title: si-zuc

description:
Library name: si-zuc
Sequencing of total small-RNAs after depletion of 2s rRNA

source_name: OSC

growth_protocol: Ovarian somatic cells (OSCs) were maintained at 27 °C in a humidified incubator with 2.5% CO₂, as previously described (Niki, Yamaguchi et al. 2006, Saito, Inagaki et al. 2009) Cells were cultured in M3 basal medium supplemented with 10% fetal bovine serum (FBS), insulin, glutathione, and fly extract.

extract_protocol:
Total RNA was extracted from ovarian somatic cells (OSCs) using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Briefly, cells were lysed in TRIzol, followed by phase separation with chloroform. The aqueous phase was recovered, and RNA was precipitated with isopropanol, washed with 75% ethanol, and resuspended in nuclease-free water. RNA concentration and purity were assessed by NanoDrop spectrophotometry (A260/280 and A260/230 ratios). To enrich for small RNAs and deplete ribosomal RNA, 10 µg of total RNA was subjected to 2S rRNA depletion using a biotinylated antisense oligonucleotide (5'–Bio-AGTCTTACAACCCTCAACCATATGTAGTCCAAGCAGCACT–3') immobilized on MyOne Streptavidin C1 magnetic beads (Invitrogen). RNA was denatured at 80 °C for 2 min, hybridized to the bead-bound probe at 50 °C for 1 h with rotation, and the rRNA-depleted supernatant was recovered by magnetic separation and ethanol precipitation. The depleted RNA was resuspended in nuclease-free water and used directly for library preparation.
Small RNAs were isolated by resolving the mixture on a 12.5% polyacrylamide–urea gel and excising the region flanked by the spike-in signals. These spike-ins were ligated to conventional 4N adapters alongside the endogenous small RNA population. Following each ligation step, libraries were gel-purified, with band excision guided by the radioactive signal. After reverse transcription and PCR amplification, the spike-in sequences were removed from the library via restriction digestion. The libraries  were pooled at the final stage using PCR-introduced dual or single index barcodes.

value: OSC

value: ovarian somatic cells

value: wildtype

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: Male, Old, Nicotinamide Riboside, rep 1

status: Public on Feb 23 2026

type: SRA

city: Boston

first: Alexander

last: Tyshkovskiy

state: Massachusetts

address: 77 Avenue Louis Pasteur

country: USA

institute: Brigham & Women's Hospital, Harvard Medical School

description:
Library name: JL13970
Male_Old_NR_1

library_source: transcriptomic

data_processing:
Reads were mapped to mouse genome (GRCm39) with STAR (version 2.7.11b). Genes were counted via featureCounts (version 2.0.6).
Assembly: GRCm39
Supplementary files format and content: comma-separated values file includes gene counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA was extracted with PureLink RNA Mini Kit.
Libraries were prepared with TruSeq Stranded mRNA LT Sample Prep Kit according to TruSeq Stranded mRNA Sample Preparation Guide.

treatment_protocol: Mice were housed at the University of Michigan Medical School (UM), the University of Texas (UT), and The Jackson Laboratory (TJL). Animals were fed ad libitum with the Purina 5LG6 diet, produced in the same commercial diet facility (TestDiet, Richmond, IN, USA). Compounds were administered through food until the animals were sacrificed.

tag: tissue

value: Liver

tag: strain

tag: Sex

value: Male

tag: cohort

tag: site

value: JL

tag: treatment

value: Nicotinamide Riboside

tag: treatment abbreviation

value: NR

tag: dose

tag: age group

value: Old

tag: age

value: 22 months

tag: age at_start_of_treatment

value: 8 months

tag: replicate


title: Male, Old, MitoQ, rep 2

description:
Library name: UM60529
Male_Old_MitoQ_2

value: UM

value: MitoQ

value: 100 ppm

value: 7 months


title: APB25

city: Portland

first: Lisa

last: Coussens

state: OR

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
39654

library_source: genomic

data_processing:
*library strategy: TCRseq
Combine paired-end sequences with PEAR (v.0.9.6)
Custom script extracts synthetic template sequences and determines normalization factors
Align reads to TCR reference sequences using MiXCR v 4.4.2
Normalize clonotype counts using normalization factors
Calculate summary statistics, e.g. clonality, shannon diversity, Jaccard index, etc.
Assembly: Mouse TCRb from RepSeq.IO library v2.1 (Full Library MD5: 2f4877a1b3b109f2be617d38e9935b4f)
Supplementary files format and content: tab-delimited text files containing clonotype information: raw and normalized counts and frequencies, sequence information for V, D, J, and CDR3, etc.

molecule: genomic DNA

source_name: Blood

growth_protocol: Mice were maintained in standard conditions

extract_protocol:
As described by Medler et al, Cancer Cell 2019
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run

treatment_protocol: 80-day-old MMTV-PyMT female littermates were randomized by initial tumor volume and fed either with PLX3397 (Pexidartinib) formulated in mouse chow or control chow until endpoints. PLX3397 was formulated so that the average dose per animal per day was 40 mg/kg. When PLX3397-treated MMTV-PyMT mice reached 85 days of age, they were then administered PTX (Breckenridge Pharmaceutical, Inc.) every 5 days by i.v. injection into the retroorbital plexus. PTX was given at 10 mg/kg of the animal per injection, diluted in PBS. At 87 days of age, mice were treated with PD-1 (RMP1-14, BioXcell, Cat#BE0146) or Isotype control rat IgG2a (BioXcell, Cat# BE0089) at 1.0 mg/mouse for initial dose, then every 5 days at 0.5 mg/mouse for follow-up doses by i.p. injection. Primary tumor burden was determined by caliper measurements on live sedated mice every 5 days following initiation of PLX3397 treatment. At endpoints, mice were intraperitoneally injected with 50 mg/kg BrdU (Roche) for 90 min and prior to tissue collection, followed by were cardiac-perfusion with PBS containing 10 U/ml heparin (Sigma-Aldrich) to clear peripheral blood. Resected tissues were enzymatically and mechanistically digested to obtain single cell suspensions for susequent DNA extraction

value: Blood

tag: cell line

tag: cell type

value: peripheral blood mononuclear cells

tag: genotype

value: MMTV-PyMT

value: Untreated

tag: time


title: Whole-blood RNA-seq from AD(04_014_S00_08)

city: Barcelona

first: Ferran

last: Aguilar Parera

state: BARCELONA

address: Avinguda Diagonal 477, 11th floor, EF CLIF

country: Spain

institute: EF-CLIF

data_processing:
The reads were aligned to the hg38 genome assembly and the transcriptome using STAR v2.5.3a and GENCODE 26 annotation
Gene expression was quantified using STAR (–quantMode GeneCounts) and VSN-transformed (variance stabilizing normalization)
Then a quantile normalization method was applied to normalize the nonbiological variability.
Using the HUGO Genome Nomenclature Committee (HGNC), which is a resource for approved human gene nomenclature, we included protein-coding genes, and among other gene locus types, immunoglobulin genes, and T cell receptor genes. Genes brought by sexual chromosomes and mitochondrial DNA were not included in the analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited file with expected counts (RSEM) for each sample

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
RNA was isolated from blood stored in Tempus tubes using the Tempus™ Spin RNA Isolation Kit (reference 4380204, Applied Biosystems). RNA quality was assessed using Agilent RNA 6000 Nano and Pico Chips (Agilent Technologies, Cat.# 5067-1511 and Cat.# 5067-151, respectively) and concentration via Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Cat.# Q32855).
Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina Inc., Cat.# 20020612) and TruSeq RNA CD Index Plate (Illumina Inc., Cat.# 20019792) following TruSeq Stranded Total RNA Sample Prep-guide (Part # 15031048 Rev. E). Briefly, starting from 500 ng of total RNA, rRNA and globin mRNA were depleted and remaining RNA was purified, fragmented and primed for cDNA synthesis. cDNA first strand was synthesized with SuperScript-II Reverse Transcriptase (Thermo Fisher Scientific, Cat.#18064-014) for 10 min at 25°C, 15 min at 42°C, 15 min at 70°C and pause at 4°C. cDNA second strand was synthesized with Illumina reagents at 16°C for 1 hour. Then, A-tailing and adaptor ligation were performed. Finally, enrichment of libraries was achieved by PCR (30 sec at 98°C; 15 cycles of 10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C; 5min at 72°C and pause at 4°C). Afterwards, libraries were visualized on an Agilent 2100 Bioanalyzer using Agilent High Sensitivity DNA kit (Agilent Technologies, Cat. # 5067-4626), quantified using Qubit dsDNA HS DNA Kit (Thermo Fisher Scientific, Cat. # Q32854) and sequenced in a NovaSeq-6000 (Illumina Inc.) by at least 100 million paired-end 100nt reads.

value: Whole blood

value: AD


title: APB26

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
39667


title: Whole-blood RNA-seq from AD(04_011_S02_08)


title: si-GFP

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

description:
Library name: si-GFP
Sequencing of total small-RNAs after depletion of 2s rRNA

library_source: other

data_processing:
Illumina reads were processed by removing 3′ adapters with cutadapt {Martin, 2011 #646}, trimming 4 random nucleotides from each end and filtering for minimal length (>18 nt) and sequence complexity (bbduk, entropy = 0.35, entropy window = 18, k = 4) . Reads were first aligned to Drosophila rRNA precursor sequences and the mitochondrial genome using bowtie {Langmead, 2009 #656}. Remaining unmapped reads were mapped to the OSC_r1.01 genome using bowtie allowing for 1 mismatch. Alignments were separated into uniquely and all‑mapping fractions. For visualization, HOMER was used to generate tag directories (makeTagDirectory … -format bed -keepAll -single -fragLength given) and UCSC‑compatible tracks (makeUCSCfile … -fsize 1e20 -strand +/- -fragLength given -noadj -normLength 0) were generated per strand. Counts were normalized to 1M miRNAs and final BigWig tracks were created with bedGraphToBigWig (Kent Utilities), producing strand‑specific (sense and antisense) coverage profiles for genome browser display. For transposon histogram analysis, piRNA reads longer than 23 nucleotides were aligned to transposable element consensus sequences using bowtie (--best --strata -f -v 2 -a), permitting multiple mappings. Alignments were subsequently filtered to retain reads that mapped either uniquely or at most twice to a single transposon consensus, to account for long terminal repeat (LTR) redundancy. Reads mapping twice were assigned a fractional count of 0.5 to each location.
Assembly: OSC_r1.01
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense

molecule: other

organism: Drosophila melanogaster

value: OSC

value: ovarian somatic cells

value: wildtype

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: si-armi

description:
Library name: si-armi
Sequencing of total small-RNAs after depletion of 2s rRNA


title: Male, Old, MitoQ, rep 1

description:
Library name: JL12767
Male_Old_MitoQ_1

value: Liver

value: Male

value: JL

value: Old


title: si-YB

description:
Library name: si-YB
Sequencing of total small-RNAs after depletion of 2s rRNA


title: Male, Old, Minocycline, rep 3

description:
Library name: UT08533
Male_Old_Min_3

value: UT

value: Minocycline

value: Min

value: 300 ppm

value: 22 months

value: 6 months


title: APB23

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FBWT5

value: Blood

value: peripheral blood mononuclear cells

value: FVBN

value: WTNT


title: Whole-blood RNA-seq from AD(04_011_S00_08)

value: Whole blood

value: AD


title: Whole-blood RNA-seq from AD(04_002_S00_08)


title: Whole-blood RNA-seq from AD(04_002_S02_08)


title: Whole-blood RNA-seq from HS(03K003)

value: HS


title: si-vret

description:
Library name: si-vret
Sequencing of total small-RNAs after depletion of 2s rRNA

value: OSC

value: ovarian somatic cells

value: wildtype

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: si-SoYb

description:
Library name: si-SoYb
Sequencing of total small-RNAs after depletion of 2s rRNA


title: APB24

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
39647

value: MMTV-PyMT

value: Untreated


title: Male, Old, Minocycline, rep 1

description:
Library name: JL12726
Male_Old_Min_1

value: Liver

value: Male

value: JL

value: Minocycline

value: Min

value: Old


title: APB22

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FBWT4

value: Blood

value: peripheral blood mononuclear cells

value: FVBN


title: Whole-blood RNA-seq from ACLF(032020_S01)

value: Whole blood

value: ACLF


title: Male, Old, MIF098, rep 3

description:
Library name: UT09744
Male_Old_MIF098_3

value: UT

value: 240 ppm

value: 22 months

value: 8 months


title: si-piwi

description:
Library name: si-piwi
Sequencing of total small-RNAs after depletion of 2s rRNA

value: OSC

value: ovarian somatic cells

value: wildtype

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: Male, Old, Minocycline, rep 2

description:
Library name: UM59010
Male_Old_Min_2

value: Liver

value: Male

value: UM

value: 300 ppm

value: 6 months


title: APB21

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FBWT3

value: Blood

value: peripheral blood mononuclear cells

value: WTNT


title: Whole-blood RNA-seq from ACLF(032020_S00)

value: Whole blood

value: ACLF


title: si-Yb-Rep2

description:
Library name: si-Yb-Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

extract_protocol:
sRNAseq libraries were prepared by first purifying Argonaute–sRNA complexes with TraPR resin columns. OSCs were harvested using trypsin, washed 2x with PBS and stored at -70°C after snap freezing cell-pellets in liquid nitrogen. OSCs were lysed by adding 330 µL of TraPR lysis buffer. OSC lysates were clarified, normalized to equal protein amounts (depending on the experiment 70-120 µg total protein) after Bradford measurements, applied to TraPR columns, and Argonaute-bound RNAs were eluted, followed by phenol–chloroform extraction and precipitation.
To minimize ligation bias, adapters were designed with four random nucleotides (4N) adjacent to the ligating ends. The 3′ adapter carried four random bases at its 5′ terminus (5rApp/NNNN–Adaptor–/3ddC), and the 5′ RNA adapter contained four random nucleotides at its 3′ terminus (…UCUNNNN). After 3′ adapter ligation with T4 RNA ligase 2, truncated KQ, samples were spiked with fluorescently labeled and ligation-blocked oligos as size controls and gel-purified on a 12.5% polyacrylamide–urea gel. Small RNAs were isolated using the Zymo ZR small RNA PAGE Recovery kit and subjected to 5′ adapter ligation with T4 RNA ligase 1. Following cleanup with Zymo RCC5 columns, reverse transcription was performed. Libraries were PCR-amplified with KAPA HiFi polymerase and dual-index barcoded primers to enable multiplexing at the sequencing stage. Amplification was monitored in real time with EvaGreen, and reactions were stopped upon reaching 3,500–4,000 RFU to prevent overamplification. Final libraries were size-selected on low-melt agarose gels, gel-purified (Zymo), quantified with Qubit, and sequenced (SE50, Illumina NextSeq 2000).


title: APB20

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FBWT2

value: FVBN


title: Male, Old, MIF098, rep 1

description:
Library name: JL14081
Male_Old_MIF098_1

value: JL

value: 240 ppm

value: Old

value: 22 months


title: si-Yb-Rep1

description:
Library name: si-Yb-Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

value: OSC

value: ovarian somatic cells

value: wildtype


title: Whole-blood RNA-seq from ACLF(032016_S00)


title: APB19

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
FBWT1


title: si-GFP-Rep2

description:
Library name: si-GFP-Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: APB18

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37850

value: MMTV-PyMT

value: PTX


title: Whole-blood RNA-seq from ACLF(032016_S01)


title: Male, Old, MIF098, rep 2

description:
Library name: UM68789
Male_Old_MIF098_2

value: Liver

value: Male

value: UM

value: 8 months


title: Male, Old, Leucine, rep 2

description:
Library name: UM79856
Male_Old_Leu_2

value: Leucine

value: Leu

value: 5 months


title: si-GFP-Rep1

description:
Library name: si-GFP-Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: APB17

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37849

value: Blood

value: peripheral blood mononuclear cells


title: Male, Old, Leucine, rep 3

description:
Library name: UT11101
Male_Old_Leu_3

value: UT

value: Old


title: Whole-blood RNA-seq from ACLF(032014_S01)

value: Whole blood

value: ACLF


title: CHIR-U5-8-11

city: HangZhou

first: WeiKang

last: Meng

state: ZheJiang

address: A4 Floor, Teaching Building, School of Medicine, Zijingang Campus, Zhejiang University

country: China

institute: ZheJiangUniversity

description:
Library name: sample 20
Column name in raw_counts_all_samples.csv

data_processing:
Quality control for raw reads was performed by FastQC v0.11.9
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt v4.1
The trimmed-reads were mapped to human reference genome GRCh38.99 using STAR (2.7.10a). Reads with no more than 2000 mapped loci were retained, and only the best hit was kept (--outSAMprimaryFlag AllBestScore --outSAMmultNmax 1 --outFilterMultimapNmax 2000 --winAnchorMultimapNmax 2000 --genomeLoad LoadAndKeep --limitBAMsortRAM 10000000000).
Quantification was calculated by FeatureCounts (v2.0.1) (-M, -O)
Differentially expressed genes (DEGs) and transposable elements (DE-TEs) were generated by the R package edgeR (v3.30.3)
Assembly: GRCh38 (hg38)
Supplementary files format and content: bigwig

molecule: total RNA

growth_protocol: Hesc were maintained in mTESR in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were subjected to polysome fractionation followed by TRIzol RNA extraction from pooled fractions.
RNA-seq

treatment_protocol: Cells were treated with CHIR99021 and different concentrations of Ulix inhibitor for ERK modulation in CDM2 basal media.

value: human embryo stem cell

value: WT


title: CHIR-U5-6-7

description:
Library name: sample 19
Column name in raw_counts_all_samples.csv


title: Whole-blood RNA-seq from ACLF(032014_S00)


title: CHIR-U5-4-5

description:
Library name: sample 18
Column name in raw_counts_all_samples.csv


title: APB16

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37590

value: MMTV-PyMT

value: PLX+PTX


title: Whole-blood RNA-seq from AD(031016_S00)

value: AD


title: Male, Old, Leucine, rep 1

description:
Library name: JL16357
Male_Old_Leu_1

value: Liver

value: Male

value: JL

value: 22 months


title: APB14

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37817


title: APB13

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37876


title: CHIR-U5-2-3

description:
Library name: sample 17
Column name in raw_counts_all_samples.csv


title: Whole-blood RNA-seq from HS(03_K_017_S00_09)

value: HS


title: Male, Old, Geranylgeranyl acetone, rep 1

description:
Library name: JL14095
Male_Old_GGA_1

value: Geranylgeranyl acetone

value: GGA

value: 600 ppm

value: 9 months


title: APB15

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37589

value: Blood

value: peripheral blood mononuclear cells


title: Whole-blood RNA-seq from HS(03_K_014_S00_09)

value: Whole blood


title: Whole-blood RNA-seq from HS(03_K_020_S00_09)


title: CHIR-U1_25-8-11

description:
Library name: sample 15
Column name in raw_counts_all_samples.csv

value: human embryo stem cell


title: Male, Old, Late-start 17aE2, rep 3

description:
Library name: UT09674
Male_Old_Est_20_3

value: UT

value: Late-start 17aE2

value: Old

value: 20 months


title: Male, Old, Geranylgeranyl acetone, rep 2

description:
Library name: UT09761
Male_Old_GGA_2

value: Liver


title: Male, Old, Geranylgeranyl acetone, rep 3

description:
Library name: UM68243
Male_Old_GGA_3

value: Male

value: UM


title: CHIR-U1_25-6-7

description:
Library name: sample 14
Column name in raw_counts_all_samples.csv

value: WT


title: CHIR-U5-total-RNA

description:
Library name: sample 16
Column name in raw_counts_all_samples.csv


title: Male, Old, Late-start 17aE2, rep 1

description:
Library name: UM70112
Male_Old_Est_20_1

value: 22 months


title: APB11

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37592

value: MMTV-PyMT

value: PLX+PTX


title: APB10

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37869


title: Whole-blood RNA-seq from HS(03_K_012_S00_09)

value: HS


title: CHIR-U1_25-4-5

description:
Library name: sample 13
Column name in raw_counts_all_samples.csv


title: Whole-blood RNA-seq from HS(03_K_005_S00_09)


title: Whole-blood RNA-seq from HS(03_K_004_S00_09)


title: Male, Old, Middle-start 17aE2, rep 3

description:
Library name: UT09681
Male_Old_Est_16_3

value: Middle-start 17aE2

value: 16 months


title: Whole-blood RNA-seq from pre-ACLF(03_I_001_S00_09)

value: pre-ACLF


title: CHIR-U1_25-2-3

description:
Library name: sample 12
Column name in raw_counts_all_samples.csv


title: APB12

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37582

value: Blood

value: peripheral blood mononuclear cells


title: Male, Old, Late-start 17aE2, rep 2

description:
Library name: JL13977
Male_Old_Est_20_2

value: JL


title: APB9

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37868


title: APB8

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37881


title: CHIR-U1_25-total-RNA

description:
Library name: sample 11
Column name in raw_counts_all_samples.csv

value: human embryo stem cell


title: APB7

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37847


title: Male, Old, Middle-start 17aE2, rep 1

description:
Library name: UM68390
Male_Old_Est_16_1

value: Old


title: CHIR-U0_15-8-11

description:
Library name: sample 10
Column name in raw_counts_all_samples.csv


title: Male, Old, 17-DMAG, rep 3

description:
Library name: UT08543
Male_Old_DMAG_3

value: UT

value: DMAG

value: 30 ppm

value: 6 months


title: CHIR-U0_15-6-7

description:
Library name: sample 9
Column name in raw_counts_all_samples.csv

value: WT


title: Male, Old, Middle-start 17aE2, rep 2

description:
Library name: JL14008
Male_Old_Est_16_2

value: Liver

value: Male

value: 22 months


title: APB6

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37826

value: MMTV-PyMT


title: Whole-blood RNA-seq from ACLF(022005_S00)

value: Whole blood

value: ACLF


title: Whole-blood RNA-seq from ACLF(022004_S01)


title: Male, Old, 17-DMAG, rep 1

description:
Library name: JL12639
Male_Old_DMAG_1


title: Whole-blood RNA-seq from ACLF(022005_S01)


title: APB4

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37785


title: APB5

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37759


title: CHIR-U0_15-4-5

description:
Library name: sample 8
Column name in raw_counts_all_samples.csv


title: APB3

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37588


title: Male, Old, Control, rep 24

description:
Library name: UTC19X165
Male_Old_Control_24

value: Control

value: 5 months


title: Male, Old, Control, rep 23

description:
Library name: UTC19X164
Male_Old_Control_23


title: Whole-blood RNA-seq from ACLF(022004_S00)


title: APB2

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37584

value: Blood

value: peripheral blood mononuclear cells


title: CHIR-U0_15-total-RNA

description:
Library name: sample 6
Column name in raw_counts_all_samples.csv

value: human embryo stem cell


title: Whole-blood RNA-seq from ACLF(022001_S00)


title: APB1

description:
2 x 150 protocol using a Midoutput 300 sequencing kit) with a target clustering of about 160 million clusters per run
37526


title: Male, Old, Control, rep 22

description:
Library name: UT11134
Male_Old_Control_22

value: Old


title: Whole-blood RNA-seq from ACLF(022002_S00)


title: Male, Old, 17-DMAG, rep 2

description:
Library name: UM58954
Male_Old_DMAG_2

value: UM


title: CHIR-4-5

description:
Library name: sample 3
Column name in raw_counts_all_samples.csv

value: CHIR


title: Whole-blood RNA-seq from AD(021033_S01)

value: AD


title: human Thrombosomes_2

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

description: 117624-6 Thrombosomes

data_processing:
Next Gen Sequencing was performed on Illumina NextSeq with SE75 (Single-end, 75 bp) at an approximate depth of 10-15 million reads per sample.
Sequence alignment was performed using Bowtie2 (v2.5.1; Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.) local mode alignment with default parameters.  The fastq files were mapped to the human reference genome using the Ensembl GRCh38 cDNA and non-coding RNA combined reference. Normalized read counts and differential expression were calculated for each transcript by DESeq2  (v1.16.1; Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 2014, 15:550).
Assembly: GRCh38
Supplementary files format and content: excel file includes raw counts for each sample

source_name: human freeze dried platelets (Thrombosomes)

growth_protocol: Day 1 human platelets were pelleted by low spin centrifugation and pellets frozen at -80oC. Thrombosomes were resuspended in distilled water and 1ml of the suspension was spun at low spped to collect pellets that were either frozen at -80oC till RNA extraction was performed or used for RNA extraction directly.

extract_protocol:
Platelet or Thrombosome pellets were lysed and crude RNA extracted using SBI’s spin column based RNA Purification Kit. RNA quality and quantity were checked on Bioanalyzer (Agilent) using the RNA Pico kit and assessed for presence of small RNA.
Total RNA population, starting with as little as 1 ng of total RNA, was entered into small RNA library prep using Qiagen small RNA library prep kit. Successful libraries were purified by gel extraction to ensure the correct size was isolated. Libraries were amplified by qPCR and assessed for viability by the concentration (>1 nM) to be moved on to sequencing.


title: CHIR-8-11

description:
Library name: sample 5
Column name in raw_counts_all_samples.csv


title: Male, Old, Control, rep 21

description:
Library name: UT11012
Male_Old_Control_21

value: UT


title: CHIR-U0_15-2-3

description:
Library name: sample 7
Column name in raw_counts_all_samples.csv

value: WT


title: Whole-blood RNA-seq from AD(021033_S00)


title: CHIR-6-7

description:
Library name: sample 4
Column name in raw_counts_all_samples.csv


title: Male, Old, Control, rep 20

description:
Library name: UT09711
Male_Old_Control_20

value: Liver

value: 9 months


title: human Platelet

description: 117624-1 PLT

source_name: human fresh apheresis platelets

value: human fresh apheresis platelets


title: Male, Old, Control, rep 19

description:
Library name: UT09710
Male_Old_Control_19

value: Male

value: 22 months


title: human Thrombosomes_1

description: 117624-5 Thrombosomes

value: human freeze dried platelets (Thrombosomes)


title: CHIR-total-RNA

description:
Library name: sample 1
Column name in raw_counts_all_samples.csv


title: Whole-blood RNA-seq from AD(021020_S00)

value: Whole blood


title: LP10012

first: Reinhard

last: Gruber

address: Sensengasse 2a

institute: Medical University Vienna

description:
Library name: Sample12
Column name in raw_counts_All_Samples.tsv: LP10012

data_processing:
Reads in FASTQ format were generated using the Illumina bcl2fastq command-line tool (v2.19.1.403) and the Lexogen idemux tool for optimal demultiplexing of long, unique, dual indices. Libraries were amplified using 15 PCR cycles. The quality was assessed using a Bioanalyzer 2100 with a High Sensitivity DNA Kit (Agilent Technologies, Santa Clara, CA), and concentrations were measured using the Qubit dsDNA HS Assay (Invitrogen, Waltham, MA). Pooled libraries were sequenced on a P2 flow cell using a NextSeq 2000 platform (Illumina, San Diego, CA) in 1 × 75 bp single-end mode, generating approximately 7 million reads per sample. FASTQ files were generated using bcl2fastq (v2.19.1.403) and demultiplexed with the Lexogen Idemux tool. Reads were trimmed using cutadapt (v2.8) to remove poly(A) tails, discard reads containing ambiguous bases, and trim bases with Phred quality scores < 30, resulting in approximately 5 million reads per sample after processing. Reads were aligned to the human reference genome GRCh38 with GENCODE v29 annotations using STAR (v2.6.1a) in two-pass mode. Gene-level read counts were generated by STAR, and differential expression analysis was performed using DESeq2 (v1.22.2).
Assembly: Reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using STAR aligner version 2.6.1a in 2-pass mode
Supplementary files format and content: raw_counts_All_Samples.tsv contains a matrix with raw gene counts, gene symbols, and gene types for each sample.

source_name: human gingiva

growth_protocol: Gingival fibroblasts were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Sigma-Aldrich, St. Louis, MO, USA) containing penicillin, streptomycin (Sigma Aldrich, St. Louis, MO), and 10% fetal bovine serum (Bio&Sell GmbH, Nuremberg, Germany).

extract_protocol:
Total RNA was extracted using the GeneMATRIX Universal RNA Purification Kit (EURX, Gdańsk, Poland) with rDNase set (Macherer-Nagel, Düren, Germany ).
Sequencing libraries from total RNA were prepared at the Core Facility Genomics, Medical University of Vienna, using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD (protocol v2) with unique dual indices (Lexogen GmbH, Vienna, Austria). Libraries were amplified using 15 PCR cycles.

treatment_protocol: Low-passage gingival fibroblasts were seeded at 1 × 10⁵ cells/mL and treated with either 5.0% Listerine® or a combination of IL-1β and TNF-α as a positive inflammatory control. Following a 3-hour incubation (37 °C, 5% CO2, and 95% humidity), total RNA was isolated for analysis.

value: human gingiva

value: gingival fibroblast

value: treated with 5% Listerine®


title: Male, Old, Control, rep 18

description:
Library name: UT08488
Male_Old_Control_18

value: Control

value: 7 months


title: LP10011

description:
Library name: Sample11
Column name in raw_counts_All_Samples.tsv: LP10011

value: treated with 5% Listerine® + IL-1β + TNF-α


title: Male, Old, Control, rep 17

description:
Library name: UT08486
Male_Old_Control_17

value: Old


title: KG-1A, Decitabine, 2Day, rep2

city: Duarte

first: Hung-Ping

last: Shih

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

description:
Library name: Sample 4
hsa_4_Deci_plus_KG1A

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 with a single read mode of 51 cycles. HiSeq Real-Time Analysis (RTA) 2.2.38 software was used to process the image analysis.
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone Marrow

growth_protocol: KG-1A cells (ATCC, CCL-246.1) were cultured in Iscove's Modified Dulbecco's Media (IMDM) medium containing 10% FBS

extract_protocol:
RNA was extracted from KG-1A cells by using the Rneasey Mini Kit (QIAGEN, 74104)
RNA sequencing libraries were prepared with the Kapa mRNA HyperPrep Kit (Kapa Biosystems, KR1352) according to the manufacturer's protocol, and the final libraries were validated using the Agilent Bioanalyzer DNA High Sensitivity Kit (Agilent, 5067-4626) and quantified with a Qubit Fluorometer (Thermo Fisher)

treatment_protocol: KG-1A cells were treated with Decitabine (100nM) or DMSO for 2 day

value: Bone Marrow

value: promyeloblast, macrophage

value: Decitabine (100 nM), 2 Day


title: Whole-blood RNA-seq from AD(021014_S00)

value: AD


title: Whole-blood RNA-seq from AD(021020_S01)


title: Whole-blood RNA-seq from AD(021002_S00)


title: KG-1A, DMSO, 2Day, rep2

description:
Library name: Sample 2
hsa_2_DMSO_plus_KG1A

value: WT

value: DMSO, 2 Day


title: KG-1A, DMSO, 2Day, rep1

description:
Library name: Sample 1
hsa_1_DMSO_plus_KG1A


title: Male, Old, Control, rep 15

description:
Library name: UM78498
Male_Old_Control_15

value: Liver

value: Male

value: UM

value: 5 months


title: Whole-blood RNA-seq from AD(02_I_056_S00_09)

value: Whole blood


title: Male, Old, Control, rep 16

description:
Library name: UM78505
Male_Old_Control_16

value: 22 months


title: hESC (H1), N2B27, 48h, [Re-Mix1_204055]

data_processing:
Quality control for raw reads was performed by FastQC v0.11.9
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt v4.1
The trimmed-reads were mapped to human reference genome GRCh38.99 using STAR (2.7.10a). Reads with no more than 2000 mapped loci were retained, and only the best hit was kept (--outSAMprimaryFlag AllBestScore --outSAMmultNmax 1 --outFilterMultimapNmax 2000 --winAnchorMultimapNmax 2000 --genomeLoad LoadAndKeep --limitBAMsortRAM 10000000000).
Quantification was calculated by FeatureCounts (v2.0.1) (-M, -O)
Differentially expressed genes (DEGs) and transposable elements (DE-TEs) were generated by the R package edgeR (v3.30.3)
Assembly: GRCh38 (hg38)
Supplementary files format and content: row_counts.txt

source_name: human embryo

growth_protocol: hESC were matained in 50% DMEM:F12 and 50% Neurobasal supplemented with 1% N2 ,2% B27, 1% L-glutamine, 1% NEAA,  0.18% 2-Mercaptoethanol,  50ug/mL BSA (N2B27) in humidfied atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using AccuraCode HTP OneStep RNAseq Kit (1071065) to carry out adaptor ligation and prepare RNAseq libraries
RNA libraries for RNA-seq were prepared using AccuraCode HTP OneStep RNAseq Kit following manufacture's protocols.

treatment_protocol: hESC in N2B27 media was induced by different combination of CHIR and other individual growth factor until 48h.

value: human embryo

value: hESC (H1)

value: human embryonic stem cell

value: growth factor induction


title: LP10009

description:
Library name: Sample9
Column name in raw_counts_All_Samples.tsv: LP10009

value: human gingiva

value: gingival fibroblast

value: untreated


title: LP10008

description:
Library name: Sample8
Column name in raw_counts_All_Samples.tsv: LP10008

value: treated with 5% Listerine®


title: Whole-blood RNA-seq from pre-ACLF(02_I_048_S00_09)

value: pre-ACLF


title: Whole-blood RNA-seq from AD(02_I_055_S00_09)

value: AD


title: KG-1A, Decitabine, 2Day, rep1

description:
Library name: Sample 3
hsa_3_Deci_plus_KG1A

value: Bone Marrow

value: promyeloblast, macrophage

value: WT

value: Decitabine (100 nM), 2 Day


title: Male, Old, Control, rep 14

description:
Library name: UM70357
Male_Old_Control_14

value: Liver

value: Male

value: UM

value: Control

value: Old

value: 9 months


title: LP10010

description:
Library name: Sample10
Column name in raw_counts_All_Samples.tsv: LP10010

value: treated with IL-1β + TNF-α


title: Male, Old, Control, rep 13

description:
Library name: UM70133
Male_Old_Control_13

value: 22 months

value: 7 months


title: Whole-blood RNA-seq from AD(02_I_042_S00_09)

value: Whole blood


title: LP10006

description:
Library name: Sample6
Column name in raw_counts_All_Samples.tsv: LP10006

value: human gingiva

value: gingival fibroblast


title: hESC (H1), mixed-sample [Re-Mix4_204025]

value: human embryo

value: hESC (H1)

value: human embryonic stem cell

value: growth factor induction


title: Male, Old, Control, rep 12

description:
Library name: UM69811
Male_Old_Control_12


title: LP10007

description:
Library name: Sample7
Column name in raw_counts_All_Samples.tsv: LP10007

value: treated with 5% Listerine® + IL-1β + TNF-α


title: PRC2cKO_CT_P6NGO_H2AK119ub_rep2

city: Davis

first: Satoshi

last: Namekawa

address: One Shields Avenue

institute: UC Davis

description: Library name: Sample 32

data_processing:
For CUT&Tag data processing, we basically followed the online tutorial posted by Henikoff Lab (https://protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-bjk2kkye.html).
Raw paired-end reads were trimmed by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.10)
Trimmed reads were aligned with the mouse genome (GRCm38/mm10) using Bowtie2 83 (version 2.4.5) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. D. melanogaster DNA delivered by Drosophila S2 cells was used as spike-in DNA for CUT&Tag. For mapping D. melanogaster spike-in fragments, we also use the --no-overlap --no-dovetail options to avoid cross-mapping. PCR duplicates from all mapped bam files were removed using the ‘MarkDuplicates’ command in Picard tools (version 3.0.0) (https://broadinstitute.github.io/picard/ ).
To compare replicates, Pearson correlation coefficients were calculated and plotted by ‘multiBamSummary bins’ and ‘plot correlation’ commands from deepTools 84 (version 3.5.5). Biological replicates were pooled using the ‘merge’ command in samtools for visualization and other analyses after confirming reproducibility (Pearson correlation coefficient > 0.85). Spike-in normalization was implemented using the exogenous scaling factor computed from the dm6 mapping files (scale factors = 10,000 / aligned spike-in reads).
Spike-in normalized genome coverage tracks with 1 bp resolution in BigWig format were generated using ‘bamCoverage’ from deepTools with the parameters ‘--binSize 1 --extendReads --samFlagInclude 64 --normalizeUsing RPKM --scaleFactor $scale_factor’. Track views were visualized and exported from Integrative Genomics Viewer 85 (version 2.14.1).
Assembly: mm10
Supplementary files format and content: bigWig, spike-in normalized tracks
Supplementary files format and content: bed, peaks
Library strategy: CUT&Tag

source_name: ovary

extract_protocol:
CUT&Tag libraries of oocytes were prepared as previously described32,33 with some modifications (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3 ) using CUTANA™ pAG-Tn5 (Epicypher, 15-1017). To perform quantitative spike-in CUT&Tag, Drosophila S2 cells were added to mouse oocytes at a fixed ratio (e.g. 2000 S2 cells to 1000 mouse oocytes) at the beginning of each reaction.
CUT&Tag libraries were prepared using NEBNext HiFi 2x PCR Master mix (NEB, M0541L) according to the protocol (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3 ).

value: ovary

value: primary cells

value: P6 non-growing oocytes

value: EedF/-; Ddx4-Cre

tag: antibody

tag: reads length


title: Whole-blood RNA-seq from AD(02_I_040_S00_09)

tag: tissue

value: AD


title: PRC2cKO_CT_P6NGO_H2AK119ub_rep1

description: Library name: Sample 31


title: Male, Old, Control, rep 11

description:
Library name: UM69804
Male_Old_Control_11

value: Liver

tag: strain

tag: Sex

value: Male

value: UM

value: Control

value: Old


title: Whole-blood RNA-seq from ACLF(022002_S01)

value: Whole blood

value: ACLF


title: Male, Old, Control, rep 10

description:
Library name: UM69643
Male_Old_Control_10

tag: cohort

tag: site

value: 22 months

value: 9 months


title: Whole-blood RNA-seq from pre-ACLF(02_I_028_S00_09)

value: pre-ACLF


title: LP10004

description:
Library name: Sample4
Column name in raw_counts_All_Samples.tsv: LP10004

value: human gingiva

value: gingival fibroblast

tag: treatment

value: treated with 5% Listerine®


title: PRC2ctrl_CT_P6NGO_H2AK119ub_rep2

description: Library name: Sample 30

value: ovary

value: primary cells

value: EedF/+; Ddx4-Cre


title: LP10003

description:
Library name: Sample3
Column name in raw_counts_All_Samples.tsv: LP10003

value: treated with 5% Listerine® + IL-1β + TNF-α


title: Whole-blood RNA-seq from pre-ACLF(02_I_027_S00_09)


title: PRC2ctrl_CT_P6NGO_H2AK119ub_rep1

description: Library name: Sample 29

value: P6 non-growing oocytes


title: Male, Old, Control, rep 9

description:
Library name: UM68509
Male_Old_Control_9

value: Liver

value: Male

tag: treatment abbreviation

tag: dose

value: 6 months


title: Male, Old, Control, rep 8

description:
Library name: UM60473
Male_Old_Control_8

value: UM

value: Control

tag: age group

value: Old

tag: age

value: 7 months


title: CHIR-2-3

description:
Library name: sample 2
Column name in raw_counts_all_samples.csv

value: human embryo stem cell

value: WT

value: CHIR


title: LP10005

description:
Library name: Sample5
Column name in raw_counts_All_Samples.tsv: LP10005

value: human gingiva

value: gingival fibroblast

value: untreated


title: PRC2cKO_CT_P6NGO_H3K27me3_rep2

description: Library name: Sample 28

value: ovary

value: primary cells

value: EedF/-; Ddx4-Cre


title: LP10002

description:
Library name: Sample2
Column name in raw_counts_All_Samples.tsv: LP10002

value: treated with IL-1β + TNF-α


title: Whole-blood RNA-seq from AD(02_I_022_S00_09)

value: Whole blood

value: AD


title: LP10001

description:
Library name: Sample1
Column name in raw_counts_All_Samples.tsv: LP10001


title: Whole-blood RNA-seq from pre-ACLF(02_I_027_A00_09)

value: pre-ACLF


title: Male, Old, Control, rep 7

description:
Library name: UM60438
Male_Old_Control_7

value: Liver

value: Male

value: UM

value: 22 months

tag: age at_start_of_treatment

tag: replicate


title: 643/P/21

city: New Delhi

first: Anuradha

last: Chowdhary

state: Delhi

address: M6R5+7X4 University of Delhi, Vijay Nagar Marg, Art Faculty, University Enclave

department: Medical Mycology

country: India

institute: Vallabhbhai Patel Chest Institute

description: Library name: 1521

data_processing:
The raw FASTQ reads were quality controlled and aligned to the reference strain of MYA-3404 using  HISAT2 with default settings. The mapped transcripts read counts were quantified using FeatureCounts. Differentially expressed genes were analyzed using DESeq2. Genes with false discovery rate (FDR) ≤0.05 and absolute log2 fold changes ≥0.585 (1.5-fold change) were called differentially expressed genes for each comparison.
Assembly: Candida tropicalis MYA-3404 (GCF_000006335.3)
Supplementary files format and content: tab-delimited text file includes differential expression data

organism: Candida tropicalis

source_name: Candida tropicalis isolate

growth_protocol: Candida tropicalis 17-h cultures were inoculated into YPD (OD 600 of 0.1) broth and incubated at 37°C for three h until the logarithmic growth phase was achieved.

extract_protocol:
RNA was extracted using Maxwell® RSC Plant RNA Kit (Promega, Madison, Wisconsin, USA) as recommended by the manufacturer.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA library preparation kit (New England Biolabs, Ipswich, MA, USA).

tag: cell type

value: Candida tropicalis isolate

value: Fluconazole Susceptible


title: PRC2cKO_CT_P6NGO_H3K27me3_rep1

description: Library name: Sample 27

tag: cell line

value: P6 non-growing oocytes

tag: genotype


title: Male, Old, Control, rep 6

description:
Library name: JL16272
Male_Old_Control_6

value: JL

value: Control

value: Old

value: 5 months


title: Whole-blood RNA-seq from AD(011017_S01)

tag: time


title: Whole-blood RNA-seq from AD(011017_S00)


title: 311/P/20

description: Library name: 1511

value: Fluconazole Resistant


title: PRC2ctrl_CT_P6NGO_H3K27me3_rep1

description: Library name: Sample 25

value: ovary

value: primary cells

value: EedF/+; Ddx4-Cre

tag: antibody

tag: reads length


title: Male, Old, Control, rep 5

description:
Library name: JL16270
Male_Old_Control_5

tag: tissue

tag: strain


title: Whole-blood RNA-seq from AD(011011_S00)

value: Whole blood

value: AD


title: Male, Old, Control, rep 4

description:
Library name: JL14027
Male_Old_Control_4

value: Liver

tag: Sex

tag: cohort

value: 9 months


title: Whole-blood RNA-seq from ACLF(01020_S00)

value: ACLF


title: PRC2ctrl_CT_P6NGO_H3K27me3_rep2

description: Library name: Sample 26


title: E. coli + riboflavin, biol rep 2

city: Baltimore

first: Franck

last: Housseau

state: MD

address: 1651 E.Jefferson St

institute: Johns Hopkins University School of Medicine

description:
Library name: A17
A17

data_processing:
Raw data (raw reads) in FASTQ format were first processed using fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapters, reads containing poly-N, and low-quality reads from the raw data. At the same time, Q20, Q30, and GC content of the clean data were calculated. All downstream analyses were based on the high-quality clean data. Reference genome and gene model annotation files were downloaded directly from the genome website. An 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. Hisat2 was selected as the mapping tool because it can generate a database of splice junctions based on the gene model annotation file, thereby producing better mapping results than other non-splice mapping tools. featureCounts v1.5.0-p3 was used to count the number of reads mapped to each gene, and FPKM for each gene was calculated based on gene length and the number of reads mapped to that gene. FPKM, or expected number of fragments per kilobase of transcript sequence per million base pairs sequenced, considers the effects of sequencing depth and gene length simultaneously and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCh38.p12
Supplementary files format and content: xls file containing FPKM values for all samples
Supplementary files format and content: xls file containing gene counts for all samples

source_name: cell line

growth_protocol: U266 cells were cultured in RPMI media with 10% HI FBS

extract_protocol:
Qiagen Rneasy kit was used to extract RNA
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: 600k Cells were treated overnight with 5-A-RU (6.25 uM) or 125 MOI of fixed E.fecalis or fixed E.coli

value: cell line

value: Myeloma cell line

value: WT

tag: treatment

value: E.coli + 5-A-RU, overnight


title: PRC1cKO_CT_P6NGO_H3K27me3_rep1

description: Library name: Sample 19

value: P6 non-growing oocytes

value: Ring1-/-; Ring1F/-; Ddx4-Cre


title: PRC1cKO_CT_P6NGO_H3K27me3_rep2

description: Library name: Sample 20


title: E. coli + riboflavin, biol rep 1

description:
Library name: A16
A16


title: E. coli, biol rep 3

description:
Library name: A15
A15

value: E.coli (DHFa) 125 MOI, overnight


title: PRC1ctrl_CT_P6NGO_H3K27me3_rep2

description: Library name: Sample 18

value: Ring1-/-; Rnf2F/+; Ddx4-Cre


title: E. coli + riboflavin, biol rep 3

description:
Library name: A18
A18


title: E. coli, biol rep 2

description:
Library name: A14
A14


title: Male, Old, Candesartan Cilexetil, rep 3

description:
Library name: UM68369
Male_Old_CC_3

value: Male

tag: site

value: UM

value: Candesartan Cilexetil

tag: treatment abbreviation

value: CC

value: 30 ppm

value: Old

value: 22 months

value: 8 months


title: Male, Old, Control, rep 2

description:
Library name: JL12725
Male_Old_Control_2

value: Liver

value: JL

value: Control

tag: dose

tag: age group

value: 7 months


title: PRC1ctrl_CT_P6NGO_H3K27me3_rep1

description: Library name: Sample 17

value: ovary

value: primary cells


title: Whole-blood RNA-seq from ACLF(01020_A01)

value: Whole blood

value: ACLF


title: Male, Old, Control, rep 1

description:
Library name: JL12700
Male_Old_Control_1

tag: age

tag: age at_start_of_treatment


title: Whole-blood RNA-seq from AD(01_I_007_S00_09)

value: AD


title: Whole-blood RNA-seq from ACLF(01015_A01)


title: WT_CT_P7GO_H3K27me3_rep2

description: Library name: Sample 16

tag: cell type

value: P7 growing oocytes

value: WT


title: Male, Old, Candesartan Cilexetil, rep 2

description:
Library name: JL14023
Male_Old_CC_2

value: Male

value: Candesartan Cilexetil

tag: replicate


title: E. coli, biol rep 1

description:
Library name: A13
A13

value: cell line

tag: cell line

value: Myeloma cell line

tag: genotype

value: E.coli (DHFa) 125 MOI, overnight


title: WT_CT_P7GO_H3K27me3_rep1

description: Library name: Sample 15

tag: antibody


title: Male, Old, Control, rep 3

description:
Library name: JL14026
Male_Old_Control_3

value: Old

value: 22 months

value: 9 months


title: Whole-blood RNA-seq from ACLF(01015_S00)

tag: time


title: E. fecalis + riboflavin, biol rep 3

description:
Library name: A12
A12

tag: tissue

value: E.fecalis + 5-A-RU, overnight


title: Male, Old, Candesartan Cilexetil, rep 1

description:
Library name: UT09777
Male_Old_CC_1

value: Liver

tag: strain

value: UT

value: CC

value: 30 ppm

value: 8 months


title: WT_CT_P6NGO_H3K27me3_rep2

description: Library name: Sample 14

value: ovary

value: primary cells

value: P6 non-growing oocytes

tag: reads length


title: E. fecalis + riboflavin, biol rep 2

description:
Library name: A11
A11

value: WT


title: 03-235_C1D1

type: protein

hyb_protocol: 25 uL of each sample combined with 50 uL of capture beads and 25 uL of universal assay buffer were incubated with shaking at room temperature for 2 hours. 25 uL Detection Antibody Mix was added to each sample and incubated with shaking at room temperature for 30 min. 50 uL of Streptavidin-PE was added to each sample and incubated with shaking at room temperature for 30 minutes. 120 uL of wash buffer was added and shaken at room temperature for 5 minutes. Values read on xMAP Multi-Analyte Profiling system.

scan_protocol: follow manufacture sample preparation protocol and scan on xMAP system

data_processing:
Proteins in the raw.txt file with expression less than the lower limit of detection were assigned to the lower limit of detection and saved as clean.txt (included in the sample data table)
Changes in concentration between time-points for each sampleID in clean.txt were calculated as log2(time2/time1) and saved in processed.txt, Where time2 is either C1D1, C2D1, or C4D1; time1 is Screen from characteristics: Timepoint

label: RPE

molecule: protein

source_name: blood plasma

label_protocol: use antigen-specific detection antibodies bind to antigens, RPE fluorescence identifies the antibodies

extract_protocol: Human blood samples were collected with EDTA tubes. Plasma was separated from buffy coats by centrifugation for 15 min at 2000 rpm at 4 deg C with brake off. Supernatant transferred into separate 1.8 mL cryovials until all plasma was removed. Samples stored at -80 deg C.

value: primary breast cancer

tag: timepoint

tag: sourceID

tag: outcome

value: discretion

tag: outcome type

value: toxicity

tag: best clinical response

value: SD

tag: survival


title: Male, Old, Captopril, rep 3

description:
Library name: UT11143
Male_Old_Capt_3

tag: Sex

value: Male

tag: cohort

tag: site

tag: treatment

value: Captopril

tag: treatment abbreviation

value: Capt

tag: dose

value: 180 ppm

tag: age group

value: Old

tag: age

value: 23 months

value: 5 months


title: Male, Old, Captopril, rep 2

description:
Library name: UM79394
Male_Old_Capt_2

tag: tissue

value: Liver

value: UM

tag: age at_start_of_treatment

tag: replicate


title: WT_CT_P6NGO_H3K27me3_rep1

description: Library name: Sample 13

value: ovary

tag: cell line

tag: cell type

tag: genotype

tag: antibody

tag: reads length


title: E. fecalis + riboflavin, biol rep 1

description:
Library name: A10
A10

value: cell line

value: Myeloma cell line

value: E.fecalis + 5-A-RU, overnight


title: WT_CT_P1O_H3K27me3_rep2

description: Library name: Sample 12

value: primary cells

value: P1 oocytes

value: WT


title: 01-234_C1D1

value: primary breast cancer

tag: timepoint

tag: sourceID

tag: outcome

value: radiographic

tag: outcome type

value: progression

tag: best clinical response

value: PD

tag: survival


title: E.fecalis, biol rep 3

description:
Library name: A9
A9

tag: treatment

value: E.fecalis 125 MOI, overnight


title: 03-235_Screen

value: Screen

value: discretion

value: toxicity

value: SD


title: WT_CT_P1O_H3K27me3_rep1

description: Library name: Sample 11


title: E.fecalis, biol rep 2

description:
Library name: A8
A8


title: Male, Old, Canagliflozin, rep 7

description:
Library name: UT09707
Male_Old_Cana_7

value: Liver

tag: strain

tag: Sex

value: Male

tag: cohort

tag: site

value: UT

value: Canagliflozin

tag: treatment abbreviation

value: Cana

tag: dose

value: 180 ppm

tag: age group

value: Old

value: 22 months

value: 7 months


title: Male, Old, Captopril, rep 1

description:
Library name: JL16318
Male_Old_Capt_1

tag: tissue

value: JL

value: Captopril

value: Capt

tag: age

value: 23 months

tag: age at_start_of_treatment

value: 5 months

tag: replicate


title: 01-234_Screen

value: primary breast cancer

tag: timepoint

value: Screen

tag: sourceID

value: radiographic

value: progression

value: PD


title: E.fecalis, biol rep 1

description:
Library name: A7
A7

value: cell line

tag: cell line

tag: cell type

value: Myeloma cell line

tag: genotype

value: WT

value: E.fecalis 125 MOI, overnight


title: WT_CT_E18O_H3K27me3_rep1

description: Library name: Sample 9

value: ovary

value: primary cells

value: E18.5 oocytes

tag: antibody

tag: reads length


title: 01-239_C2D1

tag: outcome

tag: outcome type

tag: best clinical response

tag: survival


title: WT_CT_E18O_H3K27me3_rep2

description: Library name: Sample 10


title: 01-239_C1D1


title: Male, Old, Canagliflozin, rep 5

description:
Library name: UM69629
Male_Old_Cana_5

value: Liver

tag: strain

tag: Sex

value: Male

tag: cohort

tag: site

value: UM

tag: treatment

value: Canagliflozin

tag: treatment abbreviation

value: Cana

tag: dose

value: 180 ppm

value: Old

value: 22 months

value: 7 months


title: Riboflavin, biol rep 3

description:
Library name: A6
A6

tag: tissue

value: 5-A-RU (6.25 uM), overnight


title: WT_CT_P7GO_H2AK119ub_rep2

description: Library name: Sample 8

tag: cell line

value: P7 growing oocytes


title: Riboflavin, biol rep 2

description:
Library name: A5
A5

value: cell line

tag: cell type

value: Myeloma cell line


title: Male, Old, Canagliflozin, rep 4

description:
Library name: UM69622
Male_Old_Cana_4

tag: age group

tag: age

tag: age at_start_of_treatment

tag: replicate


title: Riboflavin, biol rep 1

description:
Library name: A4
A4

tag: genotype

value: WT


title: 01-239_Screen

value: primary breast cancer

tag: timepoint

value: Screen

tag: sourceID

tag: outcome

value: radiographic

tag: outcome type

value: progression

tag: best clinical response

value: PD


title: WT_CT_P7GO_H2AK119ub_rep1

description: Library name: Sample 7

value: ovary

value: primary cells

tag: antibody

tag: reads length


title: Male, Old, Canagliflozin, rep 6

description:
Library name: UM69951
Male_Old_Cana_6

value: Liver

tag: strain

tag: Sex

value: Male

tag: cohort

tag: site

value: UM

tag: treatment

value: Canagliflozin

tag: treatment abbreviation

value: Cana


title: 01-237_C2D1

tag: tissue

tag: survival


title: WT_CT_P6NGO_H2AK119ub_rep2

description: Library name: Sample 6

tag: cell line

tag: cell type

value: P6 non-growing oocytes


title: Male, Old, Canagliflozin, rep 3

description:
Library name: UM69062
Male_Old_Cana_3

tag: dose

value: 180 ppm

tag: age group

value: Old

tag: age

value: 22 months

tag: age at_start_of_treatment

value: 7 months

tag: replicate


title: no antigen, biol rep3

description:
Library name: A3
A3

value: cell line

value: Myeloma cell line

tag: genotype

value: WT

value: No antigen


title: Male, Old, Canagliflozin, rep 2

description:
Library name: UM69055
Male_Old_Cana_2


title: 01-237_Screen

value: primary breast cancer

tag: timepoint

value: Screen

tag: sourceID

tag: outcome

value: radiographic

tag: outcome type

value: progression

tag: best clinical response

value: PD


title: WT_CT_P6NGO_H2AK119ub_rep1

description: Library name: Sample 5

value: ovary

value: primary cells

tag: antibody

tag: reads length


title: no antigen, biol rep2

description:
Library name: A2
A2

tag: tissue

tag: treatment


title: Male, Old, Canagliflozin, rep 1

description:
Library name: JL14046
Male_Old_Cana_1

value: Liver

tag: strain

tag: Sex

value: Male

tag: cohort

tag: site

value: JL

value: Canagliflozin

tag: treatment abbreviation

value: Cana


title: 01-237_C1D1

tag: survival


title: 01-236_C2D1


title: Male, Old, bGPA, rep 3

description:
Library name: UT08493
Male_Old_bGPA_3

value: UT

value: bGPA

tag: dose

tag: age group

value: Old

tag: age

value: 22 months

tag: age at_start_of_treatment

value: 6 months

tag: replicate


title: WT_CT_P1O_H2AK119ub_rep1

description: Library name: Sample 3

tag: cell line

tag: cell type

value: P1 oocytes

tag: genotype

value: WT


title: no antigen, biol rep1

description:
Library name: A1
A1

value: cell line

value: Myeloma cell line

value: No antigen


title: WT_CT_P1O_H2AK119ub_rep2

description: Library name: Sample 4

value: ovary

tag: antibody

tag: reads length


title: 01-236_C1D1

tag: tissue

value: primary breast cancer

tag: timepoint

tag: sourceID

tag: outcome

value: radiographic

tag: outcome type

value: progression

tag: best clinical response

value: PD


title: A549 SA 1249-5p_3

city: León

first: Pablo

last: Castañera

address: Cjón. Campus Vegazana, s/n

institute: Universidad de León

description: Library name: A_SA_1249_3

data_processing:
Raw RNA-seq reads were aligned to the Homo sapiens reference genome using STAR. Gene-level count matrices were generated with featureCounts. Normalization and differential gene expression analyses were performed in R using DESeq2, and variance-stabilized counts were obtained using the variance-stabilizing transformation (VST). Functional enrichment analyses were carried out using Gene Ontology and Reactome databases, and weighted gene co-expression network analysis (WGCNA) was performed to identify gene modules associated with experimental conditions.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: pumlmonary epithelium

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA concentration and purity were assessed using a NanoDrop One/OneC spectrophotometer (Thermo Fisher Scientific) prior to RNA sequencing.
Messenger RNA (mRNA) was isolated from total RNA using oligo(dT)-conjugated magnetic beads. Following fragmentation, first-strand cDNA synthesis was performed using random hexamer primers. Second-strand synthesis incorporated dUTP to generate strand-specific (directional) libraries. Libraries were prepared through end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification, including a USER enzyme digestion step prior to amplification for strand specificity. Library concentration was measured using a Qubit fluorometer, and library quality and fragment size distribution were assessed using a Bioanalyzer. Libraries were pooled equimolarly and sequenced on an Illumina platform

value: pumlmonary epithelium

tag: treatment


title: A549 SA 1249-5p_2

description: Library name: A_SA_1249_2


title: Male, Old, bGPA, rep 2

description:
Library name: UM59129
Male_Old_bGPA_2

value: Liver

tag: strain

tag: Sex

value: Male

tag: cohort

tag: site

value: UM

tag: treatment abbreviation

tag: dose


title: A549 SA 1249-5p_1

description: Library name: A_SA_1249_1

tag: cell line


title: WT_CT_E18O_H2AK119ub_rep2

description: Library name: Sample 2

value: primary cells

tag: cell type

value: E18.5 oocytes

tag: genotype


title: WT_CT_E18O_H2AK119ub_rep1

description: Library name: Sample 1

tag: antibody

tag: reads length


title: 01-233_C2D1

tag: tissue

tag: timepoint

value: rash

value: toxicity

value: SD

tag: survival


title: RNAseq_PRC2cKO_P7GO_rep2

data_processing:
Raw RNA-seq reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.10) with the parameter ‘--paired’
Trimmed reads were aligned to the mouse (GRCm38/mm10) genome using HISAT2 77 (version 2.2.1) with default parameters. All unmapped reads, non-uniquely mapped reads, and reads with low mapping quality (MAPQ < 30) were filtered out by samtools 78 (version 1.16.1) with the parameter '-q 30' before being subjected to downstream analyses.
Raw read counts for each gene were generated using the featureCounts79 part of the Subread package (version 2.0.3) based on mouse gene annotations (gencode.vM25.annotation.gtf, GRCm38/mm10).
DESeq280 (version 1.44.0) was used for differential gene expression analyses with cutoffs FoldChange > 1.5  and Padj values < 0.05.
The TPM values of each gene were generated using RSEM (version 1.3.3).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN, Cat # 74034) according to the manufacturer's instructions.
Library preparation was performed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB, E6420S) according to the manufacturer’s instructions.  Prepared RNA-seq libraries were sequenced on the HiSeq 4000 system (Illumina) with paired-ended 150-bp reads.

value: P7 growing oocytes

value: EedF/-; Ddx4-Cre


title: A549 SA 147a_3

description: Library name: A_SA_147a_3


title: 01-233_C1D1

tag: sourceID

tag: outcome

tag: outcome type


title: 01-233_Screen

value: Screen

tag: best clinical response


title: Male, Old, 1,3-butanediol, rep 3

description:
Library name: UT11032
Male_Old_BD_3

tag: strain

tag: Sex

value: UT

tag: treatment

value: BD

tag: age group

value: Old

tag: age

value: 22 months

tag: age at_start_of_treatment

value: 6 months

tag: replicate


title: Male, Old, bGPA, rep 1

description:
Library name: JL12769
Male_Old_bGPA_1

tag: cohort

tag: site

value: JL

value: bGPA

tag: treatment abbreviation

tag: dose


title: Male, Old, 1,3-butanediol, rep 1

description:
Library name: JL16277
Male_Old_BD_1

tag: tissue

value: Liver

value: Male


title: RNAseq_PRC2ctrl_P7GO_rep2

value: ovary

tag: cell line

value: primary cells

tag: cell type

tag: genotype

value: EedF/+; Ddx4-Cre

tag: reads length


title: Male, Old, 1,3-butanediol, rep 2

description:
Library name: UM78617
Male_Old_BD_2

value: UM


title: RNAseq_PRC2cKO_P7GO_rep1


title: 01-236_Screen

value: primary breast cancer

tag: timepoint

tag: sourceID

tag: outcome

value: radiographic

tag: outcome type

value: progression

tag: best clinical response

value: PD

tag: survival


title: Female, Young, Control, rep 6

description:
Library name: JLFemale2
Female_Young_Control_6

tag: strain

tag: Sex

value: Female

tag: treatment

value: Control

tag: age group

value: Young

tag: age

value: 5 months

tag: age at_start_of_treatment


title: A549 SA 147a_2

description: Library name: A_SA_147a_2

tag: tissue

value: pumlmonary epithelium


title: 03-232_C2D1


title: 03-232_C1D1


title: A549 SA 4430_3

description: Library name: A_SA_4430_3

tag: cell line


title: RNAseq_PRC2ctrl_P7GO_rep1

tag: cell type

value: P7 growing oocytes


title: 03-232_Screen

value: Screen


title: A549 SA 147a_1

description: Library name: A_SA_147a_1


title: Female, Young, Control, rep 5

description:
Library name: JLFemale1
Female_Young_Control_5

value: Liver

tag: cohort

tag: site

value: JL

tag: treatment abbreviation

tag: dose

tag: replicate


title: 02-231_C2D1

tag: timepoint

tag: sourceID

tag: outcome

value: fatigue

tag: outcome type

value: toxicity

value: SD


title: RNAseq_PRC2cKO_P6NGO_rep1

value: ovary

value: primary cells

value: P6 non-growing oocytes

tag: genotype

value: EedF/-; Ddx4-Cre

tag: reads length


title: A549 SA 4430_1

description: Library name: A_SA_4430_1

tag: treatment


title: RNAseq_PRC2ctrl_P6NGO_rep2

value: EedF/+; Ddx4-Cre


title: RNAseq_PRC2cKO_P6NGO_rep2


title: A549 SA 4430_2

description: Library name: A_SA_4430_2


title: Female, Young, Control, rep 3

description:
Library name: YC11
Female_Young_Control_3

tag: strain

tag: Sex

value: Female

value: UM

tag: age group

tag: age

value: 4 months


title: A549 SA C-_3

description: Library name: A549_SA_C_3

tag: tissue

tag: cell line


title: Female, Young, Control, rep 4

description:
Library name: YC12
Female_Young_Control_4

tag: cohort

tag: site

value: Control

value: Young

tag: age at_start_of_treatment


title: 02-231_C1D1

value: primary breast cancer

tag: best clinical response

tag: survival


title: RNAseq_PRC2ctrl_P6NGO_rep1

tag: cell type


title: Female, Young, Control, rep 2

description:
Library name: YC04
Female_Young_Control_2

tag: treatment abbreviation

tag: dose

value: 6 months

tag: replicate


title: A549 SA C-_2

description: Library name: A549_SA_C_2

value: pumlmonary epithelium


title: 03-229_C2D1

tag: timepoint

tag: sourceID

tag: outcome

value: radiographic

tag: outcome type

value: progression

value: PD


title: control progenitor, batch 3

city: Shanghai

first: Yuejun

last: Chen

state: Shanghai

address: 320 Yueyang Road

institute: Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences

data_processing:
Clean sequencing reads were mapped to the UCSC human GRCh38 genome with HISAT2 software (v2.1.0).
Bam files were generated using Samtools (v1.7).
Reads were counted by the ‘summarizeOverlaps’ function in the GenomicFeatures R package (v1.38.2) and a RangedSummarizedExperiment object was obtained.
RangedSummarizedExperiment object was processed by DeSeq2 (v1.26.0).
Differential expression analysis was performed using the ‘glmTreat’ function in edgeR R package (v3.28.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Cells were pelleted at 400 g for 5 min and lysed with TRIzol (Thermo Scientific).
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) and index codes were added to attribute sequences to each sample.

value: H9-derive neurons


title: 02-231_Screen

value: Screen

value: fatigue

value: toxicity

value: SD


title: A549 SA C-_1

description: Library name: A549_SA_C_1

tag: treatment


title: Female, Young, Control, rep 1

description:
Library name: YC03
Female_Young_Control_1

value: Liver

tag: strain

tag: Sex

tag: age group

tag: age


title: Female, Old, Syringaresinol, rep 3

description:
Library name: UT10937
Female_Old_Syr_3

tag: tissue

value: Female

tag: cohort

tag: site

value: UT

value: Syringaresinol

value: Syr

value: 300 ppm

value: Old

value: 22 months

value: 5 months


title: control progenitor, batch 2

tag: cell line


title: Female, Old, Syringaresinol, rep 2

description:
Library name: UM79016
Female_Old_Syr_2

value: UM

tag: age at_start_of_treatment


title: 03-229_C1D1

value: primary breast cancer

value: radiographic

value: progression

tag: best clinical response

tag: survival


title: control progenitor, batch 1

tag: cell type

value: H9-derive neurons


title: A2780 Cisplatin  R3

city: Washington

first: Sreejith

last: Nair

institute: Georgetown University

description: Library name: Sample 6

data_processing:
Raw sequencing data were quality-checked using FastQC, and adapter sequences were trimmed using Cutadapt (minimum read length = 1 bp).
Trimmed reads were aligned to the human reference genome (GRCh38, GENCODE v46 annotation) using STAR (v2.7.11) with local alignment parameters allowing up to 100 multi-mapped reads.
Gene and isoform abundance was quantified with RSEM v1.3.1.
Assembly: GRCh38
Supplementary files format and content: RSEM Normalized Gene Abundance Text File
Supplementary files format and content: RSEM Normalized Isoform Abundance Text File

extract_protocol:
Total RNA was isolated using the Zymo Quick RNA MiniPrep Kit (Zymo Research, R1054) with on-column DNase I digestion, following the manufacturer’s protocols.
RNA-seq libraries were prepared from 1 µg of total RNA using the KAPA HyperPrep Kit (Roche, KK8540) and sequenced on an Illumina NovaSeq X Plus platform to generate paired-end reads.

treatment_protocol: A2780 ovarian cancer cells were treated with 10 μM cisplatin or vehicle (DMF) for 24 h, in three independent biological replicates per condition.


title: A2780 Cisplatin  R2

description: Library name: Sample 5


title: 01-227_C2D1

tag: timepoint

value: PD


title: 03-229_Screen

value: Screen

tag: sourceID


title: Female, Old, Sulindac, rep 3

description:
Library name: UT10924
Female_Old_Sul_3

data_processing:
Reads were mapped to mouse genome (GRCm39) with STAR (version 2.7.11b). Genes were counted via featureCounts (version 2.0.6).
Assembly: GRCm39
Supplementary files format and content: comma-separated values file includes gene counts for each sample

extract_protocol:
RNA was extracted with PureLink RNA Mini Kit.
Libraries were prepared with TruSeq Stranded mRNA LT Sample Prep Kit according to TruSeq Stranded mRNA Sample Preparation Guide.

value: Sulindac

tag: treatment abbreviation

value: Sul

tag: dose

value: 5 ppm

tag: replicate


title: A2780 Cisplatin R1

description: Library name: Sample 4


title: GAD treated progenitor, batch 2


title: Female, Old, Syringaresinol, rep 1

description:
Library name: JL16279
Female_Old_Syr_1

value: Liver

tag: strain

value: Female

value: JL

tag: treatment


title: GAD treated progenitor, batch 3


title: GAD treated progenitor, batch 1


title: A2780 Vehicle R3

description: Library name: Sample 3


title: Female, Old, Sulindac, rep 1

description:
Library name: JL16262
Female_Old_Sul_1

tag: Sex

tag: age group


title: A2780 Vehicle R1

description: Library name: Sample 1


title: 01-227_Screen

tag: tissue

tag: outcome

tag: outcome type


title: Female, Old, Sulindac, rep 2

description:
Library name: UM79198
Female_Old_Sul_2

tag: cohort

tag: site

tag: age


title: A2780 Vehicle R2

description: Library name: Sample 2

tag: cell line


title: 01-227_C1D1

tag: best clinical response

tag: survival


title: 02-224_C2D1

tag: timepoint

tag: sourceID

value: toxicity

value: SD


title: a9-protocol-derived TH+ neurons, scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
scRNA-seq data were aligned with the human reference genome, GRCh38-3.0.0, and demultiplexed using the default parameters of Cellranger software (10x Genomics, v3.0.2 or v4.0.0). Obtained filtered count matrix was used for downstream analysis.The filtered count matrix was analyzed and processed using Seurat (v3.1.4) and Scanpy (v3.0.46), including data filtering, normalization, highly variable genes selection, scaling, dimension reduction, and clustering.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Output files of cellranger: Filtered feature-barcode matrix.  a9a10.Robj: R object which contain all excitatory neurons.  a9a10_d46_meta_anno.csv: metadata file containing clustering and annotation results of a9a10.Robj.

source_name: TH-tdT

extract_protocol:
Attached cells in the 6-well plate (day 46) were digested using TrypLE Express Enzyme (1.5 ml per well) for 10-15 minutes at 37°C. Digestion was terminated by adding 3 ml neural basal medium supplemented with 1% N2 supplement、2% B-27 supplement. Cells were then passed through a 35-μm cell sieve (BD) to obtain a single-cell suspension for cell sorting. Sorted tdTomato-positive cells were loaded for scRNA-seq (10X Chromium).
Chromium Single Cell 3' Reagent Kits (v3) were used for library preparation (10X Genomics). Libraries were sequenced on an Illumina Novaseq 6000 system.

tag: cell type

value: H9-derived neurons

value: TH-tdT

tag: genotype

value: WT

value: day 46


title: a10-protocol-derived TH+ neurons, scRNAseq

description: 10x Genomics


title: CUT&TAG_DMF + RNase A

description: Library name: Sample 6

data_processing:
DRIP-seq samples were processed using the nf-core cutandrun pipeline (v3.2.2) with default parameters.
Read counts were quantified for 5’ UTR regions using featureCounts from Subread (v2.1.1) and TPM normalized with a custom R script. Only transcripts with abundance ≥ 1 TPM in both replicates were retained for downstream analysis.
CPM normalized bigWig files of merged replicates were generated using deeptools (v3.5.3)
Assembly: GRCh38
Supplementary files format and content: TPM normalized Cisplatin 5'UTR Read Counts Text File
Supplementary files format and content: CPM normalized bigWig
Library strategy: CUT&Tag

growth_protocol: A2780 human ovarian carcinoma cells were cultured under standard conditions and seeded to approximately 70% confluency prior to treatment.

extract_protocol:
Cells were collected by gentle scraping in PBS, washed once, and pelleted for subsequent R-loop profiling.
A2780  cells were treated with cisplatin (25 µM) for 6 hours, , or vehicle control in biological replicates. Following treatment, cells were collected and washed  in PBS. Genome-wide mapping of R-loops was performed using the CUT&Tag-IT R-loop Assay Kit (Active Motif, 53167) according to the manufacturer’s instructions, Sequencing libraries were prepared using the reagents provided in the kit, following the manufacturer’s instructions. Libraries were amplified using Q5 polymerase. Final libraries were eluted in 20 µL of elution buffer, quantified by Qubit fluorometry, and assessed for quality by TapeStation D1000 High Sensitivity assay. Pooled libraries were sequenced on an Illumina platform to generate paired-end 150-bp reads, with a sequencing depth of ~50 million reads per sample.

treatment_protocol: Cells were exposed to cisplatin (25 µM, 6 h), 1,3-platin (50 µM, 6 h), or vehicle control in biological replicates.


title: 02-224_C1D1

value: primary breast cancer


title: Female, Old, Late-start Rapamycin, rep 3

description:
Library name: UT08557
Female_Old_Rapa_20hi_3

tag: strain

value: UT

value: Late-start Rapamycin

tag: treatment abbreviation

tag: dose

value: 42 ppm

value: Old

value: 22 months

tag: age at_start_of_treatment

value: 20 months

tag: replicate


title: Female, Old, Late-start Rapamycin, rep 2

description:
Library name: UM59367
Female_Old_Rapa_20hi_2

tag: tissue

tag: Sex

value: UM

tag: treatment

tag: age group


title: 02-224_Screen

value: Screen

tag: outcome

tag: outcome type


title: Female, Old, Late-start Rapamycin, rep 1

description:
Library name: JL12784
Female_Old_Rapa_20hi_1

value: Liver

value: Female

tag: cohort

tag: site

tag: age


title: 02-238_C4D1

tag: timepoint

tag: sourceID

value: radiographic

value: progression

tag: best clinical response

tag: survival


title: CUT&TAG_DMF R1

description:
Library name: Sample 4
dmf_merged.cpm.bw

tag: cell line


type: RNA

description:
BLQ_1_CD25-
CD25-negative cells from human BCR-ABL1+ ALL xenograft sample BLQ1.

hyb_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual).

data_processing: The CEL files were processed with Affymetrix Gene Expression Console software (Version 1.1) using RMA normalization to the gene level expression.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual).

extract_protocol: Qiagen RNeasy Kit.

tag: xenograft sample

tag: cell type

value: CD25-negative BCR-ABL1 ALL cells


title: Female, Old, Rapamycin+Acarbose, rep 3

description:
Library name: UT11008
Female_Old_RaAc9_3

tag: strain

value: Rapamycin+Acarbose

tag: treatment abbreviation

tag: dose

tag: age at_start_of_treatment

value: 9 months

tag: replicate


title: 02-238_C2D1

tag: tissue

tag: outcome

value: SD


title: CUT&TAG_Cisplatin + RNase A

description: Library name: Sample 3


description:
BLQ_1_CD25+
CD25-positive cells from human BCR-ABL1+ ALL xenograft sample BLQ1.

scan_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual).

value: CD25-positive BCR-ABL1 ALL cells


title: 02-238_C1D1

value: primary breast cancer

tag: outcome type


title: Female, Old, Rapamycin+Acarbose, rep 2

description:
Library name: UM79086
Female_Old_RaAc9_2

tag: Sex

tag: cohort

tag: site

tag: treatment

tag: age group


title: CUT&TAG_DMF R2

description:
Library name: Sample 5
dmf_merged.cpm.bw


description:
LAX_9_CD25-
CD25-negative cells from human BCR-ABL1+ ALL xenograft sample LAX9.


title: Female, Old, Rapamycin+Acarbose, rep 1

description:
Library name: JL16313
Female_Old_RaAc9_1

value: JL

tag: age


title: CUT&TAG_Cisplatin R2

description:
Library name: Sample 2
cis_merged.cpm.bw

tag: cell line


title: Female, Old, Middle-start Rapamycin+Acarbose, rep 3

description:
Library name: UT11019
Female_Old_RaAc16_3

value: UT

value: Middle-start Rapamycin+Acarbose

value: 16 months


title: Female, Old, Middle-start Rapamycin+Acarbose, rep 2

description:
Library name: UM78939
Female_Old_RaAc16_2

value: Old

value: 22 months


title: 03-228_C4D1

tag: timepoint

tag: sourceID

tag: best clinical response

value: PR

tag: survival


title: 02-238_Screen

value: Screen


title: Female, Old, Middle-start Rapamycin+Acarbose, rep 1

description:
Library name: JL16306
Female_Old_RaAc16_1

value: Liver

tag: strain

value: Female

tag: treatment abbreviation

tag: dose


title: A27cpds13_In_1

description: Library name: Sample 7

data_processing:
Paired-end FASTQ files were quality checked using FastQC (v0.11.9) .
Sequencing adapters were trimmed using CutAdapt (v4.0)  in paired-end mode.
Trimmed reads were aligned to the human reference genome (GRCh38.p14, GENCODE Release 46) using STAR (v2.7.11).
Peaks were called using the peak calling software CLAM (CLIP-seq Analysis of Multi-mapped reads) (v1.2.3).
RPKM normalized bigWig files were generatd using deeptools v3.5.3 for visualization.
Assembly: GRCh38
Supplementary files format and content: RPKM Normalized BigWig File

source_name: 1,3 Platin + cPDS Input R1

growth_protocol: A2780 cells were maintained in DMEM supplemented with 10% FBS and 1% penicillin–streptomycin at 37 °C with 5% CO₂.

extract_protocol:
Total RNA was extracted with TRIzol (Thermo Fisher, MAN0001271) according to the manufacturer’s protocol. RNA were fragmented by sonication and pre-cleared buy incubation with streptaidin Dynabeads T1. RNA was re-extracted using Trizol LS(Thermo Fisher, MAN0000806). Ten percent lysate was saved as input. Pre-cleared RNA was reacted with 100 µM DBCO-PEG4-Biotin in aqueous solution for 16 h at 37 °C. Following labeling, samples were treated with DNase  at 37 °C for 30 min. RNA was purified from unreacted DBCO-PEG4-Biotin with TRIzol LS. Labeled RNA was incubated with Dynabeads T1 for 30 min at room temperature with rotation. Bead–RNA complexes were washed 12 times: 6 times with 1 ml bead wash buffer II (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl) pre-warmed to 65 °C, followed by 6 times at room temperature. After the final wash, RNA was eluted with TRIzol.
Pulldown and input RNA samples were depleted of rRNA using the RiboErase kit (Roche, KK8560) following the manufacturer’s protocol. The rRNA-depleted RNAs were processed for stranded cDNA library construction using the KAPA RNA HyperPrep Kit (Roche, KR1351 v4.21).

treatment_protocol: A2780 cells were treated with  30 µM concentrations of 1,3-Platin or DMF for 16 hours. For competition samples, the cells were treated with 5 µM cPDS for 8 hours, followed by 1,3-Platin for an additional 16 hours.


title: 03-228_C2D1

tag: tissue

value: radiographic

value: progression


title: A27cpds13_In_2

description: Library name: Sample 8

source_name: 1,3 Platin + cPDS Input R2


title: GFP+ cells at 15 days after LD damage

city: Ann arbor

first: Thanh

last: Hoang

state: Michigan

address: 1000 wall street

institute: University of Michigan ann arbor

description:
Library name: 12222-ZF-1
10xscRNA 3' GEX mmp9Cre/EGFP

data_processing:
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Scanpy was used to perform downstream analysis following the standard pipeline.
Assembly: Danio rerio (GRCz11 / danRer11, Ensembl release 105)
Supplementary files format and content: HDF5 (.h5) files generated with Scanpy/AnnData.

organism: Danio rerio

source_name: retina

extract_protocol:
papain dispase dissociation
10x Genomics Chromium Single Cell System

value: retina


description:
BLQ_11_CD25-
CD25-negative cells from human BCR-ABL1+ ALL xenograft sample BLQ11.

tag: xenograft sample

tag: cell type

value: CD25-negative BCR-ABL1 ALL cells


title: CUT&TAG_Cisplatin R1

description:
Library name: Sample 1
cis_merged.cpm.bw


title: 03-228_C1D1

tag: outcome

tag: outcome type


description:
BLQ_11_CD25+
CD25-positive cells from human BCR-ABL1+ ALL xenograft sample BLQ11.


title: GFP+ cells at 15 days after NMDA damage

description:
Library name: 12222-ZF-2
10xscRNA 3' GEX mmp9Cre/EGFP


title: Female, Old, PB125, rep 3

description:
Library name: UT11049
Female_Old_PB125_3

source_name: Liver

tag: Sex

tag: cohort

tag: site

value: 100 ppm

tag: age at_start_of_treatment

value: 5 months

tag: replicate


title: 03-228_Screen

value: primary breast cancer

tag: timepoint


description:
LAX_9_CD25+
CD25-positive cells from human BCR-ABL1+ ALL xenograft sample LAX9.

value: CD25-positive BCR-ABL1 ALL cells


title: KO med 6

city: Birmingham

first: Shinichi

last: Kano

state: AL

address: 1720 7th Ave South

department: Psychiatry

institute: University of Alabama at Birmingham

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used to convert bcl images to FASTQ files.
FASTQ files were uploaded to Qiagen's GeneGlobe web tool for alignment and UMI transcript abundance calculations.
Assembly: mm10
Supplementary files format and content: tab-delimited Excel file containing UMI values for each microRNA in each sample

source_name: Blood (sera)

extract_protocol:
Freshly collected sera were immediately used to enrich extracellular vesicle fractions using differential ultracentrifugation. The small RNAs were extracted from extracellular vesicle fractions with miRNeasy mini kit (Qiagen).
Libraries were prepared with Qiagen miRNA library prep kit (Qiagen)

value: Blood (sera)

value: Primary tissues

tag: genotype

tag: treatment

value: Vehicle injection


title: A27cpds13_1

description: Library name: Sample 5

source_name: 1,3 Platin + cPDS IP R1

tag: cell line


title: KO med 3


title: Female, Old, PB125, rep 2

description:
Library name: UM78708
Female_Old_PB125_2

tag: strain

value: UM

tag: age group

value: Old

tag: age


title: KO med 5

tag: tissue


title: A27cpds13_2

description: Library name: Sample 6

source_name: 1,3 Platin + cPDS IP R2


title: A27_13_2

description: Library name: Sample 2

source_name: 1,3 Platin IP R2


title: KO med 4


title: 01-226_Screen

tag: sourceID

value: toxicity

tag: best clinical response

value: SD

tag: survival


title: KO med 1

tag: cell type


title: Female, Old, Nicotinamide Riboside, rep 2

description:
Library name: UM68341
Female_Old_NR_2

value: Liver

tag: Sex

value: Nicotinamide Riboside

tag: treatment abbreviation

value: NR

tag: dose

value: 22 months

value: 8 months


title: A27_13_In_2

description: Library name: Sample 4

source_name: 1,3 Platin Input R2


title: 02-223_Screen

value: Screen

tag: outcome

value: radiographic

tag: outcome type

value: progression

value: PD


title: Female, Old, PB125, rep 1

description:
Library name: JL16258
Female_Old_PB125_1

value: Female

tag: cohort

tag: site

value: JL

value: 100 ppm

tag: age at_start_of_treatment

value: 5 months

tag: replicate


title: 01-226_C1D1

value: primary breast cancer

tag: timepoint


title: KO med 2

value: Blood (sera)

value: Primary tissues

tag: genotype

tag: treatment

value: Vehicle injection


title: 1,3 Platin Input R2

description: Library name: Sample 8

growth_protocol: A549 cells were maintained in DMEM supplemented with 10% FBS and 1% penicillin–streptomycin at 37 °C with 5% CO₂.

treatment_protocol: Two biological replicates of A549 cells were treated with  30 µM concentrations of 1,3-Platin or DMF for 16 hours. For competition samples, the cells were treated with 10 µM cisplatin for 8 hours, followed by 1,3-Platin for an additional 16 hours.

tag: cell line


title: Female, Old, MitoQ, rep 3

description:
Library name: UT08579
Female_Old_MitoQ_3

tag: tissue

value: Liver

tag: strain

value: UT

value: MitoQ

tag: age group

value: Old

tag: age

value: 7 months


title: 02-223_C2D1

tag: sourceID

tag: best clinical response

tag: survival


title: 02-223_C1D1

tag: outcome


title: Female, Old, Nicotinamide Riboside, rep 3

description:
Library name: UT09584
Female_Old_NR_3

tag: Sex

value: Nicotinamide Riboside

tag: treatment abbreviation

value: NR

tag: dose

value: 22 months

value: 8 months


title: KO T cell 6

tag: cell type

value: Sytemic T cell injection


title: 01-222_Screen

value: Screen

value: clinical

tag: outcome type

value: progression

value: PD


title: A27_13_1

description: Library name: Sample 1

source_name: 1,3 Platin IP R1


title: Female, Old, Nicotinamide Riboside, rep 1

description:
Library name: JL14032
Female_Old_NR_1

value: Female

tag: cohort

tag: site

value: JL

tag: age at_start_of_treatment

tag: replicate


title: A27_13_In_1

description: Library name: Sample 3

source_name: 1,3 Platin Input R1

tag: cell line


title: KO T cell 5

tag: tissue

value: Blood (sera)

value: Primary tissues

tag: genotype

tag: treatment


title: 1,3 Platin Input R1

description: Library name: Sample 7


title: Female, Old, MitoQ, rep 2

description:
Library name: UM60081
Female_Old_MitoQ_2

value: Liver

tag: strain

value: UM

value: 100 ppm

tag: age group

tag: age


title: 01-222_C1D1

value: primary breast cancer

tag: timepoint

tag: sourceID

tag: outcome

tag: best clinical response

tag: survival


title: 1,3 Platin IP R2

description: Library name: Sample 6


title: Female, Old, Minocycline, rep 3

description:
Library name: UT08459
Female_Old_Min_3

tag: Sex

value: UT

value: Minocycline

tag: treatment abbreviation

value: Min

tag: dose

value: 300 ppm

value: Old

value: 6 months


title: KO T cell 2

tag: cell type

value: Sytemic T cell injection


title: 1,3 Platin IP R1

description: Library name: Sample 5


title: KO T cell 1


title: KO T cell 4


title: 02-221_C4D1

value: radiographic

tag: outcome type

value: progression

value: SD


title: 1,3 Platin  + Cisplatin IP R1

description: Library name: Sample 1

tag: cell line


title: KO T cell 3

tag: tissue


title: Female, Old, Minocycline, rep 2

description:
Library name: UM59241
Female_Old_Min_2

value: Female

tag: cohort

tag: site

value: 22 months

tag: age at_start_of_treatment

tag: replicate


title: Female, Old, Minocycline, rep 1

description:
Library name: JL12683
Female_Old_Min_1

tag: strain

value: JL

tag: treatment

tag: age group

tag: age


title: Cisplatin R2

description:
Library name: Sample 2
A27G4cisII

data_processing:
Paired-end samples were aligned to transcripts using the comprehensive gene annotation from GENCODE (Ensembl 112, GRCh38.p14) with STAR v1.0.2.
Gene-level read counts were computed with featureCounts from Subread v2.1.1.
Read counts were normalized to transcripts per million (TPM). Only transcripts with abundance ≥ 1 TPM in both replicates were retained for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: TPM Normalized Read Counts Text File

extract_protocol:
The cells were collected, washed twice in ice-cold PBS, and pelleted at 300 × g for 5 min at 4 °C. Pellets were resuspended in 500 µL lysis buffer provided with RNA immunoprecipitation kit (MBL Life Science, RN1005) , vortexed, incubated for 10 min at 4 °C, and centrifuged at 12,000 × g for 5 min. . The lysates were incubated overnight at 4 °C with15 µg of BG4 antibody (Anti-DNA/RNA BG4, scFv fragment, FLAG-tagged, Absolute antibody, Ab00174-30.126). Llysates were incubated with washed M2 beads for 2 hours at 4 °C. The beads were then washed three times with 1 mL of wash buffer. Bead-bound RNA was extracted using the TRIzol method.
The rRNA-depleted stranded libraries were prepared with the KAPA RNA HyperPrep Kit with HMR RiboErase (Roche, KR1351 v4.21). Library quality was assessed using the TapeStation D1000 High Sensitivity assay. The libraries were sequenced at a depth of 40 million reads.

treatment_protocol: Two biological replicates of A2780 cells were treated under the following conditions: 25 µM cisplatin for 6 h (replicates 1 and 2).

value: anti-BG4 antibody


title: 02-221_Screen

tag: timepoint

value: Screen

tag: sourceID

tag: outcome

tag: best clinical response


title: 1,3 Platin  + Cisplatin Input R1

description: Library name: Sample 3


title: 02-221_C1D1

tag: survival


title: Female, Old, MIF098, rep 1

description:
Library name: JL14006
Female_Old_MIF098_1

value: Liver

tag: Sex

tag: treatment abbreviation

tag: dose

value: 240 ppm

value: 8 months


title: Female, Old, MitoQ, rep 1

description:
Library name: JL12749
Female_Old_MitoQ_1

tag: tissue

value: MitoQ

value: 100 ppm

value: 7 months


title: 02-225_C1D1

value: primary breast cancer


title: WT_med_3

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used to convert raw bcl images to FASTQ files
Raw FASTQ files were aligned with STAR (version 2.7.5c) using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattribtues All
Transcript abundances were calculated from the aligned BAM file using HTSeq-count (version 0.11.1) using parameters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Assembly: Gencode GRCm38 p6 Release M24
Supplementary files format and content: tab-delimited Excel file containing Ensembl ID# and raw count values for each ID in each sample

source_name: Brain (prefrontal cortex)

extract_protocol:
Freshly dissected PFC tissues were immediately frozen and ketp at -80ºC until use. The frozen tissues were directly dissolved in lysis buffer and the total RNAs were extracted with RNeasy micro kit (Qiagen).
Libraries were prepared with NEB Next Ultra II Directional RNA Library Prep kit (New England BioLabs).

value: Brain (prefrontal cortex)

tag: cell type

value: Primary tissues

tag: genotype

value: WT


title: 02-220_C1D1

value: radiographic

tag: outcome type

value: progression

value: PD


title: 1,3 Platin  + Cisplatin Input R2

description: Library name: Sample 4

tag: cell line


title: 02-220_C2D1


title: Female, Old, MIF098, rep 2

description:
Library name: UM68292
Female_Old_MIF098_2

tag: strain

value: Female

tag: cohort

tag: site

value: UM

value: Old

value: 22 months

tag: age at_start_of_treatment

tag: replicate


title: Female, Old, MIF098, rep 3

description:
Library name: UT09617
Female_Old_MIF098_3

value: Liver

value: UT

tag: treatment

tag: age group

tag: age


title: WT_med_6


title: WT_med_1


title: 1,3 Platin  + Cisplatin IP R2

description: Library name: Sample 2


title: 02-225_Screen

tag: timepoint

value: Screen

tag: sourceID


title: DMF Rep 2

description: Library name: Sample 5

data_processing:
Raw sequencing reads were evaluated for quality using FastQC v0.11.9. Reads were aligned to the GRCh38 reference genome using Bowtie2 v2.3.5.1.
Aligned reads were converted to BAM format, sorted, and indexed using SAMtools v1.10.
For stalling index analysis, read counts were computed using BEDtools v2.27.1 within regions surrounding transcription start sites (TSS; -500 bp to +300 bp) and across gene bodies (+300 bp to transcription end sites). Region counts were normalized to RPM/bp, and input signal was subtracted.
BigWig files were generated with CPM normalization for visualization.
Assembly: GRCh38
Supplementary files format and content: CPM Normalized BigWig file

growth_protocol: Human ovarian adenocarcinoma A2780 cells were maintained in RPMI supplemented with 10% FBS and 1% penicillin–streptomycin at 37 °C with 5% CO₂.

extract_protocol:
Cells were fixed for 10 minutes with 1% formaldehyde and quenched  by adding Glycine (0.125M). Chromatin DNA was fragmented by sonication. RNA PolII was  immunoprecipitated with  antibody (clone CTD4H8; Millipore Sigma, Cat. No. 05-623-Z) overnight at 4°C. Next day, lysates were incubated in prewashed protein G dynabeads . After washing and elution, the protein–DNA complex was decross-linked and  DNA was purified by using QIAquick PCR purificaion kit.
ChIP–Seq libraries were prepared using the KAPA Hyper Prep Kit (Roche, 7962347001) following the manufacturer’s protocol, and sequenced on an Illumina NovaSeq X Plus platform.

treatment_protocol: Two biological replicates of A2780 cells were treated with 12.5 µM cisplatin or equal volume DMF for 1 hour, followed by formaldehyde crosslinking.


title: Female, Old, Leucine, rep 2

description:
Library name: UM78806
Female_Old_Leu_2

tag: Sex

value: Leucine

tag: treatment abbreviation

value: Leu

value: 5 months


title: 02-220_Screen

tag: tissue

value: primary breast cancer

tag: outcome

tag: best clinical response

tag: survival


title: KO_med_3

value: Brain (prefrontal cortex)

tag: cell type

tag: genotype

value: Vehicle


title: Female, Old, Leucine, rep 3

description:
Library name: UT11053
Female_Old_Leu_3

tag: strain

tag: cohort

tag: dose


title: DMF Input

description: Library name: Sample 6

tag: cell line


title: Female, Old, Leucine, rep 1

description:
Library name: JL16267
Female_Old_Leu_1

tag: site

value: JL

tag: treatment

tag: age at_start_of_treatment

tag: replicate


title: 01-219_C4D1

tag: timepoint

tag: sourceID

value: radiographic

tag: outcome type

value: PR


title: Cisplatin Input

description: Library name: Sample 3


title: 01-219_C2D1

tag: tissue

value: progression


title: KO_EV_3

value: Primary tissues

value: Extracellular vesicles


title: 02-230_C1D1

tag: outcome

value: PD


title: KO_EV_2


title: KO_med_2


title: KO_med_1


title: DMF Rep 1

description: Library name: Sample 4


title: Female, Old, Geranylgeranyl acetone, rep 2

description:
Library name: UT09642
Female_Old_GGA_2

tag: Sex

value: Female

value: Geranylgeranyl acetone

tag: treatment abbreviation

value: GGA

value: 600 ppm

tag: age group

value: Old

tag: age

value: 22 months

value: 9 months


title: Cisplatin Rep 2

description: Library name: Sample 2


title: KO_EV_5

tag: cell type

tag: genotype


title: Female, Old, Geranylgeranyl acetone, rep 1

description:
Library name: JL13903
Female_Old_GGA_1

value: Liver

tag: strain

tag: cohort

tag: dose


title: Cisplatin Rep 1

description: Library name: Sample 1

tag: cell line


title: 01-219_Screen

value: primary breast cancer

value: Screen

tag: best clinical response

tag: survival


title: 02-230_Screen

tag: timepoint


title: Female, Old, 17-DMAG, rep 3

description:
Library name: UT08576
Female_Old_DMAG_3

tag: site

value: UT

tag: treatment

value: DMAG

value: 30 ppm

tag: age at_start_of_treatment

value: 6 months

tag: replicate


title: Cisplatin R1

description:
Library name: Sample 1
A27G4cisI

value: anti-BG4 antibody


title: Female, Old, Geranylgeranyl acetone, rep 3

description:
Library name: UM68628
Female_Old_GGA_3

tag: tissue

tag: Sex

value: UM


title: 01-217_C2D1

tag: sourceID

tag: outcome

value: radiographic

tag: outcome type

value: progression

value: PD