H3K37ac_Input_young_sirt6_tg_1

city: Ramat-Gan

first: Haim

middle: Yosef

last: Cohen

address: Max & Anna Webb

country: Israel

institute: Bar-Ilan University

description: Library name: Sample64

data_processing:
Adapters were trimmed using the cutadapt tool. Following adapter removal, reads that were shorter than 40 nucleotides were discarded (cutadapt option –m 30)
The reads were aligned uniquely to the mouse genome (mm10) using bowtie (version 1.0.0)
Bound regions were detected using MACS2 (version 2.0.10.20131216)
Assembly: mm10
Supplementary files format and content: csv file of normalized counts for each sample and Bigwig for each sample

source_name: Liver

extract_protocol:
Trizol extraction (Phenol/chlorophorm)
Chip-seq libraries were prepared at the Crown Genomics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science starting from 1-20ng of DNA as previously described (Blecher-Gonen R et al. Nat. prot. (2013)).Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent). Sequencing was done on a Novaseq X Plus instrument (Illumina) using a Novaseq X 1.5B 100 cycles kit, allocating 20M reads per sample (paired end sequencing for H3K9ac & H3K56ac and single end for H3K27ac).

value: Liver

tag: strain

tag: chip antibody


title: H3K56ac_old_sirt6_tg_25

description: Library name: Sample57

data_processing:
Adapters were trimmed using the cutadapt tool. Following adapter removal, reads that were shorter than 40 nucleotides were discarded (cutadapt option –m 30)
The reads were aligned uniquely to the mouse genome (mm10) using bowtie (version 1.0.0)
Bound regions were detected using MACS2 (version 2.0.10.20131216)
Assembly: mm10
Supplementary files format and content: csv file of normalized counts for each sample

extract_protocol:
Trizol extraction (Phenol/chlorophorm)
Chip-seq libraries were prepared at the Crown Genomics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science starting from 1-20ng of DNA as previously described (Blecher-Gonen R et al. Nat. prot. (2013)).Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent). Sequencing was done on a Novaseq X Plus instrument (Illumina) using a Novaseq X 1.5B 100 cycles kit, allocating 20M reads per sample (paired end sequencing).

value: old

value: SIRT6 tg

value: H3K56ac (Epigentek; A-4026)


title: H3K27ac_young_wt_1

description: Library name: Sample70

value: H3K27ac (Abcam; EP16602)


title: H3K27ac_old_sirt6_tg_1

description: Library name: Sample76


title: H3K27ac_young_sirt6_tg_2

description: Library name: Sample71


title: H3K37ac_Input_young_wt_1

description: Library name: Sample62


title: H3K27ac_old_wt_1

description: Library name: Sample74


title: H3K27ac_old_wt_2

description: Library name: Sample73


title: H3K27ac_young_sirt6_tg_1

description: Library name: Sample72


title: H3K56ac_old_sirt6_tg_23

description: Library name: Sample55


title: H3K37ac_Input_old_wt_1

description: Library name: Sample66


title: H3K37ac_Input_young_wt_2

description: Library name: Sample61


title: H3K27ac_old_sirt6_tg_2

description: Library name: Sample75


title: H3K37ac_Input_old_sirt6_tg_2

description: Library name: Sample67


title: H3K56ac_old_wt_20

description: Library name: Sample52

value: WT


title: H3K37ac_Input_young_sirt6_tg_2

description: Library name: Sample63


title: H3K37ac_Input_old_sirt6_tg_1

description: Library name: Sample68


title: H3K56ac_old_sirt6_tg_28

description: Library name: Sample60


title: H3K37ac_Input_old_wt_2

description: Library name: Sample65


title: H3K56ac_old_sirt6_tg_24

description: Library name: Sample56


title: H3K56ac_old_sirt6_tg_26

description: Library name: Sample58


title: H3K56ac_old_sirt6_tg_27

description: Library name: Sample59


title: H3K27ac_young_wt_2

description: Library name: Sample69


title: H3K56ac_old_wt_22

description: Library name: Sample54


title: H3K56ac_old_wt_21

description: Library name: Sample53


title: H3K56ac_young_sirt6_tg_14

description: Library name: Sample49

value: young


title: H3K56ac_young_sirt6_tg_11

description: Library name: Sample48


title: H3K56ac_old_wt_19

description: Library name: Sample51


title: H3K56ac_young_wt_2

description: Library name: Sample43


title: H3K56ac_young_wt_1

description: Library name: Sample42


title: H3K9ac_old_sirt6_tg_28

description: Library name: Sample41

value: H3K9ac (Abcam; ab32129)


title: H3K56ac_young_sirt6_tg_10

description: Library name: Sample47


title: H3K56ac_young_sirt6_tg_9

description: Library name: Sample46


title: H3K9ac_old_wt_18

description: Library name: Sample31


title: H3K56ac_young_wt_6

description: Library name: Sample45


title: H3K9ac_old_wt_15

description: Library name: Sample30


title: H3K9ac_young_sirt6_tg_11

description: Library name: Sample27


title: H3K9ac_old_sirt6_tg_27

description: Library name: Sample40


title: H3K9ac_old_sirt6_tg_26

description: Library name: Sample39


title: H3K9ac_old_wt_21

description: Library name: Sample34


title: H3K9ac_young_sirt6_tg_10

description: Library name: Sample26


title: H3K9ac_old_sirt6_tg_24

description: Library name: Sample37


title: H3K56ac_young_wt_5

description: Library name: Sample44


title: H3K9ac_old_sirt6_tg_23

description: Library name: Sample36


title: H3K9ac_old_wt_22

description: Library name: Sample35


title: H3K9ac_old_wt_20

description: Library name: Sample33


title: H3K9ac_young_wt_5

description: Library name: Sample23


title: H3K9ac_young_sirt6_tg_14

description: Library name: Sample28


title: H3K9ac_young_sirt6_tg_9

description: Library name: Sample25


title: H3K9ac_old_sirt6_tg_25

description: Library name: Sample38


title: H3K9ac_young_wt_1

description: Library name: Sample21


title: H3K9ac_H3K56ac_Input_old_sirt6_tg_28

description: Library name: Sample20


title: H3K9ac_young_wt_6

description: Library name: Sample24


title: H3K9ac_old_wt_19

description: Library name: Sample32


title: H3K9ac_H3K56ac_Input_old_sirt6_tg_27

description: Library name: Sample19


title: H3K9ac_H3K56ac_Input_old_sirt6_tg_26

description: Library name: Sample18


title: H3K9ac_H3K56ac_Input_old_wt_22

description: Library name: Sample14


title: H3K9ac_H3K56ac_Input_old_wt_21

description: Library name: Sample13


title: H3K9ac_young_wt_2

description: Library name: Sample22


title: H3K9ac_H3K56ac_Input_old_sirt6_tg_25

description: Library name: Sample17


title: H3K9ac_H3K56ac_Input_old_sirt6_tg_24

description: Library name: Sample16


title: H3K9ac_H3K56ac_Input_old_sirt6_tg_23

description: Library name: Sample15


title: H3K9ac_H3K56ac_Input_old_wt_18

description: Library name: Sample10


title: H3K9ac_H3K56ac_Input_old_wt_15

description: Library name: Sample9


title: H3K9ac_H3K56ac_Input_young_wt_5

description: Library name: Sample3


title: H3K9ac_H3K56ac_Input_young_sirt6_tg_11

description: Library name: Sample7


title: H3K9ac_H3K56ac_Input_young_sirt6_tg_14

description: Library name: Sample8


title: H3K9ac_H3K56ac_Input_young_wt_2

description: Library name: Sample2


title: H3K9ac_H3K56ac_Input_young_sirt6_tg_9

description: Library name: Sample5


title: H3K9ac_H3K56ac_Input_old_wt_19

description: Library name: Sample11


title: H3K9ac_H3K56ac_Input_young_sirt6_tg_10

description: Library name: Sample6


title: H3K9ac_H3K56ac_Input_young_wt_1

description: Library name: Sample1


title: H3K9ac_H3K56ac_Input_young_wt_6

description: Library name: Sample4


title: sirt6_15

description: Library name: Sample15

data_processing:
Adapters were trimmed using the cutadapt tool. Following adapter removal, reads that were shorter than 25 nucleotides were discarded (cutadapt option –m 25).An additional 3 bases were trimmed from the end of the read.
The reads were aligned uniquely to the M. musculus GRCm38 reference genome using bowtie (version 2.0.0). Reads that were mapped to the mitochondrial chromosome were excluded. Duplicate reads were excluded using Picard tools. Fragments that were longer than 120 nucleotides were excluded from the analysis.
Open regions were detected using MACS371. Merged peaks were conducted using Bedtools intersect. Peak annotation was performed using ChIPseeker. Additional analysis used csaw and EdgeR packages in R. Peaks were annotated with genes, defined as the closest gene to the peak.
Differentially accessible peaks were identified using DESeq2. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.
Assembly: mm10
Supplementary files format and content: csv file of normalized counts for each sample

extract_protocol: ATAC-Seq Kit from active motif (cat: 53150)

value: AAV8 SIRT6


title: sirt6_13

description: Library name: Sample13


title: sirt6_14

description: Library name: Sample14


title: sirt6_12

description: Library name: Sample12


title: H3K9ac_H3K56ac_Input_old_wt_20

description: Library name: Sample12


title: sirt6_8

description: Library name: Sample8


title: gfp_7

description: Library name: Sample7

value: GFP


title: sirt6_11

description: Library name: Sample11


title: sirt6_9

description: Library name: Sample9


title: sirt6_10

description: Library name: Sample10


title: gfp_5

description: Library name: Sample5


title: gfp_2

description: Library name: Sample2


title: gfp_4

description: Library name: Sample4


title: ALS48_deltarae1::Spc_ermBL_ermB_3FLAG_1Ery

city: Chicago

first: Mee-Ngan

middle: F.

last: Yap

state: IL

address: 320 E Superior St

department: Microbiology-Immunology

institute: Northwestern University Feinberg School of Medicine

description: Library name: ALS48

data_processing:
Quality control and adapter trimming was performed with Trim Galore 16. BBSplit and SortMeRNA were used to remove genome containimants and rRNAs. Salmon and RSEM were used for alignment and quantification. Raw, quantified total counts of each locus are available in the “.tsv” file.
Assembly: GenBank accession CP000255.1
Supplementary files format and content: Text delimited file showing read couts (RPKM) of every locus

organism: Staphylococcus aureus

source_name: whole cell

growth_protocol: S. aureus cells were grown in TSB until early-log phase (OD600~ 0.2) at 37ºC and either treated with and without sublethal 1ug/mL or lethal 400 ug/ml of erythromycin for 120 min.

extract_protocol:
Bacterial cells were disrupted by Lysing Matrix B beads on a MP Biomedical FastPrep 24 instrument for 2 cycles of 40M/s.  Cell lysates were extracted with acidic phenol-chloroform (pH 4.7) at least 2-3 times before subjecting to isopropanol precipitation. Crude RNAs were further cleaned up using the Qiagen RNeasy mini columns. Final total RNA were digested with Turbo DNase I to remove genomic DNA contamination
Ribo-Zero rRNA depletion and cDNA libraries was performed by NUSeq core (Northwestern Univ) using Illumina Unique Dual Indexes.

treatment_protocol: antibiotic (erythromycin) exposure

value: whole cell

tag: cell line

value: delta_rae1::Spc ermBL-ermB_3_FLAG

value: 1 ug/mL Erythromycin


title: ALS44_deltapurR::Spc_ermBL_ermB_3FLAG_0Ery

description: Library name: ALS44

tag: genotype

value: delta_purR::Spc ermBL-ermB_3_FLAG

value: ethanol mock


title: gfp_1

description: Library name: Sample1


title: ALS46_deltapurR::Spc_ermBL_ermB_3FLAG_400Ery

description: Library name: ALS46

tag: treatment

value: 400 ug/mL Erythromycin


title: ALS47_deltarae1::Spc_ermBL_ermB_3FLAG_0Ery

description: Library name: ALS47

tag: tissue


title: gfp_3

description: Library name: Sample3

tag: cell type


title: ALS42_deltapurR::Spc_0Ery

description: Library name: ALS42


title: ALS38_parental_1Ery

description: Library name: ALS38

value: parental


title: ALS43_deltapurR::Spc_1Ery

description: Library name: ALS43


title: ALS37_parental_0Ery

description: Library name: ALS37


title: ALS40_ermBL_ermB_3FLAG_1Ery

description: Library name: ALS40


title: gfp_6

description: Library name: Sample6

value: Liver