title: 18_PCD14 Heifer N°18 at day 14 post-estrus of Preconceptional cycle

description:
Heifer N°18 at day 14 post-estrus of Preconceptional cycle
253680910014_2_1

value: Preconceptional cycle (estrus cycle)


title: Sample_15_Polish women with BC

status: Public on Aug 13 2025

type: genomic

city: Szczecin

first: Tomasz

middle: K

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

country: Poland

institute: Pomeranian Medical University

description: DNA extracted from peripheral blood of Polish women with BC

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Data were processed in R, normalized using BMIQ normalization.
The data_table.csv contains normalized beta-value (BMIQ)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral Blood

label_protocol: Standard Illumina Protocol

extract_protocol: The DNA from the whole blood samples was extracted using salting out method.

tag: subject status

value: Polish women with BC

tag: age

tag: as

tag: Sex

value: F

tag: tissue

value: Peripheral Blood


title: NAc, VEH-VEH,  Female, 2

type: SRA

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

country: USA

institute: Virginia Tech

description: V-V Female NAc

library_source: genomic

data_processing:
Illumina NovaSeq X  with paired-end 150-nt read was used to sequence each library, generating an average of 19 million reads per sample and input. However, only the forward (R1) strand was used for data analysis.
Read trimming was performed using default settings by Trim Galore!
Reads were subsampled to 95% to generate two artificial replicates using seqtk package.
Raw ChIP-seq reads and input data were then mapped to mouse mm10 genome (GRCm38) using Bowtie2 (2.2.5).
Peaks called using MACS2 (2.2.7.1) using a q-value cutoff of 0.05.
MM10 blacklisted regions (ENCODE) were removed using SAMtools
Mapped reads were extended by 100bp on either side (350 bp total) using BEDtools
Each library was randomly sub-sampled twice to 95% of its original raw reads to generate two artificial replicates using the seqtk package. The artificial replicates were used as input into diffbind (3.12.0) R package for generating a consensus peakset. Consensus peaksets were created independently for each brain region (PFC and NAc) using dba.peakset in diffbind (DBA_BLACKLIST_MM10, consensus = DBA_TREATMENT, minOverlap = 2). The raw read counts were extracted using the diffbind function dba.count (data_blacklist_remove, summits = FALSE, peaks = ConsensusPeaks, filter=1, bScaleControl = TRUE, minCount=1, score=DBA_SCORE_TMM_MINUS_FULL). This count file was then used as the input to DESeq2 (1.42.1) package in R. Uniform Manifold Approximation and Projection (UMAP) was used to identify principal components with outsized impact. The following covariates were regressed out: demographic covariates (sex, condition) and technical covariates (align rate, unique rate, FRiP, NSC, the number of identified peaks, and sequencing batch) by correlating the top 6 principal components (Pearson correlation > 0.7) with these covariates. Differential peak analysis was then performed to identify differential peaks between the conditions (VEH-VEH, VEH-PSI, OXY-VEH, OXY-PSI), and sexes for each brain region (FDR <0.05). The p-values were adjusted by performing a standard Bonferroni correction. For more accurate annotation, enhancers (defined as identified H3K27ac peaks that do not fall within ±2000bp of TSS) were first checked for regional overlap with published Hi-C data on neurons in mice (Bonev et al., Cell, 171, 557-572, e524 (2017)). Overlapped peak regions were annotated based on these existing Hi-C gene links, and the rest of the enhancers were associated with their nearest-neighbor genes. K-means clustering and unsupervised hierarchical clustering (UHC) were performed on differential enhancers for each sex and region. Count files were filtered based on differential peak callouts to form a new consensus peakset comprising the count files of all differential peaks between any two of the three groups (VEH-VEH, OXY-VEH, and OXY-PSI). To normalize the counts based on the number of samples, each row of the count file was divided by √(sum〖(X)〗^2 ). The optimal number of clusters for k-means was determined using Silhouette method. UHC was performed using the default settings of the pheatmap library in R, with cluster position on the x-axis rotated about their dendrogram tentacle for continuity. Gene ontology (GO) biological enrichment analysis was performed on annotated peaks using the bioconducter clusterProfiler package. KEGG pathway analysis was performed using shinyGO version 0.838.  Both GO and KEGG analysis were performed using FDR adjusted P values < 0.05 to ensure generation of high-confidence terms.
Assembly: mm10
Supplementary files format and content: bedGraph

organism: Mus musculus

source_name: Nucleus Accumbens

extract_protocol:
Neuronal neclei extracted performed following previously published protocol (Ma et al., Sci Adv., Vol 4, Issue 4, ( 2018); de la Fuente Revenga et al., Cell Rep., Volume 37, Issue 3, (2021)). Each step was performed on ice unless otherwise noted. A small slice (20-30mg) of frozen FC or NAc tissue was plunged into a tissue grinder (D9063, Sigma-Aldrich) filled with 3 ml of ice-cold nuclei extraction buffer (NEB) [0.32M sucrose, 5mM CaCl2, 3mM Mg(Ac)2, 0.1mM EDTA, 10 mM tris-HCl, and 0.1%(v/v) Triton X-100] along with 30 μl of freshly prepared protease inhibitor cocktail (PIC, Sigma-Aldrich), 3 μl of 1 M dithiothreitol (DTT, Sigma-Aldrich), 3 μl of 100mM phenylmethylsulfonyl fluoride (PMSF, Sigma-Aldrich) in isopropyl alcohol, and 4.5 μl of recombinant ribonuclease (RNase) inhibitor (2313A,Takara Bio). The tissue was then homogenized by douncing 25 times with pestle A and 15 times with pestle B. A 40-μm cell strainer (22-363-547, ThermoFisher Scientific) was then used to filter the homogenate, which was then collected into a 15 ml centrifuge tube. Next, the cell suspension was centrifuged at 1000 RCF for 10 min. The supernatant was then discarded, and the collected pellet was resuspended in 0.5 ml of ice-cold NEB with freshly added 5 μl of PIC, 0.5 μl of PMSF, 0.5 μl of DTT, and 0.75 μl of RNase inhibitor. 500 μl of the sample was mixed with 750 μl of 50%(w/v) iodixanol (created by mixing 4 ml of OptiPrepTM gradient (Sigma-Aldrich)) and 0.8 ml of diluent [150 mM KCl, 30 mM MgCl2, and 120 mM Tris-HCl]), along with 7.5 μl of PIC, 0.75 μl of PMSF, 0.75 μl of DTT, and 1.125 μl of RNase inhibitor. The mixture was centrifuged at 10,000 RCF at 4°C for 20 min. The supernatant was then removed and 300 μl of 2% (w/v) normal goat serum (50062Z, Life technologies) in Dulbecco’s PBS (DPBS, Life technologies), and 0.3 μl of RNase inhibitor was gently added to the sample and incubated on ice for 10 min, before resuspending the nuclei pellet by pipetting. In order to label and separate neuronal and glial fractions by FACS, 10 μl of 2 ng/ml anti-NeuN antibody conjugated with Alexa 488 (MAB377X, Millipore) in DPBS was added into the nuclei suspension. This suspension was mixed well by pipetting before being placed on a roto-mixer (Labnet) without light at 4°C for 1 h. Next, NeuN+ and NeuN- fractions were sorted using a BD FACSAriaTM cell sorter (BD Biosciences). Around 192 μl of the sorted solution containing ~24,000 NeuN+ nuclei was then added into 192 μl of 2x lysis buffer [4% (vol/vol) Triton X-100, 100 mM Tris-HCl (pH 8.0), 100 mM NaCl and 30 mM MgCl2 in Milli-Q water], along with 1.92 μl of PIC and 1.92 μl PMSF. This solution was mixed well and incubated at room temperature for 10 min, before addition of 38.4 μl of 100 mM CaCl2 and 4.8 μl of 100U/ul MNase (88216, ThermoFIsher). The solution was mixed by vortex and incubated at room temperature for 10 min. 42.24 μl of 0.5 M UltraPure EDTA (15575-038, Life Technologies) was added and allowed to incubate on ice for 10 min to halt the digestion. The resulting mixture was centrifuged at 16,100g for 10 min at 4°C and all of the supernatant was collected as chromatin sample.
ChIP-seq was performed using previously reported MOWChIP microfluidic platform (Zhu et al., Nat Protocols, 14, 3366–3394, (2019)) from chromatin extracted from 10,000 nuclei per sample, and 2000 nuclei per input. Libraries prepared using Accel-NGS 2 S Plus DNA Library kit (IDT, 1000987). Libraries amplified 10-12 cycles. Enrichment valideated by qPCR and size selected using Agilent tapestation.

treatment_protocol: Mice received three separate administrations of OXY (3 mg/kg) or vehicle on consecutive days (days 1-3), with 24-hour intervals between doses, followed by a single dose of PSI (1 mg/kg) or vehicle (day 4), resulting in four distinct experimental groups: VEH-VEH, VEH-PSI, OXY-VEH, and OXY-PSI. On day 5, tissue samples were collected for H3K27ac profiling

value: Nucleus Accumbens

tag: cell type

value: Neuron

tag: treatment

value: Vehicle-Vehicle


title: 21_PCD7 Heifer N°21 at day 7 post-estrus of Preconceptional cycle

type: RNA

city: Jouy-en-Josas

first: Mariam

last: Raliou

address: Allée de Vilvert

department: PHASE

country: France

institute: INRAE

description:
Heifer N°21 at day 7 post-estrus of Preconceptional cycle
253680910015_2_2

hyb_protocol: Labelled cRNA were hybridized on the custom bovine gene expression 8x60K array for 17 hours, centrifuge at 10 rpm for 65°C. Following washing, the slides were scanned using an Agilent G2565CA microarray Scanner System, at a 3 μm resolution in a 20-bit scan mode, according to the “AgilentG3_GX_1Color” protocol.

scan_protocol: The slides were scanned using an Agilent G2565CA microarray Scanner System, at a 3 μm resolution in a 20-bit scan mode, according to the “AgilentG3_GX_1Color” protocol.

data_processing: Raw.tiff images were then extracted using Agilent “Feature Extraction, version 10.10.1.1” following “GE1_1010_Sep10” protocol. Median raw expression values were further normalized by quantile method

molecule: total RNA

organism: Bos taurus

source_name: Peripheral White Blood Cells

label_protocol: RNA labeling was performed according to Agilent protocol “One-Color Microarray-Based Gene Expression Analysis – Low Input Quick Amp Labelling” version 6.5, May 2010 (Cat # G4140-90050). Complementary RNA (cRNA) samples were linearly amplified and labelled with cyanine 3 starting from 100 ng of total RNA.

extract_protocol: Total RNA of circulating white blood cells was isolated from PAXgene blood samples using the PAXgene Blood RNA system (PreAnalytiX, Qiagen/BD Company, France).

tag: breed

value: heifer

value: Peripheral White Blood Cells

tag: stage of postpartum period


title: 15_1ETD7 Heifer N°1 at the day (7) of the first embryo transfer

description:
Heifer N°1 at the day (7) of the first embryo transfer
253680910015_1_3

value: Day (7) of the first embryo transfer


title: 18_PCD7 Heifer N°18 at day 7 post-estrus of Preconceptional cycle

description:
Heifer N°18 at day 7 post-estrus of Preconceptional cycle
253680910019_1_4


title: 18_2ETD7 Heifer N°18 at the day (7) of the second embryo transfer

description:
Heifer N°18 at the day (7) of the second embryo transfer
253680910017_2_2

value: Day (7) of the second embryo transfer


title: 17_1ETD7 Heifer N°1 at the day (7) of the first embryo transfer

description:
Heifer N°1 at the day (7) of the first embryo transfer
253680910014_2_2


title: genomic DNA from clinical gastric cancer case [GC264T]

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

description:
SAMPLE 31
low DNA methylation epigenotype

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

data_processing: BeadStudio software v3.2

extract_protocol: genomic DNA was extracted and purified from clinical samples using QIAquick DNA mini kit according to standard instructions

tag: gender

value: Female

value: gastric cancer

tag: sample type

value: clinical sample

tag: disease state


title: Sample_14_Polish women with BC


title: 15_2ETD7 Heifer N°15 at the day (7) of the second embryo transfer

description:
Heifer N°15 at the day (7) of the second embryo transfer
253680910012_1_2


title: 15_PCD14 Heifer N°15 at day 14 post-estrus of Preconceptional cycle

description:
Heifer N°15 at day 14 post-estrus of Preconceptional cycle
253680910012_2_4


title: FC, VEH-VEH, Female, 5

description: V-V Female FC

source_name: Frontal Cortex

value: Frontal Cortex


title: Sample_12_Polish women with BC


title: genomic DNA from clinical gastric cancer case [GC277T]

description:
SAMPLE 33
extremely high DNA methylation epigenotype

value: Male


title: FC, VEH-VEH, Female, 3

description: V-V Female FC


title: genomic DNA from clinical gastric cancer case [GC270T]

description:
SAMPLE 32
low DNA methylation epigenotype


title: Sample_11_Polish women with BC


title: FC, VEH-VEH, Female, 2

description: V-V Female FC


title: 15_PCD7 Heifer N°15 at day 7 post-estrus of Preconceptional cycle

description:
Heifer N°15 at day 7 post-estrus of Preconceptional cycle
253680910014_2_3


title: genomic DNA from clinical gastric cancer case [GC287T]

description:
SAMPLE 35
extremely high DNA methylation epigenotype


title: FC, VEH-VEH, Female, 1

description: V-V Female FC


title: Sample_10_Polish women with BC


title: 14_2ETD7 Heifer N°14 at the day (7) of the second embryo transfer

description:
Heifer N°14 at the day (7) of the second embryo transfer
253680910017_1_3


title: Sample_13_Polish women with BC


title: 14_1ETD7 Heifer N°1 at the day (7) of the first embryo transfer

description:
Heifer N°1 at the day (7) of the first embryo transfer
253680910016_2_4


title: NAc, VEH-VEH, Male, 5

description: V-V Male NAc


title: genomic DNA from clinical gastric cancer case [GC280T]

description:
SAMPLE 34
extremely high DNA methylation epigenotype


title: Sample_9_Polish women with BC


title: genomic DNA from clinical gastric cancer case [GC219T]

description:
SAMPLE 27
extremely high DNA methylation epigenotype


title: FC, VEH-VEH,  Female, 4

description: V-V Female FC


title: genomic DNA from clinical gastric cancer case [GC250T]

description:
SAMPLE 29
extremely high DNA methylation epigenotype


title: Sample_8_Polish women with BC

description: DNA extracted from peripheral blood of Polish women with BC


title: NAc, VEH-VEH, Male, 4

description: V-V Male NAc


title: genomic DNA from clinical gastric cancer case [GC215T]

description:
SAMPLE 25
high DNA methylation epigenotype_MLH1(+)


title: 14_PCD14 Heifer N°14 at day 14 post-estrus of Preconceptional cycle

description:
Heifer N°14 at day 14 post-estrus of Preconceptional cycle
253680910014_1_4


title: genomic DNA from clinical gastric cancer case [GC256T]

description:
SAMPLE 30
extremely high DNA methylation epigenotype


title: NAc, VEH-VEH, Male, 3

description: V-V Male NAc


title: genomic DNA from clinical gastric cancer case [GC226T]

description:
SAMPLE 28
high DNA methylation epigenotype_MLH1(+)


title: genomic DNA from clinical gastric cancer case [GC216T]

description:
SAMPLE 26
high DNA methylation epigenotype_MLH1(-)


title: Sample_6_Polish women with BC


title: NAc, VEH-VEH, Male, 2

description: V-V Male NAc


title: genomic DNA from clinical gastric cancer case [GC209T]

description:
SAMPLE 22
extremely high DNA methylation epigenotype


title: 13_1ETD7 Heifer N°1 at the day (7) of the first embryo transfer

description:
Heifer N°1 at the day (7) of the first embryo transfer
253680910014_1_3


title: Sample_7_Polish women with BC


title: 13_PCD14 Heifer N°13 at day 14 post-estrus of Preconceptional cycle

description:
Heifer N°13 at day 14 post-estrus of Preconceptional cycle
253680910015_1_4


title: genomic DNA from clinical gastric cancer case [GC211T]

description:
SAMPLE 23
extremely low DNA methylation epigenotype


title: genomic DNA from clinical gastric cancer case [GC214T]

description:
SAMPLE 24
Outlier


title: Sample_4_Polish women with BC


title: genomic DNA from clinical gastric cancer case [GC192T]

description:
SAMPLE 20
high DNA methylation epigenotype_MLH1(-)


title: 14_PCD7 Heifer N°14 at day 7 post-estrus of Preconceptional cycle

description:
Heifer N°14 at day 7 post-estrus of Preconceptional cycle
253680910018_1_2


title: NAc, VEH-VEH, Male, 1

description: V-V Male NAc


title: FC, VEH-VEH, Male, 5

description: V-V Male FC


title: Sample_5_Polish women with BC


title: 12_2ETD7 Heifer N°12 at the day (7) of the second embryo transfer

description:
Heifer N°12 at the day (7) of the second embryo transfer
253680910013_2_2


title: FC, VEH-VEH, Male, 4

description: V-V Male FC


title: 13_PCD7 Heifer N°13 at day 7 post-estrus of Preconceptional cycle

description:
Heifer N°13 at day 7 post-estrus of Preconceptional cycle
253680910013_2_3


title: FC, VEH-VEH, Male, 6

description: V-V Male FC


title: genomic DNA from clinical gastric cancer case [GC194T]

description:
SAMPLE 21
extremely low DNA methylation epigenotype


title: Sample_1_Polish women with BC


title: Sample_3_Polish women with BC


title: FC, VEH-VEH, Male, 3

description: V-V Male FC


title: Sample_2_Polish women with BC


title: 11_PCD14 Heifer N°11 at day 14 post-estrus of Preconceptional cycle

description:
Heifer N°11 at day 14 post-estrus of Preconceptional cycle
253680910012_1_3


title: 11_PCD7 Heifer N° 11 at day 7 post-estrus of Preconceptional cycle

description:
Heifer N° 11 at day 7 post-estrus of Preconceptional cycle
253680910012_2_3


title: 12_1ETD7 Heifer N°1 at the day (7) of the first embryo transfer

description:
Heifer N°1 at the day (7) of the first embryo transfer
253680910014_1_1


title: FC, VEH-VEH, Male, 2

description: V-V Male FC


title: genomic DNA from clinical gastric cancer case [GC191T]

description:
SAMPLE 19
high DNA methylation epigenotype_MLH1(-)


title: 11_1ETD7 Heifer N°1 at the day (7) of the first embryo transfer

description:
Heifer N°1 at the day (7) of the first embryo transfer
253680910013_2_4


title: Nepro_IP_rep2

city: Cambridge

first: Jimmy

last: Ly

state: Massachusetts

address: 455 main street

department: Biology

institute: Whitehead Institute

description: Library name: Nepro_IP_rep2

library_source: transcriptomic

data_processing:
Samples were demultiplexed with bcl2fastq v2.20 to generate fastq files.
Reads were aligned using STAR v2.7.1.a with options ---runThreadN 6 --runMode alignReads --outFilterMultimapNmax 1 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate for mRNA seq; --runThreadN 2 --limitBAMsortRAM 10000000000 --runMode alignReads --outFilterMultimapNmax 5000 --winAnchorMultimapNmax 1000 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate for rRNA analysis.
Transcript counts were quantified using Htseq-count
Differential expression analysis was performed using DEseq2
Assembly: hg38 (gencode v25) for mRNA sequencing. Custom human pre-rRNA (Gene ID: 100861532) for rRNA analysis.
Supplementary files format and content: Transcript counts are stored in tab-delimited files with one row per transcript, quantification done using Htseq-count.

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum, 2 mM L-glutamine, and 100 U/mL penicillin/streptomycin

extract_protocol:
After dox induction cells were harvested after incubation with 5 mM EDTA in 1X PBS for 5 minutes at 37 °C. Harvested cells were pelleted by centrifugation at 200 x g. Cells were washed once with 1X PBS and then once with 1x lysis buffer (25 mM HEPES pH 8.0, 2 mM MgCl2, 0.1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 300 mM KCl and 10% glycerol). Cells were pelleted between each wash step. Finally, the cells were resuspended in a 1:1 ratio in 1x lysis buffer and flash frozen in liquid nitrogen before being stored at -80 °C. Polysome lysis buffer (20 mM Hepes pH 7.5, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100) supplemented with 1% CHAPS, 1 cOmplete EDTA-free protease inhibitor cocktail (Roche), and 0.02 U/μl of SUPERaseIn (Invitrogen) was added to each frozen cell pellet before thawing the cells in a 37 °C water bath. Cells were lysed by 10 cycles of sonication at high amplitude with a 30 second on time and 1 minute off time (Bioruptor, Diagenode). The lysate was clarified by centrifugation at 21,000 x g for 30 minutes at 4 °C. Clarified lysate was then incubated with Protein A beads (BioRad) coupled to a rabbit anti-GFP antibody at 4 °C for 2 hours on a rotating wheel.  Following incubation with the clarified lysate the beads were washed 4 times for 5 minutes with polysome lysis buffer supplemented with 1 mM DTT, 10 µg/ml leupeptin/pepstatin/chymostatin, and 0.02 U/ml of SUPERaseIn. RNA was eluted from the beads by addition of TRI reagent. For analysis of knockout cells, cells were washed once with PBS then directly lyzed in Tri reagent.
For RIP-seq library preparation, libraries were prepared with the Watchmaker library prep kit (Watchmaker Genomics) with a QiaFast Select rRNA kit (Qiagen) module for rRNA depletion and each step was performed according to the manufacturer’s instructions. For the analysis of rRNA from knockout cells, the total RNA was directly prepped using the Kapa HyperPrep kit without any depletion/enrichment modules according the manufacturer’s instructions.  For the analysis of mRNA from knockout cells, the Kapa HyperPrep kit with oligo dT enrichment was performed according the manufacturer’s instructions.

treatment_protocol: GFP transgene expression was induced with 1 ug/mL doxycycline for 2 days and cells were harvested for RIP-seq. Knockout cells were harvested 3 days post puromycin selection or 6 days post infection.

tag: cell line

value: HeLa


title: FC, VEH-VEH, Male, 1

description: V-V Male FC


title: 35S GPT2 stem tissue,overexpression line, sample 3, Rep 4

city: College station

first: Wayne

last: Versaw

state: Texas

address: Nagle St

institute: Texas A&M University

data_processing:
Reads were mapped to the Arabidopsis genome (TAIR10.1; using RNA STAR). After mapping, differential expression analysis was conducted using DESeq2
Galaxy (HPRC- TAMU) was used to execute a complete RNA-seq analysis pipeline
Assembly: TAIR10.1
Supplementary files format and content: tab-delimited excel files include counts for each sample

organism: Arabidopsis thaliana

source_name: Stem

growth_protocol: Plant lines used for transcriptomic analysis were grown in 0.5 x Noren medium for 9-10 weeks prior to harvesting stem tissues.

extract_protocol:
Total RNA was isolated using the QIAGEN RNeasy plant mini kit (QIAGEN, Inc., Valencia, CA) according to the manufacturer's instructions
The mRNA sequencing library was prepared using the TruSeq stranded mRNA library method

value: Stem

tag: genotype


title: GFP_IP_rep2

description: Library name: GFP_IP_rep2


title: genomic DNA from clinical gastric cancer case [GC153T]

description:
SAMPLE 16
high DNA methylation epigenotype_MLH1(-)


title: genomic DNA from clinical gastric cancer case [GC159T]

description:
SAMPLE 17
extremely high DNA methylation epigenotype


title: Nepro_IP_rep1

description: Library name: Nepro_IP_rep1


title: GFP_IP_rep1

description: Library name: GFP_IP_rep1


title: 35S GPT2 stem tissue,overexpression line, sample 3, Rep 2


title: 35S GPT2 stem tissue,overexpression line, sample 3, Rep 1


title: 35S GPT2 stem tissue,overexpression line, sample 3, Rep 3


title: 10_2ETD7 Heifer N°10 at the day (7) of the second embryo transfer

description:
Heifer N°10 at the day (7) of the second embryo transfer
253680910015_1_1


title: Nepro_Input_rep1

description: Library name: Nepro_Input_rep1


title: Nepro_Input_rep2

description: Library name: Nepro_Input_rep2


title: 8_PCD14 Heifer N°8 at day 14 post-estrus of Preconceptional cycle

description:
Heifer N°8 at day 14 post-estrus of Preconceptional cycle
253680910017_1_1

value: Preconceptional cycle (estrus cycle)


title: 35S GPT2 stem tissue,overexpression line, sample 2, Rep 4


title: 8_PCD7 Heifer N° 8 at day 7 post-estrus of Preconceptional cycle

description:
Heifer N° 8 at day 7 post-estrus of Preconceptional cycle
253680910019_1_3


title: 10_1ETD7 Heifer N°1 at the day (7) of the first embryo transfer

description:
Heifer N°1 at the day (7) of the first embryo transfer
253680910015_2_3


title: 7_2ETD7 Heifer N°7 at the day (7) of the second embryo transfer

description:
Heifer N°7 at the day (7) of the second embryo transfer
253680910018_1_4


title: 6_2ETD7 Heifer N°6 at the day (7) of the second embryo transfer

description:
Heifer N°6 at the day (7) of the second embryo transfer
253680910017_2_1


title: 6_1ETD7 Heifer N°1 at the day (7) of the first embryo transfer

description:
Heifer N°1 at the day (7) of the first embryo transfer
253680910018_2_3


title: GFP_Input_rep2

description: Library name: GFP_Input_rep2


title: GFP_Input_rep1

description: Library name: GFP_Input_rep1


title: 35S GPT2 stem tissue,overexpression line, sample 2, Rep 2


title: 35S GPT2 stem tissue,overexpression line, sample 2, Rep 3


title: genomic DNA from clinical gastric cancer case [GC136T]

description:
SAMPLE 14
high DNA methylation epigenotype_MLH1(+)


title: Rpp14_day3_rep2_total

description: Library name: Rpp14_day3_rep2_total


title: 35S GPT2 stem tissue,overexpression line, sample 2, Rep 1


title: genomic DNA from clinical gastric cancer case [GC131T]

description:
SAMPLE 13
high DNA methylation epigenotype_MLH1(-)


title: genomic DNA from clinical gastric cancer case [GC151T]

description:
SAMPLE 15
high DNA methylation epigenotype_MLH1(+)


title: genomic DNA from clinical gastric cancer case [GC094T]

description:
SAMPLE 12
extremely low DNA methylation epigenotype


title: genomic DNA from clinical gastric cancer case [GC092T]

description:
SAMPLE 11
Outlier


title: C18orf21_day3_rep2_total

description: Library name: C18orf21_day3_rep2_total


title: Rpp21_day3_rep2_total

description: Library name: Rpp21_day3_rep2_total


title: 35S GPT2 stem tissue,overexpression line, sample 1, Rep 4


title: 35S GPT2 stem tissue,overexpression line, sample 1, Rep 3


title: genomic DNA from clinical gastric cancer case [GC064T]

description:
SAMPLE 8
high DNA methylation epigenotype_MLH1(-)


title: genomic DNA from clinical gastric cancer case [GC184T]

description:
SAMPLE 18
extremely low DNA methylation epigenotype


title: 2_2ETD7 Heifer N°2 at the day (7) of the second embryo transfer

description:
Heifer N°2 at the day (7) of the second embryo transfer
253680910017_1_2


title: genomic DNA from clinical gastric cancer case [GC052T]

description:
SAMPLE 6
low DNA methylation epigenotype


title: 4_2ETD7 Heifer N°4 at the day (7) of the second embryo transfer

description:
Heifer N°4 at the day (7) of the second embryo transfer
253680910016_2_1


title: 35S GPT2 stem tissue,overexpression line, sample 1, Rep 2


title: 1_1ETD7 Heifer N°1 at the day (7) of the first embryo transfer

description:
Heifer N°1 at the day (7) of the first embryo transfer
253680910013_1_1


title: genomic DNA from clinical gastric cancer case [GC063T]

description:
SAMPLE 7
extremely low DNA methylation epigenotype


title: 2_1ETD7 Heifer N°1 at the day (7) of the first embryo transfer

description:
Heifer N°1 at the day (7) of the first embryo transfer
253680910017_1_4


title: 35S GPT2 stem tissue,overexpression line, sample 1, Rep 1


title: Neutrophil, Female, Zika, rep3

city: Detroit

first: Gil

middle: G.

last: Mor

state: Michigan

address: 275 E. Hancock

department: C.S. Mott Center for Human Growth and Development

institute: Wayne State University School of Medicine

description:
Library name: Sample 28
FZ3

data_processing:
Base calling was conducted using HiSeq Control Software, converted to fastq files and de-multiplexed using Illumina bcl2fastq 2.17 software
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.36
Trimmed sequence reads were mapped to GRCm39 using Hisat2 v2.2.1
Unique gene hit counts were calculated using the featureCounts function from the Subread package v1.5.2
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: Neutrophil

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

treatment_protocol: Pregnant C57/BL6 mice were exposed to 50PFU  Zika virus on E8.5. Placentas were collected on E12.5. And in another cohort, pups were delivered and sacrificed on PND35, bone marrow neutrophils of offspring from Zika-exposed dams were isolated and sent for RNAseq.

value: Neutrophil

value: Zika

tag: batch


title: Control_day3_rep2_total

description: Library name: Control_day3_rep2_total


title: C18orf21_day3_rep1_total

description: Library name: C18orf21_day3_rep1_total


title: Neutrophil, Female, Zika, rep2

description:
Library name: Sample 27
FZ2


title: genomic DNA from clinical gastric cancer case [GC087T]

description:
SAMPLE 10
extremely low DNA methylation epigenotype


title: GaHV-2-infected ESCDL-1 cell line

city: Namur

first: Damien

last: Coupeau

address: Rue de Bruxelles, 61

department: Namur Research Institute for Life Sciences

country: Belgium

institute: University of Namur

data_processing:
Viral reads recovery (alignment using BWA mem -a -T15) (BWA v0.7.11)
Adapter trimming (Trimmomatic v0.39. Included the trimming of the adapters, quality trimming (Sliding Window 4:15), and a minimal length filter of 70 nucleotides
PCR duplicates removal (dedupe.sh (BBMap v1.0))
vCircTrappist v1.0 pipeline for circRNA-originating reads identification (including Samtools v1.10 and BWA v0.7.11)
Assembly: KX905135.1 ; KT122858.1 ; AC_000008.1 ; NC_001436.1 ; EF523390.1
Supplementary files format and content: tab-delimited text file including raw circRNA-derived reads count, circularization sites sequences, splicing pattern, strandness of the reads, 5' and 3' positions of the circularization sites, max size of the circRNAs, colocalized genes, common k-mers between circularization sites, viral segment, read identifiers

organism: Gallus gallus

extract_protocol:
RNA was extracted using TRI-reagent (Thermofisher) and 4ug were sent to sequencing (Novogene).
1µg of total RNA was sent to Novogene for the library preparation and sequencing. Library preparation include : ribosomal depletion, linear RNA degradation, RNA fragmentation, reverse transcription, second strand synthesis (using dUTPs), end-repair, A-tailing, adapter ligation, enzyme digestion to remove dUTPs-containing second strand cDNAs, size selection, PCR amplification

value: WT


title: Col-0 stem tissue, control trial for comparison with 35S GPT2, sample 3, Rep 4


title: Rpp21_day3_rep1_total

description: Library name: Rpp21_day3_rep1_total


title: 1_PCD14 Heifer N°1 at day 14 post-estrus of Preconceptional cycle

description:
Heifer N°1 at day 14 post-estrus of Preconceptional cycle
253680910012_1_4


title: H3K27me3_wt_21-24hr_exp8_chrom2

city: Martinsried

first: Jürg

last: Müller

state: Bavaria

address: Am Klopferspitz

country: Germany

institute: Max Planck Institute of Biochemistry

description: Library name: sample 10

data_processing:
Reads from fastq files were aligned to the dm6 genome (and to the D. pseudoobscura dp3 genome for subsequent normalization) using STAR (Dobin et al., 2013). Only sequences that mapped uniquely to the genome with a maximum of two mismatches were considered for further analyses.
Bam files were used as inputs to run Bioconductor packages.
The STAN Bioconductor package (Zacher et al., 2014) was used to refine the subdivision of H3K27me3 enriched domains (see Bonnet et al., 2022) into canonical and non-canonical H3K27me3 domains.
The proportion of D. pseudoobscura reads as compared to D. melanogaster reads in input and in samples was used to normalize the ChIP-seq datasets for histone marks in embryos. Reference samples for normalization with D. pseudoobscura chromatin are indicated. Other samples were normalized based on total read number per million reads. Normalization factor for each sample is indicated.
Assembly: dm6
Supplementary files format and content: Normalized bigwig files (bin size = 1) were generated with deepTools (Ramirez et al., 2016).

organism: Drosophila melanogaster

source_name: 21-24hr old embryos

growth_protocol: Drosophila embryos and larvae were grown on standard medium at 25˚C

extract_protocol:
Lysates were clarified from sonicated fixed nuclei. Histone/Protein-DNA complexes were isolated with antibody. D. pseudoobscura chromatin was spiked in at a 1:5 ratio of dm / dp chromatin before the addition of the antibody.
Libraries were prepared according to manufacturer's instructions.

value: 21-24hr old embryos

value: wt

tag: antibodies

value: H3K27me3 (Cell Signaling (#9733))

tag: normalization factor


title: genomic DNA from clinical gastric cancer case [GC008T]

description:
SAMPLE 2
Outlier


title: H3K27me3_wt_21-24hr_exp8_chrom1

description: Library name: sample 9


title: Neutrophil, Female, Zika, rep1

description:
Library name: Sample 26
FZ1


title: H3K27me3_Jarid2^0_21-24hr_exp8_chrom2

description: Library name: sample 7


title: Rpp14_day3_rep1_total

description: Library name: Rpp14_day3_rep1_total


title: Control_day3_rep1_total

description: Library name: Control_day3_rep1_total


title: Neutrophil, Male, Zika, rep3

description:
Library name: Sample 25
MZ3


title: genomic DNA from clinical gastric cancer case [GC024T]

description:
SAMPLE 4
Outlier


title: genomic DNA from clinical gastric cancer case [GC075T]

description:
SAMPLE 9
extremely low DNA methylation epigenotype


title: 5_2ETD7 Heifer N°5 at the day (7) of the second embryo transfer

description:
Heifer N°5 at the day (7) of the second embryo transfer
253680910013_1_4

value: heifer

value: Peripheral White Blood Cells


title: H3K27me3_Jarid2^0_21-24hr_exp8_chrom1

description: Library name: sample 6


title: Rpp14_day3_rep2_mRNA

description: Library name: Rpp14_day3_rep2_mRNA


title: 1_PCD7 Heifer N°1 at day 7 post-estrus of Preconceptional cycle

description:
Heifer N°1 at day 7 post-estrus of Preconceptional cycle
253680910019_1_2


title: Neutrophil, Male, Zika, rep2

description:
Library name: Sample 24
MZ2


title: Col-0 stem tissue, control trial for comparison with 35S GPT2, sample 3, Rep 2


title: genomic DNA from clinical gastric cancer case [GC039T]

description:
SAMPLE 5
extremely low DNA methylation epigenotype


title: C18orf21_day3_rep2_mRNA

description: Library name: C18orf21_day3_rep2_mRNA


title: genomic DNA from clinical gastric cancer case [GC017T]

description:
SAMPLE 3
low DNA methylation epigenotype


title: genomic DNA from clinical gastric cancer case [GC003T]

description:
SAMPLE 1
extremely low DNA methylation epigenotype


title: input_wt_21-24hr_exp8_chrom1

description: Library name: sample 4


title: input_Jarid2^0_21-24hr_exp8_chrom2

description: Library name: sample 3


title: Neutrophil, Male, Zika, rep1

description:
Library name: Sample 23
MZ1


title: Control_day3_rep2_mRNA

description: Library name: Control_day3_rep2_mRNA


title: Col-0 stem tissue, control trial for comparison with 35S GPT2, sample 2, Rep 3


title: Neutrophil, Female, Control, rep2

description:
Library name: Sample 21
FC2

value: Control


title: Rpp21_day3_rep2_mRNA

description: Library name: Rpp21_day3_rep2_mRNA


title: Neutrophil, Female, Control, rep3

description:
Library name: Sample 22
FC3

value: Female


title: Col-0 stem tissue, control trial for comparison with 35S GPT2, sample 2, Rep 4


title: Neutrophil, Female, Control, rep1

description:
Library name: Sample 20
FC1


title: input_Jarid2^0_21-24hr_exp8_chrom1

description: Library name: sample 2


title: input_wt_21-24hr_exp8_chrom2

description: Library name: sample 5


title: Col-0 stem tissue, control trial for comparison with 35S GPT2, sample 3, Rep 1


title: Col-0 stem tissue, control trial for comparison with 35S GPT2, sample 2, Rep 1


title: Col-0 stem tissue, control trial for comparison with 35S GPT2, sample 3, Rep 3


title: Col-0 stem tissue, control trial for comparison with 35S GPT2, sample 2, Rep 2


title: Rpp14_day3_rep1_mRNA

description: Library name: Rpp14_day3_rep1_mRNA


title: H3K27me3_l(3)73Ah^0_21-24hr_exp2_chrom2

description: Library name: sample 1


title: Neutrophil, Male, Control, rep3

description:
Library name: Sample 19
MC3


title: Rpp21_day3_rep1_mRNA

description: Library name: Rpp21_day3_rep1_mRNA


title: Col-0 stem tissue, control trial for comparison with 35S GPT2, sample 1, Rep 4


title: Col-0 stem tissue, control trial for comparison with 35S GPT2, sample 1, Rep 3


title: RNAseq_sa_rep2

city: Stanford

first: Neuza

last: Reis Matias

state: CA

address: 279 Campus Drive

department: Developmental Biology

institute: Stanford University

description: Library name: RNAseq_sa_rep2

data_processing:
Adapters and low-quality bases were trimmed with trimGalore (0.6.6) (Martin 2011); reads were mapped to Drosophila genome assembly: BDGP6.32 (GCA_000001215.4) using STAR (2.7.9a) (Dobin et al. 2013); DeepTools (3.3.0) was used to generate normalized coverage tracks (BigWig files)
Input raw files to run SQANTI3 (Pardo-Palacios et al. 2024), which used Kallisto to map reads to transcriptome (generated from PacBio analysis) and quantify transcript isoforms. tappAS was used for transcript and gene expression analysis, and expression of predicted protein isoforms (Fuente et al. 2020).
To quantify expression from a given promoter (defined by CAGE cluster), the expression from all transcripts starting at that promoter was summed. DEseq2 was used for differential promoter expression analysis (Love, Huber, and Anders 2014)
Analysis scripts are available at https://github.com/NeuzaRM/Kmg_FullerPaper2025
Assembly: dm6
Supplementary files format and content: BigWig (for fw, rv, or both direction reads)
Supplementary files format and content: tsv files (output of tappAS) with expression data of transcripts, genes, or proteins
Supplementary files format and content: text files with promoter expression data

molecule: polyA RNA

source_name: Testes

extract_protocol:
RNA was extracted from 150 pairs of testes using the RNeasy Plus Mini Kit from QIAGEN (74104)
Library preparation was carried out using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (#E7760S), with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (#E7490S).

value: Testes

value: Fly crosses were kept for 3 days at 25°C. Adults were then flipped to a new bottle, while the eggs and early larvae were shifted to 29°C. Testes were dissected from 0–2 day old males in 1xPBS.


title: Neutrophil, Male, Control, rep1

description:
Library name: Sample 17
MC1


title: RNAseq_sa_rep1

description: Library name: RNAseq_sa_rep1


title: Col-0 stem tissue, control trial for comparison with 35S GPT2, sample 1, Rep 2


title: Placenta, Male, Zika, rep3

description:
Library name: Sample 16
Z8R4M

source_name: Placenta

value: Placenta

tag: mother


title: Placenta, Male, Zika, rep2

description:
Library name: Sample 15
Z6L4M

value: Male


title: RNAseq_aly_rep1

description: Library name: RNAseq_aly_rep1


title: Neutrophil, Male, Control, rep2

description:
Library name: Sample 18
MC2


title: Col-0 stem tissue, control trial for comparison with 35S GPT2, sample 1, Rep 1


title: gpt2-1 stem tissue, mutant, sample 3, Rep 4


title: Control_day3_rep1_mRNA

description: Library name: Control_day3_rep1_mRNA

value: HeLa


title: C18orf21_day3_rep1_mRNA

description: Library name: C18orf21_day3_rep1_mRNA


title: Senescent + 2uM Ruxolitinib, replicate1

city: La Jolla

first: Xue

last: Lei

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

description: Library name: Sen_Ruxo_1

data_processing:
Trim adapters and low‑quality bases with Trimmomatic 0.38.1.
Align reads to the human hg38 genome with HISAT2 2.2.1.
Count reads per gene using featureCounts 2.0.3.
Generate QC reports (FastQC 0.74, then summarize with MultiQC) and perform PCA for sample relationships.
Perform differential expression analysis and generate Normalized counts with DESeq2 2.11.40.8.
Assembly: Homo sapiens GRCh38 (hg38)
Supplementary files format and content: Normalized_counts_RNA_seq_IMR90_Palbo.csv

growth_protocol: IMR90 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), L-glutamine, and penicillin-streptomycin, and maintained at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
TRIzol extraction: lyse, add chloroform, centrifuge, collect aqueous phase, precipitate with ethanol, wash, air‑dry, resuspend.
PolyA capture

treatment_protocol: IMR90 fibroblasts were exposed to 20 Gy ionizing radiation (IR) over a 10‑minute period. Beginning on day 4 post‑IR, cells were treated with 2 μM Palbociclib or 2 μM Ruxolitinib on days 4, 6, 8, and 10. All samples (IR‑DMSO, IR + Palbociclib, and IR + Ruxolitinib) were harvested on day 11 post‑irradiation.

value: Human Lung Fibroblasts

value: Ruxolitinib, 2uM


title: Senescent + 2uM Ruxolitinib, replicate3

description: Library name: Sen_Ruxo_3


title: Senescent + 2uM Palbocicilb, replicate3

description: Library name: Sen_Palbo_3

value: Palbocilib, 2uM


title: RNAseq_KmgKD_sa_rep2

description: Library name: RNAseq_KmgKD_sa_rep2

value: UAS-Kmg RNAi/+; sa1,bamGal4/sa3


title: Placenta, Female, Zika, rep5

description:
Library name: Sample 13
Z8R2F

value: Zika


title: RNAseq_KmgKD_sa_rep1

description: Library name: RNAseq_KmgKD_sa_rep1

value: UAS-Kmg RNAi/+; sa1,bamGal4/sa2


title: Senescent + 2uM Palbocicilb, replicate2

description: Library name: Sen_Palbo_2

value: WT


title: gpt2-1 stem tissue, mutant, sample 3, Rep 2

value: Stem


title: Placenta, Male, Zika, rep1

description:
Library name: Sample 14
Z5L1M


title: RNAseq_aly_rep2

description: Library name: RNAseq_aly_rep2


title: gpt2-1 stem tissue, mutant, sample 3, Rep 1


title: RNAseq_KmgKD_aly_rep2

description: Library name: RNAseq_KmgKD_aly_rep2

value: UAS-Kmg RNAi/+; aly2,bamGal4/aly5p


title: Placenta, Female, Zika, rep4

description:
Library name: Sample 12
Z8L1F


title: Senescent + 2uM Ruxolitinib, replicate2

description: Library name: Sen_Ruxo_2


title: Senescent + 2uM Palbocicilb, replicate1

description: Library name: Sen_Palbo_1


title: Placenta, Female, Zika, rep3

description:
Library name: Sample 11
Z6R1F


title: RNAseq_KmgKD_aly_rep1

description: Library name: RNAseq_KmgKD_aly_rep1


title: gpt2-1 stem tissue, mutant, sample 2, Rep 4


title: Senescent DMSO, replicate3

description: Library name: Sen_DMSO_3

value: DMSO


title: Placenta, Female, Zika, rep2

description:
Library name: Sample 10
Z6L1F


title: RNAseq_SimjKD_rep2

description: Library name: RNAseq_SimjKD_rep2

value: bamGAL4/ SimjRNAi


title: Senescent DMSO, replicate2

description: Library name: Sen_DMSO_2


title: gpt2-1 stem tissue, mutant, sample 3, Rep 3


title: gpt2-1 stem tissue, mutant, sample 2, Rep 2


title: RNAseq_SimjKD_rep1

description: Library name: RNAseq_SimjKD_rep1


title: Placenta, Male, Control, rep5

description:
Library name: Sample 8
C12R2M

value: Control


title: RNAseq_Mi2KD_rep2

description: Library name: RNAseq_Mi2KD_rep2

value: Testes

value: bamGAL4/ Mi2RNAi


title: gpt2-1 stem tissue, mutant, sample 2, Rep 1


title: gpt2-1 stem tissue, mutant, sample 1, Rep 4


title: Proliferating replicate 2

description: Library name: Prolif_2

value: No treatment


title: Proliferating replicate 3

description: Library name: Prolif_3


title: gpt2-1 stem tissue, mutant, sample 2, Rep 3


title: Placenta, Male, Control, rep4

description:
Library name: Sample 7
C12L5M

value: Placenta

value: Male


title: Proliferating replicate 1

description: Library name: Prolif_1

value: Human Lung Fibroblasts


title: Placenta, Male, Control, rep3

description:
Library name: Sample 6
C7R2M


title: RNAseq_DanyKD_rep2

description: Library name: RNAseq_DanyKD_rep2

value: bamGAL4/ DanyRNAi

value: Fly crosses were kept for 3 days at 25°C. Adults were then flipped to a new bottle, while the eggs and early larvae were shifted to 29°C. Testes were dissected from 0–2 day old males in 1xPBS.


title: Placenta, Female, Zika, rep1

description:
Library name: Sample 9
Z5L6F

value: Female


title: RNAseq_DanyKD_rep1

description: Library name: RNAseq_DanyKD_rep1


title: gpt2-1 stem tissue, mutant, sample 1, Rep 2


title: Senescent DMSO, replicate1

description: Library name: Sen_DMSO_1


title: Senescent CCND1 knockdown, replicate3

description: Library name: Sen_siD1_3

data_processing:
Trim adapters and low‑quality bases with Trimmomatic 0.38.1.
Align reads to the human hg38 genome with HISAT2 2.2.1.
Count reads per gene using featureCounts 2.0.3.
Generate QC reports (FastQC 0.74, then summarize with MultiQC) and perform PCA for sample relationships.
Perform differential expression analysis and generate Normalized counts with DESeq2 2.11.40.8.
Assembly: Homo sapiens GRCh38 (hg38)
Supplementary files format and content: Normalized_Counts_RNA_seq_IMR90_siRNAKD.csv

treatment_protocol: siRNA KD (days 4 & 7 post‑IR): use 5 nM siRNA with DharmaFECT in serum‑free media; incubate complexes RT 30 min; add to cells for 18–20 h; then replace with regular media. Harvest day 10.

value: CCND1 knockdown

value: Irradiation, siRNA knockdown


title: Placenta, Male, Control, rep2

description:
Library name: Sample 5
C7R1M


title: Placenta, Male, Control, rep1

description:
Library name: Sample 4
C7L1M


title: gpt2-1 stem tissue, mutant, sample 1, Rep 1


title: Senescent CCND1 knockdown, replicate2

description: Library name: Sen_siD1_2


title: RNAseq_Mi2KD_rep1

description: Library name: RNAseq_Mi2KD_rep1


title: RNAseq_KmgKD_rep2

description: Library name: RNAseq_KmgKD_rep2

value: bamGAL4/ KmgRNAi


title: RNAseq_KmgKD_rep1

description: Library name: RNAseq_KmgKD_rep1


title: gpt2-1 stem tissue, mutant, sample 1, Rep 3

value: Stem


title: Placenta, Female, Control, rep3

description:
Library name: Sample 3
C8R5F


title: HCT-RNAi stem tissue, lignin mutant, sample 3, Rep 4

value: HCT-RNAi


title: HCT-RNAi stem tissue, lignin mutant, sample 3, Rep 3


title: Placenta, Female, Control, rep2

description:
Library name: Sample 2
C8L1F


title: Senescent CDK4, CDK6 dual knockdown, replicate3

description: Library name: Sen_siK4_K6_3

value: CDK4, CDK6 knockdown


title: RNAseq_Control_rep2

description: Library name: RNAseq_Control_rep2


title: RNAseq_Control_rep1

description: Library name: RNAseq_Control_rep1


title: HCT-RNAi stem tissue, lignin mutant, sample 3, Rep 2


title: Placenta, Female, Control, rep1

description:
Library name: Sample 1
C7L2F


title: ChIPaKmg_Mi2KD_rep2_INPUT

description: Library name: ChIPaKmg_Mi2KD_rep2_INPUT

data_processing:
Adapters and low-quality bases were trimmed using trimGalore (0.6.6), reads were mapped to Drosophila genome assembly: BDGP6.32 (GCA_000001215.4) using bwa aln (0.7.18) (Li and Durbin 2009)
DeepTools (3.1.0) was used to generate normalized coverage files (BibWig)
Analysis scripts are available at https://github.com/NeuzaRM/Kmg_FullerPaper2025
Assembly: dm6
Supplementary files format and content: BigWig

extract_protocol:
ChIP-seq was performed using the Low Cell ChIP Kit from Active Motif (#53086). Please see publication for details.
Libraries were made using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® NEB (#E7645L).

value: bamGAL4 / Mi2 RNAi

tag: chip antibody


title: Senescent CDK4, CDK6 dual knockdown, replicate1

description: Library name: Sen_siK4_K6_1


title: H3K27me3_Psc-Su(z)2^0_21-24hr_exp5_chrom1

description: Library name: sample 8

value: 21-24hr old embryos

value: H3K27me3 (Cell Signaling (#9733))


title: ChIPaKmg_Mi2KD_rep2

description: Library name: ChIPaKmg_Mi2KD_rep2

value: Testes

value: anti-Kmg (Kim et al. 2017)


title: CAGEseq_KmgKD_rep2

description:
Library name: CAGEseq_KmgKD_rep2
150bp PE but only sed only R1 for this analysis

data_processing:
Low-quality bases were trimmed using TrimGalore (0.6.6) (Martin 2011) and mapped to Drosophila genome assembly: BDGP6.32 (GCA_000001215.4) using STAR (2.7.11b) (Dobin et al. 2013).
The most 5′ nucleotide of each mapped read was counted using bedtools coverage (2.27.1) (Quinlan and Hall 2010) and used as input into CAGEr to build CAGE clusters (1.20.0) (Haberle et al. 2015)
Created bigwig files with bedGraphToBigWig
Analysis scripts are available at https://github.com/NeuzaRM/Kmg_FullerPaper2025
Assembly: dm6
Supplementary files format and content: tab-delimited text files include CAGE cluster information for each sample and for consensus cluster.
Supplementary files format and content: BigWig (for fw, rv, or both direction reads)

extract_protocol:
RNA was extracted from 150 pairs of testes using the RNeasy Plus Mini Kit from QIAGEN (74104)
10ug of total RNA were sent to DNAform (https://www.dnaform.jp/en/products/library/cage/) for CAGE library preparation using published protocol nAnTi-CAGE (non-amplifying-non-tagging illumina CAGE) (Murata et al. 2014)


title: HCT-RNAi stem tissue, lignin mutant, sample 2, Rep 4


title: ChIPaKmg_Mi2KD_rep1_INPUT

description: Library name: ChIPaKmg_Mi2KD_rep1_INPUT


title: Senescent CDK6 knockdown, replicate3

description: Library name: Sen_siK6_3

value: CDK6 knockdown


title: HCT-RNAi stem tissue, lignin mutant, sample 2, Rep 3


title: Senescent CDK6 knockdown, replicate2

description: Library name: Sen_siK6_2


title: CAGEseq_KmgKD_rep1

description:
Library name: CAGEseq_KmgKD_rep1
150bp PE but only sed only R1 for this analysis


title: HCT-RNAi stem tissue, lignin mutant, sample 2, Rep 2


title: ChIPaKmg_DanyKD_rep2_INPUT

description: Library name: ChIPaKmg_DanyKD_rep2_INPUT

value: bamGAL4 / Dany RNAi


title: ChIPaKmg_Mi2KD_rep1

description: Library name: ChIPaKmg_Mi2KD_rep1


title: Senescent CCND1 knockdown, replicate1

description: Library name: Sen_siD1_1

value: Human Lung Fibroblasts


title: CAGEseq_Control_rep1

description:
Library name: CAGEseq_Control_rep1
76bp SR


title: HCT-RNAi stem tissue, lignin mutant, sample 2, Rep 1


title: Senescent CDK4 knockdown, replicate3

description: Library name: Sen_siK4_3

value: CDK4 knockdown


title: ChIPaKmg_DanyKD_rep2

description: Library name: ChIPaKmg_DanyKD_rep2


title: Senescent CDK4, CDK6 dual knockdown, replicate2

description: Library name: Sen_siK4_K6_2


title: HCT-RNAi stem tissue, lignin mutant, sample 3, Rep 1


title: Senescent CDK4 knockdown, replicate2

description: Library name: Sen_siK4_2


title: ChIPaKmg_DanyKD_rep1_INPUT

description: Library name: ChIPaKmg_DanyKD_rep1_INPUT


title: HCT-RNAi stem tissue, lignin mutant, sample 1, Rep 3


title: 3Pseq_KmgKD_rep1

description:
Library name: 3Pseq_KmgKD_rep1
sequenced as in Berry et al. 2022

data_processing:
Low-quality bases, polyA tails and adapters were trimmed using bbmap (39.01) and reads were mapped to Drosophila genome assembly: BDGP6.32 (GCA_000001215.4) using STAR (2.7.11b)
The most 3′ nucleotide of each mapped read was counted using bedtools coverage (2.27.1) and used as input into CAGEr to build 3’ end clusters (1.20.0)
Created bigwig files with bedGraphToBigWig
Analysis scripts are available at https://github.com/NeuzaRM/Kmg_FullerPaper2025
Assembly: dm6
Supplementary files format and content: tab-delimited text files include 3'seq cluster information for each sample and for consensus cluster.

extract_protocol:
RNA was extracted from 150 pairs of testes using the RNeasy Plus Mini Kit from QIAGEN (74104)
Library preparation was carried out using the Quant Seq (FWD) kit from Lexogen

value: Fly crosses were kept for 3 days at 25°C. Adults were then flipped to a new bottle, while the eggs and early larvae were shifted to 29°C. Testes were dissected from 0–2 day old males in 1xPBS.


title: ChIPaKmg_DanyKD_rep1

description: Library name: ChIPaKmg_DanyKD_rep1


title: Senescent CDK4 knockdown, replicate1

description: Library name: Sen_siK4_1


title: HCT-RNAi stem tissue, lignin mutant, sample 1, Rep 2


title: 3Pseq_Control_rep2

description:
Library name: 3Pseq_Control_rep2
sequenced as in Berry et al. 2022


title: 3Pseq_Control_rep1

description:
Library name: 3Pseq_Control_rep1
sequenced as in Berry et al. 2022


title: Senescent Non targeting#4 knockdown, replicate3

description: Library name: Sen_siNT4_3

value: WT


title: HCT-RNAi stem tissue, lignin mutant, sample 1, Rep 4


title: Senescent CDK6 knockdown, replicate1

description: Library name: Sen_siK6_1


title: Col-0 stem tissue, control, sample 3, Rep 4


title: Senescent Non targeting#4 knockdown, replicate2

description: Library name: Sen_siNT4_2


title: H3K27me3_wt_21-24hr_exp3_chrom2

description: Library name: sample 26

value: wt


title: CAGEseq_Control_rep2

description:
Library name: CAGEseq_Control_rep2
76bp SR


title: HCT-RNAi stem tissue, lignin mutant, sample 1, Rep 1


title: Senescent Non targeting#3 knockdown, replicate3

description: Library name: Sen_siNT3_3

value: Irradiation, siRNA knockdown


title: ChIPaKmg_WT_rep1

description: Library name: ChIPaKmg_WT_rep1


title: 3Pseq_KmgKD_rep2

description:
Library name: 3Pseq_KmgKD_rep2
sequenced as in Berry et al. 2022

value: bamGAL4/ KmgRNAi


title: Col-0 stem tissue, control, sample 3, Rep 3

value: Stem


title: ChIPaKmg_WT_rep1_INPUT

description: Library name: ChIPaKmg_WT_rep1_INPUT


title: H3K27me3_wt_21-24hr_exp6_chrom2

description: Library name: sample 25


title: H3K27me3_wt_21-24hr_exp6_chrom1

description: Library name: sample 24


title: ChIPaV5Dany_Hom_wt_rep2_INPUT

description: Library name: ChIPaV5Dany_Hom_wt_rep2_INPUT


title: Senescent Non targeting#3 knockdown, replicate2

description: Library name: Sen_siNT3_2


title: Col-0 stem tissue, control, sample 3, Rep 1


title: Senescent Non targeting#3 knockdown, replicate1

description: Library name: Sen_siNT3_1


title: H3K27me3_esc^0_21-24hr_exp6_chrom2

description: Library name: sample 23


title: ChIPaV5Dany_Hom_wt_rep2

description: Library name: ChIPaV5Dany_Hom_wt_rep2

value: anti-V5 (Invitrogen 46-0705)


title: Col-0 stem tissue, control, sample 3, Rep 2


title: H3K27me3_esc^0_21-24hr_exp6_chrom1

description: Library name: sample 22


title: Col-0 stem tissue, control, sample 2, Rep 4


title: Proliferating replicate3

description: Library name: Prolif_3

value: No treatment


title: ChIPaKmg_WT_rep2_INPUT

description: Library name: ChIPaKmg_WT_rep2_INPUT


title: ChIPaKmg_WT_rep2

description: Library name: ChIPaKmg_WT_rep2


title: input_Psc-Su(z)2^0_21-24hr_exp5_chrom1

description: Library name: sample 21


title: Senescent Non targeting#4 knockdown, replicate1

description: Library name: Sen_siNT4_1


title: ChIPaV5Dany_Hom_wt_rep1_INPUT

description: Library name: ChIPaV5Dany_Hom_wt_rep1_INPUT


title: ChIPaV5Dany_Hom_wt_rep1

description: Library name: ChIPaV5Dany_Hom_wt_rep1


title: input_Pcl^0_21-24hr_exp5_chrom1

description: Library name: sample 20


title: Col-0 stem tissue, control, sample 2, Rep 3


title: Col-0 stem tissue, control, sample 2, Rep 2


title: ChIPaHA_Aly_wt_rep1_INPUT

description: Library name: ChIPaHA_Aly_wt_rep1_INPUT

value: Aly-HA


title: input_wt_21-24hr_exp6_chrom2

description: Library name: sample 17

value: 21-24hr old embryos


title: ChIPaHA_Aly_wt_rep1

description: Library name: ChIPaHA_Aly_wt_rep1

value: anti-HA (Cell Signaling C29F4)


title: input_esc^0_21-24hr_exp6_chrom2

description: Library name: sample 16


title: Col-0 stem tissue, control, sample 2, Rep 1


title: Col-0 stem tissue, control, sample 1, Rep 4


title: ChIPaH3K4me3_WT_rep2_INPUT

description: Library name: ChIPaH3K4me3_WT_rep2_INPUT

value: Testes


title: Brain metastasis tissue microarray

city: Houston

first: Nadim

last: Ajami

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

description: For more information on processed data read README.txt

hyb_protocol: RNA ISH probes (6K Discovery Panel, Cat# 121500041) were denatured at 95°C before preparation of the ISH probe mix (1 nM ISH probes, 1X Buffer R, 0.1 U/μL SUPERaseIn™). Slides were incubated with ISH probe mix at 37°C overnight.

scan_protocol: After loading on the instrument, the flow cell was scanned, and 39 fields of view (FOVs) were created on each slide. Eight z-stack images (0.8 μm step size) were acquired of each FOV and the fluorophores on the reporter probes were UV cleaved and washed.

data_processing: For cell segmentation, z-stack images of immunostaining and DAPI were used for determining cell boundaries. Transcripts were assigned to cell locations and subcellular compartments using a cell segmentation pipeline. The transcript profile of individual cells was generated by combining target transcript location and cell segmentation boundaries.  Cells with fewer than 20 total transcripts were removed from the analysis.

label: SMI barcodes

source_name: Brain metastasis tissue microarray

label_protocol: Spatial molecular imaging was conducted using the CosMx SMI Platform (NanoString Technologies, Seattle, WA) using the 6K Discovery panel and a custom panel of bacterial probes.

extract_protocol: A total of 33 glioma and 19 BrM FFPE blocks were used for TMA construction. Hematoxylin and Eosin slides of each block were used for initial screening to demarcate immune-high and immune-low areas in the tumor. For each block, 2-6 cores were selected for TMA construction. TMAs were built using an ATA-100 Advanced Tissue Arrayer (Chemicon International). Slides were prepared according to NanoString protocol for FFPE slide preparation. Briefly, slides were baked at 60°C overnight, followed by deparaffinization, proteinase K digestion (3 μg/ml, 40°C, 30 min) and antigen retrieval (100°C, 15 min, in Leica buffer ER1). Samples were then fixed using 10% NBF, rinsed with Tris-glycine buffer (0.1M glycine, 0.1M Tris-base), and blocked using 100 mM N-succinimidyl acetate (NHS-acetate, ThermoFisher) in NHS-acetate buffer (0.1M NaP, 0.1% Tween pH 8 in DEPC H2O) for 15 min at RT.

value: Brain metastasis tissue


title: Glioma tissue microarray

source_name: Glioma tissue microarray

value: Glioma tissue


title: Col-0 stem tissue, control, sample 1, Rep 3


title: PRLX-93936 5uM, 6hr, Rep 3

city: Palo Alto

first: Steven

last: Corsello

state: California

address: 240 Pasteur Drive

department: Stanford School of Medicine

description:
Library name: 11-C-PANC1-PRLX-5-6h-Rep-4
Column name in processed files is library name

data_processing:
nf-core/rnaseq (3.12.0)
Salmon (1.10.1)
Assembly: hg38
Supplementary files format and content: Tab separated gene counts, columns are library names
Supplementary files format and content: Tab separated gene counts, length scaled, columns are library names
Supplementary files format and content: Tab separeted gene counts, scaled, columns are library names
Supplementary files format and content: Tab separated gene transcripts per million (TPM), columns are library names
Supplementary files format and content: Tab separated transcript counts, columns are library names
Supplementary files format and content: Tab separated transcript per million (TPM), columns are libarary names

source_name: cell line

growth_protocol: PANC-1 cells were seeded in 6-well plates in DMEM with 10% FBS and Pen/Strep

extract_protocol:
RNeasy Mini Kit (QIAGEN)
Genewiz

treatment_protocol: Treated with 0.5uM and 5uM PRLX-93936 and DMSO

value: cell line

value: pancreatic

tag: time


title: H2Aub1_Psc-Su(z)2^0_21-24hr_exp5_chrom1

description: Library name: sample 9

value: H2Aub1 (cell signaling (#8240))


title: Col-0 stem tissue, control, sample 1, Rep 2


title: PRLX-93936 5uM, 6hr, Rep 2

description:
Library name: 10-C-PANC1-PRLX-5-6h-Rep-3
Column name in processed files is library name


title: ChIPaH3K4me3_WT_rep2

description: Library name: ChIPaH3K4me3_WT_rep2

value: anti-H3K4me3 (abcam ab8580)


title: Col-0 stem tissue, control, sample 1, Rep 1

value: WT


title: ChIPaH3K4me3_WT_rep1_INPUT

description: Library name: ChIPaH3K4me3_WT_rep1_INPUT


title: Proliferating replicate1

description: Library name: Prolif_1

value: Human Lung Fibroblasts


title: input_esc^0_21-24hr_exp6_chrom1

description: Library name: sample 15


title: ChIPaH3K4me3_WT_rep1

description: Library name: ChIPaH3K4me3_WT_rep1


title: Proliferating replicate2

description: Library name: Prolif_2


title: H2Aub1_wt_21-24hr_exp6_chrom2

description: Library name: sample 5

value: wt


title: PRLX-93936 5uM, 2hr, Rep 3

description:
Library name: 23-F-PANC1-PRLX-5-2h-Rep-4
Column name in processed files is library name


title: PRLX-93936 5uM, 6hr, Rep 1

description:
Library name: 9-C-PANC1-PRLX-5-6h-Rep-2
Column name in processed files is library name


title: H2Aub1_Pcl^0_21-24hr_exp5_chrom1

description: Library name: sample 8


title: input_wt_21-24hr_exp2_chrom2

description: Library name: sample 19


title: PRLX-93936 5uM, 2hr, Rep 2

description:
Library name: 22-F-PANC1-PRLX-5-2h-Rep-3
Column name in processed files is library name


title: input_wt_21-24hr_exp2_chrom1

description: Library name: sample 18


title: H2Aub1_Sce^I48A_21-24hr_exp1_chrom1

description: Library name: sample 3


title: H2Aub1_wt_21-24hr_exp6_chrom1

description: Library name: sample 4


title: input_l(3)73Ah^0_21-24hr_exp2_chrom2

description: Library name: sample 14


title: H3K27me3_Pcl^0_21-24hr_exp5_chrom1

data_processing:
Reads from fastq files were aligned to the dm6 genome (and to the D. pseudoobscura dp3 genome for subsequent normalization) using STAR (Dobin et al., 2013). Only sequences that mapped uniquely to the genome with a maximum of two mismatches were considered for further analyses.
Bam files were used as inputs to run Bioconductor packages.
The STAN Bioconductor package (Zacher et al., 2014) was used to define the location of H3K36me2 enriched-regions and H3K27me3 enriched-regions.
The proportion of D. pseudoobscura reads as compared to D. melanogaster reads in input and in samples was used to normalize the ChIP-seq datasets for histone marks in embryos. Reference samples for normalization with D. pseudoobscura chromatin are indicated. Other samples were normalized based on total read number per million reads. Normalization factor for each sample is indicated.
Assembly: dm6
Supplementary files format and content: Normalized bigwig files (bin size = 1) were generated with deepTools (Ramirez et al., 2016).

extract_protocol:
Lysates were clarified from sonicated fixed nuclei (for embryos) and from sonicated fixed hand-dissected imaginal disc tissues (for 3rd instar larvae). Histone/Protein-DNA complexes were isolated with antibody. D. pseudoobscura chromatin was spiked in at a 1:5 ratio of dm / dp chromatin before the addition of the antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq kit.

value: H3K27me3 (Cell Signaling (#9733))


title: PRLX-93936 5uM, 2hr, Rep 1

description:
Library name: 21-F-PANC1-PRLX-5-2h-Rep-2
Column name in processed files is library name


title: PRLX-93936 0.5uM, 6hr, Rep 3

description:
Library name: 8-B-PANC1-PRLX-0-5-6h-Rep-5
Column name in processed files is library name


title: input_l(3)73Ah^0_21-24hr_exp2_chrom1

description: Library name: sample 13


title: H3K27me3_Asx^0-Pcl^0_21-24hr_exp4_chrom2


title: PRLX-93936 0.5uM, 6hr, Rep 2

description:
Library name: 6-B-PANC1-PRLX-0-5-6h-Rep-2
Column name in processed files is library name


title: PRLX-93936 0.5uM, 6hr, Rep 1

description:
Library name: 5-B-PANC1-PRLX-0-5-6h-Rep-1
Column name in processed files is library name


title: H3K27me3_wt_21-24hr_exp2_chrom1

description: Library name: sample 11


title: H3K27me3_wt_21-24hr_exp2_chrom2

description: Library name: sample 12


title: PRLX-93936 0.5uM, 2hr, Rep 3

description:
Library name: 20-E-PANC1-PRLX-0-5-2h-Rep-5
Column name in processed files is library name


title: KPUM-MS3 for 96 hours with rIL-10

city: Kamigyo-ku, Kyoto

first: Yu

last: Inoue

state: Kyoto

address: 465 Kajii-cho, Kawaramachi-Hirokoji

department: Division of Hematology and Oncology, Department of Medicine

institute: Kyoto Prefectural University of Medicine

description: gene expression data in CD33+ myeloid cells of PBMCs co-cultured with KPUM-MS3 for 96 hours with rIL-10

hyb_protocol: Following fragmentation, Biotinylated RNA were hybridized for 16 hr at 45℃ on GeneChipTM human Clariom S Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChipTM Scanner 3000 7G.

data_processing: The data were analyzed with Transcriptome Analysis Console 4.0 (TAC 4.0) using robust multi-array analysis (RMA).

label: biotin

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol from total RNA.

growth_protocol: PBMCs were isolated from healthy donors using lymphocyte separation solution (Nacalai Tesque) and cultured in RPMI-1640 (Wako) with the addition of 10% heat-inactivated fetal bovine serum (Thermo Fisher), 2 mM L-glutamine, and penicillin/streptomycin.

extract_protocol: Total RNA was extracted from CD33+ cells using the mirVana miRNA Isolation Kit (Thermo Fisher).

treatment_protocol: PBMCs were treated with rMIF and/or rIL-10, and were co-cultured with KPUM-UH1 or KPUM-MS3 for 24, 48, 96 hours, and 96 hours along with rIL-10. CD33+ myeloid cells were isolated from each condition using the EasySep Human CD33 Positive Selection Kit II (VERITAS Corporation).

value: CD33+ myeloid cells of PBMCs


title: H3K27me3_l(3)73Ah^0_21-24hr_exp2_chrom1

description: Library name: sample 10


title: H3K27me3_Pcl^0_21-24hr_exp4_chrom1


title: input_Asx^0-Pcl^0_21-24hr_exp4_chrom2


title: H3K27me3_Pcl^0_21-24hr_exp4_chrom2


title: PRLX-93936 0.5uM, 2hr, Rep 1

description:
Library name: 17-E-PANC1-PRLX-0-5-2h-Rep-1
Column name in processed files is library name


title: PRLX-93936 0.5uM, 2hr, Rep 2

description:
Library name: 19-E-PANC1-PRLX-0-5-2h-Rep-3
Column name in processed files is library name


title: H2Aub1_wt_21-24hr_exp2_chrom1

description: Library name: sample 6


title: KPUM-MS3 for 96 hours

description: gene expression data in CD33+ myeloid cells of PBMCs co-cultured with KPUM-MS3 for 96 hours

value: co-cultured with KPUM-MS3 for 96 hours


title: KPUM-UH1 for 96 hours with rIL-10

description: gene expression data in CD33+ myeloid cells of PBMCs co-cultured with KPUM-UH1 for 96 hours with rIL-10


title: KPUM-MS3 for 48 hours

description: gene expression data in CD33+ myeloid cells of PBMCs co-cultured with KPUM-MS3 for 48 hours

value: co-cultured with KPUM-MS3 for 48 hours


title: DMSO, 6hr, Rep 3

description:
Library name: 4-A-PANC1-DMSO-6h-Rep-5
Column name in processed files is library name

value: DMSO


title: KPUM-UH1 for 96 hours

description: gene expression data in CD33+ myeloid cells of PBMCs co-cultured with KPUM-UH1 for 96 hours

value: co-cultured with KPUM-UH1 for 96 hours


title: KPUM-UH1 for 48 hours

description: gene expression data in CD33+ myeloid cells of PBMCs co-cultured with KPUM-UH1 for 48 hours

value: co-cultured with KPUM-UH1 for 48 hours


title: input_Asx^0-Pcl^0_21-24hr_exp4_chrom1

value: 21-24hr old embryos


title: H2Aub1_l(3)73Ah^0_21-24hr_exp2_chrom2

description: Library name: sample 2


title: H3K27me3_Asx^0-Pcl^0_21-24hr_exp4_chrom1


title: KPUM-UH1 for 24 hours

description: gene expression data in CD33+ myeloid cells of PBMCs co-cultured with KPUM-UH1 for 24 hours

value: co-cultured with KPUM-UH1 for 24 hours


title: H2Aub1_l(3)73Ah^0_21-24hr_exp2_chrom1

description: Library name: sample 1


title: DMSO, 6hr, Rep 2

description:
Library name: 2-A-PANC1-DMSO-6h-Rep-3
Column name in processed files is library name


title: input_Pcl^0_21-24hr_exp4_chrom1


title: H2Aub1_wt_21-24hr_exp2_chrom2

description: Library name: sample 7


title: DMSO, 6hr, Rep 1

description:
Library name: 1-A-PANC1-DMSO-6h-Rep-1
Column name in processed files is library name


title: SW480-Hypoxia2-run2

city: Taipei

first: Che-Kun James

last: Shen

address: No. 128號, Section 2, Academia Rd, Nangang District

country: Taiwan

institute: Institute of Molecular Biology, Academia Sinica

data_processing:
DNA methylation analysis from the WGBS raw data were conducted by using default parameters via BatMeth2.
The complete data processing, including alignment with the human genome (GRCh38.p13; GCF_000001405.39), calculation of DNA methylation levels of CpG sites using the function "Calmeth", and identification of differentially methylated cytosine (DMC) and differentially methylated regions (DMR) using the function "batDMR".
The methylated levels of each sample from two sequencing run were summed.
Assembly: GRCh38
Supplementary files format and content: tab-separated text files include read depth and methylation level for each CpG site

source_name: Colon

growth_protocol: The colon cancer cell line SW480, breast cancer cell line MCF-7 and hepatocellular carcinoma cell line HepG2 were cultured under 5% CO2 at 37 °C in DMEM (Invitrogen) supplemented with 10% FBS (v/v) (Biological Industries) and 1% (v/v) penicillin-streptomycin (Invitrogen)

extract_protocol:
Genomic DNA was isolated from the cultured SW480 cells using QIAamp DNA mini kit (QIAGEN).
The bisulfite-converted DNA was processed for generating WGBS libraries using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences).

treatment_protocol: To induce hypoxia, the cells were transferred from a normoxic incubator (5% CO2 and 20% O2) to a hypoxic incubator (5% CO2 and 1% O2) for 24 hr. Increased levels of HIF-1α, as assayed by Western blotting, were used to assess induction of hypoxia.

value: Colon

value: Colorectal carcinoma cell line

value: Hypoxia

tag: run


title: H2Aub1_Asx^0-Pcl^0_21-24hr_exp4_chrom2

tag: tissue

value: H2Aub1 (cell signaling (#8240))


title: HiC_JE2_delta_4parS

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

institute: Indiana University at Bloomington

description: Library name: HiC_JE2_delta_4parS

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Staphylococcus aureus Hi-C, we mapped reads in each FASTQ file back to the genome of Staphylococcus aureus JE2 (NCBI Reference Sequence GCF_002085525.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.  For WGS, we mapped reads in each FASTQ file back to the genome of Staphylococcus aureus JE2 (NCBI Reference Sequence GCF_002085525.1) using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Staphylococcus aureus JE2  genome was divided into DpnII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Staphylococcus aureus JE2 was then divided into bins 5 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Assembly: Staphylococcus aureus JE2 (NCBI Reference Sequence GCF_002085525.1)
Supplementary files format and content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv files are comma-separated values files of WGS results.

organism: Staphylococcus aureus

source_name: Bacterial cell

extract_protocol:
Wild type and mutant cells of Staphylococcus aureus JE2 growing in TSB were crosslinked using 7 % formaldehyde and then lysed by treatment of lysosome and 1% SDS as previouly discribed (Wang et al 2015).
Standard library construction protocol was used for Illumina Nextseq500/Nextseq2000 sequencing platforms. Illumina Truseq indexes were used.

tag: strain

tag: cell type

value: Bacterial cell

value: JE2, delta_4parS

value: Cells were grown in TSB at 37°C with agitation until early-exponential phase (OD600 0.3-0.4)


title: SW480-Hypoxia1-run2

value: WT

tag: treatment


title: DMSO, 2hr, Rep 3

description:
Library name: 16-D-PANC1-DMSO-2h-Rep-5
Column name in processed files is library name

value: cell line

value: pancreatic


title: H2Aub1_Asx^0-Pcl^0_21-24hr_exp4_chrom1


title: KPUM-MS3 for 24 hours

description: gene expression data in CD33+ myeloid cells of PBMCs co-cultured with KPUM-MS3 for 24 hours

value: CD33+ myeloid cells of PBMCs

value: co-cultured with KPUM-MS3 for 24 hours


title: rMIF+rIL-10

description: gene expression data in CD33+ myeloid cells of PBMCs treated with rMIF+rIL-10

value: treated with rMIF+rIL-10


title: HiC_JE2_WT

description: Library name: HiC_JE2_WT

value: JE2, WT


title: DMSO, 2hr, Rep 2

description:
Library name: 14-D-PANC1-DMSO-2h-Rep-3
Column name in processed files is library name

value: DMSO


title: rIL-10

description: gene expression data in CD33+ myeloid cells of PBMCs treated with rIL-10

value: treated with rIL-10


title: rMIF

description: gene expression data in CD33+ myeloid cells of PBMCs treated with rMIF

value: treated with rMIF


title: DMSO, 2hr, Rep 1

description:
Library name: 13-D-PANC1-DMSO-2h-Rep-2
Column name in processed files is library name


title: HiC_JE2_delta_parB

description: Library name: HiC_JE2_delta_parB

value: JE2, delta_parB


title: H2Aub1_Pcl^0_21-24hr_exp4_chrom1

value: 21-24hr old embryos


title: SW480-Normoxia1-run2

value: Colon

value: Colorectal carcinoma cell line

value: Normoxia


title: HiC_JE2_delta_scpAB

description: Library name: HiC_JE2_delta_scpAB

value: Bacterial cell

value: JE2, delta_scpAB


title: H2Aub1_Pcl^0_21-24hr_exp4_chrom2

value: H2Aub1 (cell signaling (#8240))


title: RRBS_PGCs_E14.5f

status: Public on Aug 12 2025

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

institute: CNRS

data_processing:
Reads were trimmed to remove low quality bases with Trim Galore v0.4.2 (parameters --rrbs --paired -r1 30 -r2 30 -q 20 --length 20 --stringency 5 --retain_unpaired) and aligned to the mm10 genome with BSMAP v2.74 (parameters -v 2 -w 100 -r 1 -x 400 -m 30 -D C-CGG -n 1).
Methylation scores were calculated using methratio.py in BSMAP v2.74 (parameters -z -u -g) and CpGs were filtered at a minimum of 8 X sequencing depth.
Assembly: mm10
Supplementary files format and content: We provide IGV files containing methylation scores for all CGs with at least 8X sequencing depth.

source_name: Primordial germ cells

extract_protocol:
Genomic DNA samples were prepared by proteinase K digestion, phenol/chloroform/Isoamyl alcohol (25:24:1) extraction and precipitation with ethanol.
RRBS libraries were prepared as described in Bender et al. (2021), Methods Mol Biol 2214:207-220. Briefly, between 5 and 100 ng genomic DNA were digested with MspI (Thermo Fisher Scientific) for 5 h at 37°C, end-repaired and A-tailed with 5 U Klenow fragment exo- (Thermo Fisher Scientific) for 40 min at 37°C and ligated to methylated adapters overnight at 16°C with 30 U T4 DNA ligase (Thermo Fisher Scientific) in Tango 1X buffer. Fragments between 150 and 400 bp were excised from a 3% agarose 0.5X TBE gel, purified with the MinElute gel extraction kit (Qiagen) and bisulfite converted with the EpiTect bisulfite kit (Qiagen) with two consecutive rounds of conversion. Final libraries were amplified with PfU Turbo Cx hotstart DNA polymerase (Agilent) with 14-18 PCR cycles and purified with AMPure XP beads (Beckman Coulter).

value: Primordial germ cells

value: WT

tag: developmental stage

tag: Sex

value: Female


title: RRBS_PGCs_E15.5f


title: input_Pcl^0_21-24hr_exp4_chrom2


title: control

description: gene expression data in CD33+ myeloid cells of PBMCs untreated

source_name: CD33+ myeloid cells of PBMCs untreated

value: CD33+ myeloid cells of PBMCs

value: untreated


title: RRBS_PGCs_E13.5f


title: RRBS_PGCs_E17.5f


title: RRBS_PGCs_E16.5f


title: RRBS_PGCs_E12.5f


title: RRBS_PGCs_E17.5m

value: Male


title: RRBS_PGCs_E16.5m


title: RRBS_PGCs_E14.5m


title: SW480-Normoxia2-run2


title: RRBS_PGCs_E13.5m


title: RRBS_PGCs_E11.5_rep1

value: Mixed


title: RRBS_PGCs_E10.5_rep1


title: RRBS_PGCs_E12.5m


title: RRBS_PGCs_E10.5_rep2


title: RRBS_PGCs_E9.5_rep1


title: RRBS_PGCs_E9.5_rep2


title: RRBS_PGCs_E11.5_rep2


title: spinal lumbar tissue,SCI, Day14, rep1

city: Mudanjiang

first: Ying

state: Heilongjiang

address: No 3,Tongxiang Road, Aiming district

country: China

institute: Mudanjiang Medical University

description: Library name: Sample D1

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes count and FPKM values for each Sample

organism: Rattus norvegicus

source_name: spinal lumbar tissue

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

value: spinal lumbar tissue

value: SCI


title: spinal lumbar tissue,SCI, Day7, rep3

description: Library name: Sample C3


title: spinal lumbar tissue,SCI, Day3, rep2

description: Library name: Sample B2


title: spinal lumbar tissue,SCI, Day7, rep2

description: Library name: Sample C2


title: spinal lumbar tissue,SCI, Day14, rep3

description: Library name: Sample D3


title: spinal lumbar tissue,sham, Day0, rep1

description: Library name: Sample A1

value: sham


title: spinal lumbar tissue,SCI, Day3, rep1

description: Library name: Sample B1


title: pdac7

city: Baltimore

first: Dimitrios

last: Sidiropoulos

state: MD

address: 1650 Orleans St

department: Oncology

institute: Johns Hopkins University

data_processing:
Sequencing alignment and demultiplexing with Space Ranger (10x Genomics).
Quality check and filtering with Seurat.
Normalization using SCTransform in Seurat.
Dimensional reduction using PCA in Seurat.
Gene expression analysis using Seurat.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv: spatial barcodes
Supplementary files format and content: features.tsv: genes
Supplementary files format and content: matrix.mtx: sequencing counts
Library strategy: Spatial transcriptomics

source_name: pancreas

extract_protocol:
There was no extraction protocol used.
Libraries were constructed using the Visium FFPE Spatial Gene Expression Reagent Kits (10x Genomics).

value: pancreatic ductal adenocarcinoma

value: pancreas

tag: tissue subtype

value: Tumor

tag: path response

value: R

tag: sample type

value: FFPE

tag: treatment arm

value: C


title: spinal lumbar tissue,sham, Day0, rep2

description: Library name: Sample A2


title: pdac6

tag: disease state

value: A


title: spinal lumbar tissue,sham, Day0, rep3

description: Library name: Sample A3


title: pdac3

value: lymph node


title: pdac4


title: RRBS_PGCs_E15.5m

value: Primordial germ cells

tag: genotype

value: WT


title: pdac1


title: M07E

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

description: ATAC-seq profiling of CG-AMKL patient-derived cell line M-07e

data_processing:
Raw sequencing data were processed using the nf-core/atacseq pipeline v1.2.1
Downstream analysis, quality control and differential analysis was was performed in R mainly using Rsubread v.2.12.3 and DESeq2 v1.38.3 and with the aid of multiple, additional tools. For details, processing, please refer to the methods of the associated manuscript.
Supplementary files format and content: Comma-separated values  tables contatining ATAC-seq counts of all the samples included in the analysis pipeline. Please refer to Supplementary Table 1 of the associated manuscript for an overview of the processed data.
Assembly: GRCh38 human genome reference

source_name: Blood

growth_protocol: hiPSC line (Gibco A18945) was used  and routinely cultured under hypoxic conditions (37 °C, 3% O2, 5% CO2) on plates coated with hESC-qualified Matrigel (Corning) in TeSR E8 or mTeSR-Plus medium (STEMCELL Technologies). Cells were passaged every 3–4 days mostly at a split ratio of 1:6 using StemPro Accutase (Thermo Fisher Scientific), and medium was exchanged every 1-2 days

extract_protocol:
For differentiation, 2000 hiPSCs were seeded as clumps per well of a Matrigel-coated 12-well plate and 3 days later normoxic cell culture with STEMdiff hematopoietic differentiation basal medium with supplement A (containing BMP4, FGF2, VEGFA) for the first day with 3 µM CHIR99021 glycogen synthase kinase 3 inhibitor (Sigma-Aldrich) and another 2 days without. Next, cells were cultured for 9-10 days in differentiation medium with supplement B (containing BMP4, FGF2, VEGFA, SCF, FLT3L, TPO) with half media changes every 2–3 days. For CG protein degradation dTAG-13 compound (100 nM final; kindly provided by Nathanael Gray, Dana-Farber Cancer Institute, Boston, MA, USA; CG-negative isogenic control) was added from differentiation day 2 onwards.
Nuclei were prepared from 100-250k cells frozen cells by gentle lysis in 100uL isolation buffer (10uL of Tris-HCl pH 7.5 1M, 2uL of NaCl 5M, 3uL of MgCl2 1M, BSA 1%, Tween-20 0.1%, NP40 0.05% Digitonin 0.005%, 1uL of DTT 1M, 25uL of RNase inhibitor 40U/uL in 843uL of water) for 5min on ice. Nuclei were washed with 400uL of wash buffer (250uL of Tris-HCl pH 7.5 1M, 50uL of NaCl 5M, 75uL of MgCl2 1M, BSA 1%, Tween-20 0.1%, 25uL of DTT 1M, 625uL of RNase inhibitor 40U/uL in 20.925mL of water), strained (40um), and centrifuge for 5 min (500g, 4 °C). Nuclei were resuspended in nuclei buffer (50uL of 20x nuclei buffer, 1uL of 1M DTT, BSA 1%, 824uL water).
Tagmentation was performed for 50,000 targeted nuclei using the Illumina Tagment DNA TDE1 Enzyme and Buffer Kits #15027865. Post-tagmentation DNA fragment recovery was performed using a Guanidium-based method. Briefly, 25uL of guanidinium hydrochloride solution 8 M, pH 8.5 (MBS) was added for 5 minutes, followed by 120uL of binding solution (BS: 20% PEG 8000, 2.5M NaCL, 10mM Tris-HCl pH8, 1mM EDTA, 0,05% Tween 20) and 30uL of MBSpure beads. After 10 minutes of incubation, fragments were purified on a magnetic stand and washed twice with 150uL of 80% EtOH.

treatment_protocol: Parental hiPSCs (WT genotype) were genetically engineered by in trans paired nicking to carry CBFA2T3::GLIS2 (CG genotype) in one endogenous CBFA2T3 allele.

value: Blood

tag: cell line

value: M-07e (DSMZ ACC-104)

value: hematopoietic

value: CG

value: UNTREATED


title: CG_UNTREATED_LONGTERM_REP3

description: ATAC-seq profiling of hiPSC-derived long-term line CG_E5_HEM32/1 at timepoint D72

value: hiPSC (Gibco A18945)


title: CG_UNTREATED_LONGTERM_REP1

description: ATAC-seq profiling of hiPSC-derived long-term line CG_A9_HEM22 at timepoint D115


title: spinal lumbar tissue,SCI, Day14, rep2

description: Library name: Sample D2

value: spinal lumbar tissue

value: SCI


title: CG_UNTREATED_LONGTERM_REP2

description: ATAC-seq profiling of hiPSC-derived long-term line CG_A9_HEM23/1 at timepoint D115


title: CG_DTAG13_D13_REP3

description: ATAC-seq profiling of dTAG-13-treated hiPSC-derived HSPCs harboring CG allele at timepoint D13


title: CG_DTAG13_D25_REP3

description: ATAC-seq profiling of dTAG-13-treated hiPSC-derived hematopoietic cells harboring CG allele at timepoint D25


title: CG_UNTREATED_D25_REP2

description: ATAC-seq profiling of hiPSC-derived hematopoietic cells harboring CG allele at timepoint D25


title: spinal lumbar tissue,SCI, Day3, rep3

description: Library name: Sample B3


title: CG_UNTREATED_D13_REP3

description: ATAC-seq profiling of hiPSC-derived HSPCs harboring CG allele at timepoint D13


title: pdac5

value: pancreatic ductal adenocarcinoma

value: pancreas


title: spinal lumbar tissue,SCI, Day7, rep1

description: Library name: Sample C1


title: CG_UNTREATED_D25_REP3


title: CG_UNTREATED_D25_REP1


title: pdac2

value: Tumor

value: R


title: CG_DTAG13_D25_REP1


title: WT_DTAG13_D13

description: ATAC-seq profiling of dTAG-13-treated hiPSC-derived HSPCs at timepoint D13


title: WT_UNTREATED_D25

description: ATAC-seq profiling of hiPSC-derived hematopoietic cells at timepoint D25


title: CG_UNTREATED_D13_REP1


title: WT_UNTREATED_D13

description: ATAC-seq profiling of hiPSC-derived HSPCs at timepoint D13


title: WT_DTAG13_D25

description: ATAC-seq profiling of dTAG-13-treated hiPSC-derived hematopoietic cells at timepoint D25


title: CG_UNTREATED_D13_REP2


title: sub_M07E_CBFA2T3_IP

description: ChIP-seq profiling of CBFA2T3 protein of CG-AMKL patient-derived cell line M-07e, subsampled

data_processing:
Raw sequence data were processed using the nf-core/chipseq pipeline v1.2.2.
Downstream analysis, quality control and motif enrichmenet analysis was performed in R mainly using motifmatchr v1.20.0 and with the aid of multiple, additional tools. For details, processing, please refer to the methods of the associated manuscript.
Supplementary files format and content: BED file of the set of consensus peaks defined by merging overlapping peaks detected in at least two HA replicates.
Assembly: GRCh38 human genome reference

extract_protocol:
For differentiation, 2000 hiPSCs were seeded as clumps per well of a Matrigel-coated 12-well plate and 3 days later normoxic cell culture with STEMdiff hematopoietic differentiation basal medium with supplement A (containing BMP4, FGF2, VEGFA) for the first day with 3 µM CHIR99021 glycogen synthase kinase 3 inhibitor (Sigma-Aldrich) and another 2 days without. Next, cells were cultured for 9-10 days in differentiation medium with supplement B (containing BMP4, FGF2, VEGFA, SCF, FLT3L, TPO) with half media changes every 2–3 days. For CG protein degradation dTAG-13 compound (100 nM final; kindly provided by Nathanael Gray, Dana-Farber Cancer Institute, Boston, MA, USA; CG-negative isogenic control) was added from differentiation day 2 onwards.
Approx. 10^7 CG-expressing long-term or M-07e cells were fixed for 10 min at RT with 1% methanol-free formaldehyde in DPBS, and chromatin was prepared with the truChIP chromatin shearing kit according to NEXSON protocol 66 by ultrasonication for 20 min at 75 W peak incidence power, 10% duty factor, 200 cycles per burst and 7°C (Covaris M220). Immunoprecipation was performed with chromatin of 3-4 * 106 cells, 3 µg HA, CBFA2T3, or control normal mouse immunoglobulin G, and Protein G dynabeads (Invitrogen).
Libraries were prepared from input and immunoprecipitated DNA using the NEBnext Ultra II kit (New England Biolabs, E7645L) and sequenced on an Illumina NovaSeq (either 2x150 cycles in paired-end [CG_22_HA_IP_R1.1, CG_22_INPUT_R1.1, sub_M07E_CBFA2T3_IP, sub_M07E_INPUT] or 1x100 cycles in single-end [all other samples] setup) by the Vienna BioCenter Core Facilities (VBCF).


title: CG_DTAG13_D13_REP1


title: CG_22_INPUT_R1.1

description: ChIP-seq profiling of CG-dTAG-HA protein of hiPSC-derived long-term line CG_A9_HEM22


title: CG_22_HA_IP_R1.1

description: ChIP-seq input of hiPSC-derived long-term line CG_A9_HEM22


title: M07E_CBFA2T3_IP_R1

description: ChIP-seq profiling of CBFA2T3 protein of CG-AMKL patient-derived cell line M-07e


title: CG_DTAG13_D25_REP2


title: M07E_INPUT_R1

description: ChIP-seq input of patient-derived cell line M-07e


title: CG_23_HA_IP_R1

description: ChIP-seq profiling of CG-dTAG-HA protein of hiPSC-derived long-term line CG_A9_HEM23/1


title: CG_23_INPUT_R1

description: ChIP-seq input of CG-dTAG-HA protein of hiPSC-derived long-term line CG_A9_HEM23/1


title: CG_32_HA_IP_R1

description: ChIP-seq profiling of CG-dTAG-HA protein of hiPSC-derived long-term line CG_E5_HEM32/1


title: CG_22_INPUT_R1


title: CG_22_HA_IP_R1


title: SH-SY5Y cells, IR+Oligonol 3

city: Hwasun

first: Juhyun

last: Song

address: Seoyang-ro 264

department: Department of Anatomy

country: South Korea

institute: Chonnam National University Medical School

data_processing:
The FastQC was used for the initial quality check of sequencing results.
Reads for each sample were pseudoaligned to the reference(GRCh38.p13) by Kallisto(v0.46.1), producing a list of transcripts and quantify gene and transcript counts.
After applying a filter to the gene list, considering a count per million (cpm) of 2 and more in at least 1 replicate, expression values were normalized by trimmed mean of M values (TMM) of edgeR package.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited gene expression counts normalized by the total counts of genes in each sample ("c" means "count value" and "e" means "expression value").

growth_protocol: SH-SY5Y neuroblastoma cells were maintained in MEM supplemented with 10% fetal bovine serum (FBS), 1mM sodium pyruvate (SP) and antibiotics in 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted using TRIzol (Ambicon) according to the manufacturer's protocol. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Preparation Kit (Illumina) following manufacturer's protocol. The libararies were sequenced by NovaSeq 6000 (Illumina) in the paired-end 2*100 sequencing cycles.

treatment_protocol: To induce neuronal differentiation, 1 day after SH-SY5Y cells seeding, the cells were maintained in MEM supplemented with 2% FBS and antibiotics, 1mM  (SP), antibiotics, and all-trans retinoic acid (RA). Media was replaced with every 2 days.To induced insulin resistance in SH-SY5Y cells, cells were treated with 100 nM insulin and 30 mM D-glucose for 24 hours. Oligonol was treated with 500 ng/mL for 24 hours.

value: neuroblastoma cell line

value: insulin resistance + Oligonol treatment


title: SH-SY5Y cells, IR+Oligonol 2


title: CG_DTAG13_D13_REP2


title: sub_M07E_INPUT

description: ChIP-seq input of patient-derived cell line M-07e, subsampled


title: SH-SY5Y cells, IR+Oligonol 1


title: SH-SY5Y cells, IR control 3

value: insulin resistance


title: SH-SY5Y cells, IR control 1


title: SH-SY5Y cells, IR control 2