title: E16.5 Decidua, PNA, HF diet, rep 1

city: Oulu

first: Terhi

middle: T

last: Piltonen

address: Aapistie 5a

department: Department of Obstetrics and Gynecology

country: Finland

institute: University of Oulu

description:
L8FD
D_PHFvsD_PND_deg.txt
D_PHFvsD_CHF_deg.txt
D_PHFvsD_CND_deg.txt

data_processing:
Base calling software: Illumina Casava 1.8
The following data filtering steps were applied to the raw reads: 1. Remove reads with adapter contamination. 2. Remove reads when uncertain nucleotides constitute more than 10 percent of either read. 3. Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Alignment of reads was performed with HISAT2 v2.0.5.
Differentially expressed genes were screened with DESeq2 R-package (1.20.0) software. Parameters: |log2(FoldChange)| > 1 and adjusted p-value (padj) < 0.05, or p-value < 0.05.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: The *deg.txt files contain details from differential gene expression analyses between experimental groups, one analysis per each file. Each analysis concerns one experimental group being compared to one other group. For all experiments and tissues, effects of diet were assessed by comparing CHF vs. CN or PHF vs. PN groups. Effects of PNA were assessed by comparing PN vs. CN or PHF vs. CHF groups. Excel files starting with "D" represent decidua gene expression comparisons; excel files starting with "P" contain placenta (without decidua layer) gene expression comparisons. Information included in these files for every identified gene in each analysis: gene-id;  normalized read counts for each sample, average normalized read count per experimental group; log2 fold change, p-values (both regular and corrected for multiple testing (padj)); gene name; chromosome; gene start- and endpoint; gene strand; gene length; gene biotype; gene description; transcription factor family name; raw read counts for each sample; fpkm-value for each sample.

source_name: Decidua

growth_protocol: Female C57BL/6J mice (Charles River, Germany) were housed in a conventional non-barrier facility under controlled conditions (12:12 hour light:dark cycle, 23 ±2°C and 40-60% relative humidity) and received ad libitum food pellets and tap water.

extract_protocol:
Tissues were stored in RNAlater and in -80°C until processing. RNA extraction and DNase treatment of was performed using the RNeasy Mini kit (Qiagen) according to the manufacturer’s instructions. Isolated RNA was submitted to Novogene Europe for further processing for RNA sequencing (RNAseq).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification

treatment_protocol: PCOS-like mice were generated by prenatal androgenization (PNA), achieved through daily injections of 250 µg dihydrotestosterone into pregnant mice from embryonic day 16.5 to 18.5. The F1 offspring were then fed either a high-fat (HF) diet to induce obesity or a normal diet, creating four experimental groups based on PNA status and diet: CN (control, normal diet), CHF (control, high-fat diet), PN (PNA, normal diet), and PHF (PNA, high-fat diet). Three distinct experiments were conducted: (1) Following ovariectomy, estrogen (E2) and progesterone (P4) injections were administered to artificially induce the window of implantation (WOI). Uteri from four mice per group were analysed. (2) Ovariectomized F1 mice received E2 and P4 injections to induce decidualization. A 25 µl oil injection was administered to one uterine horn (stimulated), while the other horn was left untreated (unstimulated). Both uterine horns from four mice per group were used for analysis. (3) F1 mice were mated and pregnant mice were euthanized at E16.5 (with the vaginal plug considered day E0.5). The decidual layer was separated from the placenta, and both tissues were analyzed using bulk RNA sequencing (RNAseq) with 3–4 mice per group.

value: Decidua

tag: mouse strain

tag: Sex

value: Female

value: WT

value: Pregnancy


title: K562_treated_with_Flavopiridol_RNAPIIS5P_CUTnTAG_rep2_(20240408_WW1116_240329)

status: Public on Apr 10 2025

type: SRA

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

country: USA

institute: Fred Hutchinson Cancer Research Center

description: CUT&Tag targeting RNAPIIS5P in K562 in Flavopiridol replicate 2

library_source: genomic

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the hg19 Homo sapiens reference sequence obtained from UCSC.
3. We used samtools 1.14 "view" to extract properly paired reads from the hg19 alignments.
4. We combined replicates and used bedtools 2.30.0 "genomecov" to make a raw count hg19 track which is the number of fragments aligned at each position (Supplementary file .hg19.raw_counts.bw)
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: group

tag: antibody

value: Cell Signaling Technology, 13523S


title: E16.5 Decidua, PNA, HF diet, rep 4

description:
L62DD
D_PHFvsD_PND_deg.txt
D_PHFvsD_CHF_deg.txt
D_PHFvsD_CND_deg.txt

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: treatment


title: CgPho4 at 1 uM concentration

type: protein

city: Iowa City

first: Bin

last: He

email: emptyhb@gmail.com, bin-he@uiowa.edu

state: IA

address: 129 East Jefferson St., Biology Building 450

department: Biology

institute: the University of Iowa

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to 1 uM in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-488-conjugated rabbit polyclonal antibody to His (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-488-conjugated antibody (488 nm ex, 522 nm em) using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple Alexa 488 scans of the same slide were combined using masliner (MicroArray LINEar Regression) software.

data_processing: To correct for any possible non-uniformities in protein binding, we adjusted the Alexa 488 signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber. Next, the Seed-and-wobble algorithm was applied to compute enrichment scores (E-scores) and median intensities.

label: Alexa 488

molecule: protein

organism: Nakaseomyces glabratus

source_name: C. glabrata Pho4

label_protocol: Proteins were tagged with N-terminal GST by cloning. Protein-bound arrays were incubated with Alexa-488-conjugated rabbit polyclonal antibody to GST (Invitrogen).

growth_protocol: Gateway-compatible clones containing the full-length genes for ScPho4 and CgPho4 were transferred into pDEST15. Cells were grown in LB broth to an OD600 of 0.8 and then expression was induced with 1mM IPTG at 30° for 3 hours. Pelleted cells were frozen, stored at -80 C, and thawed cells were lysed with lysozyme.

extract_protocol: GST-tagged protein was run on a GST column equilibrated with the lysis buffer and eluted with a gradient to buffer B (50mM Tris, 10mM glutathione, pH 8). GST-Pho4 fractions containing the protein were pooled and loaded onto a heparin column equilibrated with low salt buffer (25mM Na2HPO4 pH 7.4, 150mM NaCl, 0.5mM THP) and eluted with a gradient to high salt buffer (25mM sodium phosphate dibasic pH 7.4, 1.5M NaCl, 0.5mM THP). Fractions containing the protein were pooled and concentrated with a 30 kDa cutoff Amicon centrifugal filter (Sigma UFC9030) and loaded onto a Superdex 200 size exclusion column equilibrated with the storage buffer (25mM HEPES pH 7.4, 500mM NaCl, 0.5mM THP). Protein was run on an SDS-PAGE and pure fractions were pooled and concentrated. 10% glycerol was added before snap freezing and storage at −80°C.

tag: transcription factor

tag: protein concentration

value: Protein concentration:1 uM


title: d8_3

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

library_source: other

data_processing:
Illumina bcl2fastq (v2.20.0.422) were performed for converting fastq files and separation by samples with default setting
To count and test the data by MAGeCK, the manufacturer's original reference file was modified by custom perl script for Set A and Set B.
"mageck count" counted guide RNA sequences and "mageck test" were used to test each gene and each guide RNA in the sample.
Assembly: https://www.addgene.org/static/cms/filer_public/a3/b1/a3b1a555-e941-46da-94af-47955f5ea5f4/hcrispri-v2-guides-weissman.zip
Supplementary files format and content: tab-delimited text file include normalized count of each guide RNA for each sample
Library strategy: CRISPRi screening

molecule: other

source_name: Primed iPSC

growth_protocol: Primed human pluripotent stem cells were maintained in StemFiT AK02N media (Ajinomoto) on iMatrix-511-coated plates at 37 ºC in a humidified incubator with 20% O2 and 5% CO2.

extract_protocol:
DNA was extracted using the manufacturer's protocotol.
Libraries were constructed following the manufacturer's protocotol.

treatment_protocol: For inducing the knockdown, 1 μg/mL of DOX were added.

tag: time

value: Day 8

tag: cell type

value: Primed iPSC

tag: library type

value: Set B


title: ScPho4 at 1 uM concentration

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae Pho4


title: AK5

city: AUBURN

first: Amit

middle: Kumar

last: Mitra

state: AL

address: HARRISON COLLEGE OF PHARMACY

department: DRUG DISCOVERY AND DEVELOPMENT

institute: AUBURN UNIVERSITY

data_processing:
Partek Genomics Suite
Read count extraction were performed from raw data using Partek Flow
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene counts in Samples

molecule: total RNA

source_name: ALL

extract_protocol:
High quality RNA was isolated using QIAshredder columns and RNAeasy Mini kit (Qiagen)
RNA-seq libraries were constructed using Illumina TruSeq RNA Library Prep Kit v2 (poly A enrichment).
RNA sequencing was performed on Illumina’s NovaSeq 6000 platform (150 bp paired-end) at >20 million reads per sample.

value: ALL

value: lymphoblast cell line


title: Kdm7c_DBA_Lamin_TwoCell_rep4

city: Munich

first: Maria-Elena

last: Torres-Padilla

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

description: Low-input LaminB1 DamID

data_processing:
Samples were sequenced using Illumina HiSeq4000 or HiSeq2500 platforms in 150 bp PE mode but only read1 was used for downstream analysis. For pre-processing of reads, first 6 random bases were discarded using trimmomatic (version 0.39). Subsequently, the reads were demultiplexed according to DamID indexes using fastx barcode splitter and the additional 15 bp of adaptors were trimmed using trimmomatic. The pre-processed reads starting with GATC were then mapped to the mm10 using bowtie2 (version 2.5.1) with default parameters. Reads aligning to the genome with quality score below 30 were discarded using samtools (version 1.17). Duplicates were removed using picard (version 3.0.0) to finally obtain unique GATC reads.
The computation of OE (Observed/Expected) values were performed in 100-kb genomic bins. To distinguish LAD domains from inter-LADs, a two-state hidden Markov model (HMM) was applied to non-zero OE mean values.
Assembly: mm10
Supplementary files format and content: Dam-LaminB1 observed over expected (OE) values calculated in 100-kb genomic bins provided in bedgraph files and LAD domain coordinates are provided in bed files.
Supplementary files format and content: Mean OE and LAD coordinates files are available on Rep 1 samples.
Library strategy: DamID-seq

source_name: 2-cell embryo

growth_protocol: Zygotes were collected from the oviduct and cumulus cells were removed upon brief incubation in M2 media containing hyaluronidase. Zygotes were placed in drops of KSOM and cultured at 37 ºC with 5% CO2.

extract_protocol:
Zona pellucida was removed by treatment with 0.5% pronase in M2 at 37 °C. Polar bodies were separated from the embryos by gentle pipetting after trypsin treatment and discarded. For each replicate, a pool of 10-20 blastomeres (10 to 20 zygotes or 5 to 10 2-cell embryos) were collected in 2 μL DamID buffer (10 mM TRIS acetate pH 7.5, 10 mM magnesium acetate, 50 mM potassium acetate) and stored at -80 °C until downstream processing.
Approximately 300 ng of PCR purified DNA was end-repaired using an End-It DNA End-Repair Kit. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Between steps, the DNA was purified with Agencourt AMPure XP beads with a 1.8 x bead volume and a 1.0 x bead volume after the ligation reaction. After adapter ligation, DNA was PCR amplified with Illumina primers for 8 cycles.

treatment_protocol: For DamID, early zygotes (18 h post hCG) were isolated and injected with 250 ng/μL Tir1, 50 ng/μL membrane-eGFP and 10 ng/μL AID-Dam-LaminB1 along with mRNA encoding candidate protein(s) and cultured in auxin (500μM)-containing medium. For mapping LADs in zygotic stage, auxin was removed from 22 h and late zygotes were collected at 28–30 h post hCG. For DamID in late 2-cell stage, auxin was washed out from 42 to 48-50 h post hCG and embryos were cultured in KSOM. The mRNA concentration of candidate proteins was decided based on size of the ORF to ensure roughly equimolar expression. For EZH2 inhibition experiment in zygote, embryos were treated with 0.01% DMSO (as control) or 5 μΜ GSK343 (Selleckchem, #S7164) from 18 h to 28 h post hCG.

value: 2-cell embryo

value: (C57BL/6J xCBA) x DBA/2J

tag: mrna injected

value: 1000 ng/μL Kdm7c


title: E16.5 Decidua, PNA, HF diet, rep 2

description:
L37ED
D_PHFvsD_PND_deg.txt
D_PHFvsD_CHF_deg.txt
D_PHFvsD_CND_deg.txt


title: Kdm7c_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID


title: d8_2

value: Set A


title: AK10


title: E16.5 Decidua, PNA, normal diet, rep 4

description:
L31ED
D_PHFvsD_PND_deg.txt
D_PNDvsD_CND_deg.txt


title: AK4


title: d8_1


title: Kdm7a_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID

value: 800 ng/μL Kdm7a


title: Kdm7a_DBA_Lamin_TwoCell_rep4

description: Low-input LaminB1 DamID


title: H3K9me3_GFP_Control_2C_rep1

data_processing:
Paired-end reads were trimmed using Cutadapt (version 3.4). After trimming, the reads were aligned to the mouse reference genome (GRCm38) using Bowtie2 (version 2.3.5). Reads were then filtered based on mapping quality scores using Samtools (version 1.3). Read pairs were imported into R (version 4.1.2) using the readGAlignmentPairs function from the GenomicAlignment package (version 1.30), where they were filtered for unique fragments. Fragments aligning to the mitochondrial genome or small scaffolds were excluded from the analysis. The fragments were counted in 100-kb genomic bins, normalized by the total fragment counts, and scaled to a million. For detailed information, see the methods of the accompanying paper.
Assembly: GRCm38
Supplementary files format and content: Normalized read counts per 100-kb bins for each replicate
Supplementary files format and content: Average normalized read counts per 100-kb bins from replicates
Library strategy: CUT&RUN

source_name: Late 2-cell embryo

growth_protocol: Zygotes were collected at 18h post-hCG, microinjected, and cultured in KSOM until 48h post-hCG (late 2-cell stage) and collected for CUT&RUN.

extract_protocol:
Low-input CUT&RUN was performed as described in detail in the methods section of the accompanying paper. Late 2-cell stage embryos (48 hours post-hCG) with intact zona pellucida were washed in a buffer containing 0.5 mM spermidine, 0.1% BSA, and 1× protease inhibitor cocktail. They were then transferred to an antibody buffer (anti-H3K9me3 antibody diluted 1:100 in wash buffer containing Triton-X and EDTA) and incubated overnight at 4 °C. After washing, the embryos were incubated with pAG-MNase (diluted 1:20 or 1:200) for 1 hour at room temperature. The embryos were washed again and transferred to a calcium buffer for 30 minutes or 2 hours at 4 °C for targeted chromatin digestion. The reaction was stopped with an EGTA-STOP buffer, followed by a 30-minute incubation at 37 °C to release chromatin fragments. The supernatant was collected, and DNA was extracted using the QIAquick kit. Illumina library preparation was carried out with 15 or 18 PCR cycles.
See methods of the accompanying paper for more information.

treatment_protocol: Embryos were microinjected with mRNAs encoding candidate protein(s). GFP-injected embryos were processed together with Suv39h1-injected embryos, whereas membrane-GFP (mGFP) injected embryos were processed with Pool J (Suv39h1, Hp1a, Hp1g).

value: Late 2-cell embryo

value: (C57BL/6J x CBA) x DBA/2J

value: Abcam, ab8898

tag: dilution of_pag-mnase

value: 1:200 dilution

tag: incubation in_calcium_buffer

value: 30 min

tag: pcr cycles

value: Control (250 ng/μL GFP)


title: E16.5 Decidua, PNA, normal diet, rep 3

description:
L30KD
D_PHFvsD_PND_deg.txt
D_PNDvsD_CND_deg.txt

value: Decidua

tag: mouse strain

value: Female

value: WT

value: Pregnancy


title: AK3

value: ALL


title: K562_treated_with_EPZ719_H3K36me3_CUTnTAG_rep2_(20240401_WW1073_240325)

description: CUT&Tag targeting H3K36me3 in K562 in EPZ719, 100nMEPZ719,24h,H152,H3K36me3

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads. 2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the repeat-masked hg19 Homo sapiens reference sequence obtained from UCSC. 3. We used samtools 1.14 "view" to extract properly paired reads from the hg19 alignments. 4. We used bedtools 2.30.0 "genomecov" to make a normalized count hg19 track which is the fraction of counts at each base pair scaled by the size of the hg19 reference sequence (3095693983) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .hg19.bw)
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

value: Epicypher, SKU:13-0058


title: AK2

value: lymphoblast cell line

value: Control


title: Kdm7a_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID

value: 2-cell embryo

value: (C57BL/6J xCBA) x DBA/2J


title: E16.5 Decidua, control, HF diet, rep 3

description:
L20ID
D_CHFvsD_CND_deg.txt
D_PHFvsD_CHF_deg.txt

tag: Sex


title: E16.5 Decidua, PNA, normal diet, rep 2

description:
L24ED
D_PHFvsD_PND_deg.txt
D_PNDvsD_CND_deg.txt


title: K562_treated_with_EPZ719_H3K36me3_CUTnTAG_rep1_(20240401_WW1072_240325)

tag: cell line


title: AK1


title: Kdm7c_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_Kdm7c_DBA_Lamin_TwoCell.bedgraph
Kdm7c_DBA_Lamin_TwoCell_LAD_coordinates.bed

value: 1000 ng/μL Kdm7c


title: Kdm7a_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_Kdm7a_DBA_Lamin_TwoCell.bedgraph
Kdm7a_DBA_Lamin_TwoCell_LAD_coordinates.bed

value: 800 ng/μL Kdm7a


title: Hp1g_DBA_Lamin_TwoCell_rep4

description: Low-input LaminB1 DamID

value: 300 ng/μL Hp1g


title: K562_treated_with_DMSO_H3K36me3_CUTnTAG_rep2_(20240401_WW1082_240325)

description: CUT&Tag targeting H3K36me3 in K562 in DMSO, 10000DMSO,24h,H152,H3K36me3

tag: group


title: p2018-107_IFNg_Pos

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the hg38 version of the mouse genome using Bowtie2 v2.2.4
bigWig files were normalized to reads per million and generated using GenomicRanges and bedGraphToBigWig function from the UCSC genome browser
Assembly: hg38
Supplementary files format and content: reads per million normalized bigWig files

source_name: Monocytes

extract_protocol:
10,000 cells were sorted into 40% FBS in complete media.
10,000 cells were centrifuged for 10 minutes at 500xg, and tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1X TD buffer (10 mM TAPS-NaOH pH 8.1, 5 mM MgCl2, 10% DMF), 2.5 μl Tn5 transposase, 0.1% Tween 20 and 0.02% Digitonin) and then incubated for 1 h at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

treatment_protocol: Monocytes from the indicated sample groups were stimulated for 18 hours with 100U IFNg or rested in media prior to ATAC-seq analysis

tag: source

value: PBMC

value: Monocytes

tag: ifng stimulation

value: Pos

tag: rs3129882 genotype

value: AA

tag: disease status

value: Healthy Control


title: E16.5 Decidua, control, HF diet, rep 2

description:
L15ED
D_CHFvsD_CND_deg.txt
D_PHFvsD_CHF_deg.txt

tag: tissue

value: Decidua

value: Female

tag: genotype

tag: treatment


title: E16.5 Decidua, PNA, normal diet, rep 1

description:
L6DD
D_PHFvsD_PND_deg.txt
D_PNDvsD_CND_deg.txt

value: WT

value: Pregnancy


title: K562_H3K36me3_CUTnTAG_5_(20240302_WW930_240206)

description: CUT&Tag targeting H3K36me3 in K562, 50K,H152,H3K36me3,dot,enzyme

tag: antibody

value: Epicypher, SKU:13-0058


title: E16.5 Decidua, control, HF diet, rep 1

description:
L14ED
D_CHFvsD_CND_deg.txt
D_PHFvsD_CHF_deg.txt


title: K562_treated_with_DMSO_H3K36me3_CUTnTAG_rep1_(20240401_WW1081_240325)


title: Hp1g_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID


title: E16.5 Decidua, control, normal diet, rep 3

description:
L12DD
D_CHFvsD_CND_deg.txt
D_PNDvsD_CND_deg.txt
D_PHFvsD_CND_deg.txt


title: E16.5 Decidua, control, normal diet, rep 2

description:
L27FD
D_CHFvsD_CND_deg.txt
D_PNDvsD_CND_deg.txt
D_PHFvsD_CND_deg.txt


title: p2018-113_IFNg_Pos

tag: cell type

value: GG

value: Parkinson's Disease


title: Hp1g_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_Hp1g_DBA_Lamin_TwoCell.bedgraph
Hp1g_DBA_Lamin_TwoCell_LAD_coordinates.bed

value: 2-cell embryo

tag: mrna injected


title: p2019-004_IFNg_Pos


title: Hp1a_DBA_Lamin_TwoCell_rep4

description: Low-input LaminB1 DamID

value: (C57BL/6J xCBA) x DBA/2J

value: 300 ng/μL Hp1a


title: K562_H3K36me3_CUTnTAG_2_(20240222_WW927_240206)

description: CUT&Tag targeting H3K36me3 in K562, 50K,H152,H3K36me3,nodot,enzyme


title: K562_H3K36me3_CUTnTAG_4_(20240302_WW929_240206)


title: Hp1g_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID


title: p2018-113_IFNg_Neg

value: Neg


title: K562_H3K36me3_CUTnTAG_3_(20240222_WW928_240206)


title: E16.5 Decidua, control, normal diet, rep 1

description:
L1FD
D_CHFvsD_CND_deg.txt
D_PNDvsD_CND_deg.txt
D_PHFvsD_CND_deg.txt


title: p2019-004_IFNg_Neg


title: Hp1a_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID


title: K562_H3K36me3_CUTnTAG_1_(20240208_WW898_240131)

description: CUT&Tag targeting H3K36me3 in K562, 50K,H152,H3K36me3


title: E16.5 Placenta, PNA, HF diet, rep 3

description:
L55DP
D_PHFvsD_PND_deg.txt
D_PHFvsD_CHF_deg.txt
D_PHFvsD_CND_deg.txt

source_name: Placenta

value: Placenta


title: Hp1a_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID


title: p2018-107_IFNg_Neg

value: PBMC


title: p2018-102_IFNg_Neg

value: Monocytes


title: K562_treated_with_ActinomycinD_RNAPIIS2P_CUTnTAG_rep2_(20240408_WW1118_240329)

description: CUT&Tag targeting RNAPIIS2P in K562 in ActinomycinD, 1uMActino,1h,P72,RNAPIIS2P

value: Cell Signaling Technology, 13499S


title: Hp1a_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_Hp1a_DBA_Lamin_TwoCell.bedgraph
Hp1a_DBA_Lamin_TwoCell_LAD_coordinates.bed


title: Ehmt2_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID

value: 1200 ng/μL Ehmt2


title: K562_treated_with_ActinomycinD_RNAPIIS2P_CUTnTAG_rep1_(20240408_WW1117_240329)


title: p2018-110_IFNg_Pos

value: Pos


title: E16.5 Placenta, PNA, HF diet, rep 2

description:
L37EP
D_PHFvsD_PND_deg.txt
D_PHFvsD_CHF_deg.txt
D_PHFvsD_CND_deg.txt


title: E16.5 Placenta, PNA, HF diet, rep 1

description:
L8FP
D_PHFvsD_PND_deg.txt
D_PHFvsD_CHF_deg.txt
D_PHFvsD_CND_deg.txt


title: K562_treated_with_Flavopiridol_RNAPIIS2P_CUTnTAG_rep1_(20240408_WW1113_240329)

description: CUT&Tag targeting RNAPIIS2P in K562 in Flavopiridol, 1uMFla,1h,P72,RNAPIIS2P


title: Ehmt2_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID


title: E16.5 Placenta, PNA, normal diet, rep 4

description:
L31EP
D_PHFvsD_PND_deg.txt
D_PNDvsD_CND_deg.txt


title: p2018-103_IFNg_Pos

value: AA


title: p2018-103_IFNg_Neg


title: E16.5 Placenta, PNA, normal diet, rep 2

description:
L24EP
D_PHFvsD_PND_deg.txt
D_PNDvsD_CND_deg.txt

value: Female


title: E16.5 Placenta, PNA, normal diet, rep 3

description:
L30KP
D_PHFvsD_PND_deg.txt
D_PNDvsD_CND_deg.txt

value: WT


title: E16.5 Placenta, PNA, HF diet, rep 4

description:
L62DP
D_PHFvsD_PND_deg.txt
D_PHFvsD_CHF_deg.txt
D_PHFvsD_CND_deg.txt

value: Pregnancy


title: K562_treated_with_Flavopiridol_RNAPIIS2P_CUTnTAG_rep2_(20240408_WW1114_240329)


title: p2018-110_IFNg_Neg


title: K562_treated_with_Triptolide_RNAPIIS2P_CUTnTAG_rep1_(20240408_WW1109_240329)

description: CUT&Tag targeting RNAPIIS2P in K562 in Triptolide, 10uMTriptolide,1h,P72,RNAPIIS2P


title: p2018-100_IFNg_Neg

value: Healthy Control


title: K562_treated_with_DMSO_RNAPIIS2P_CUTnTAG_rep2_(20240408_WW1106_240329)

description: CUT&Tag targeting RNAPIIS2P in K562 in DMSO, 1000DMSO,1h,P72,RNAPIIS2P


title: K562_treated_with_Triptolide_RNAPIIS2P_CUTnTAG_rep2_(20240408_WW1110_240329)


title: Ehmt2_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_Ehmt2_DBA_Lamin_TwoCell.bedgraph
Ehmt2_DBA_Lamin_TwoCell_LAD_coordinates.bed


title: E16.5 Placenta, PNA, normal diet, rep 1

description:
L6DP
D_PHFvsD_PND_deg.txt
D_PNDvsD_CND_deg.txt


title: p2018-102_IFNg_Pos


title: p2018-114_IFNg_Pos

value: GG


title: p2018-114_IFNg_Neg

value: Parkinson's Disease


title: K562_treated_with_DMSO_RNAPIIS2P_CUTnTAG_rep1_(20240408_WW1105_240329)


title: Suv39h1_DBA_Lamin_Zygote_rep5

description: Low-input LaminB1 DamID

source_name: Zygote

value: Zygote

value: 600 ng/μL Suv39h1


title: Ehmt1_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_Ehmt1_DBA_Lamin_TwoCell.bedgraph
Ehmt1_DBA_Lamin_TwoCell_LAD_coordinates.bed

value: 2-cell embryo

value: (C57BL/6J xCBA) x DBA/2J

value: 1200 ng/μL Ehmt1


title: E16.5 Placenta, control, HF diet, rep 4

description:
L36FP
D_CHFvsD_CND_deg.txt
D_PHFvsD_CHF_deg.txt

value: Placenta


title: K562_treated_with_ActinomycinD_RNAPIIS5P_CUTnTAG_(20240408_WW1119_240329)

description: CUT&Tag targeting RNAPIIS5P in K562 in ActinomycinD, 1uMActino,1h,P51,RNAPIIS5P

value: Cell Signaling Technology, 13523S


title: Suv39h1_DBA_Lamin_Zygote_rep4

description: Low-input LaminB1 DamID


title: p2018-009_IFNg_Neg

value: PBMC

value: Monocytes

value: Neg


title: Suv39h1_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID


title: p2018-009_IFNg_Pos

value: Pos


title: K562_treated_with_Triptolide_RNAPIIS5P_CUTnTAG_(20240408_WW1111_240329)

description: CUT&Tag targeting RNAPIIS5P in K562 in Triptolide, 10uMTriptolide,1h,P51,RNAPIIS5P


title: Ehmt1_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID


title: Suv39h1_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: E16.5 Placenta, control, HF diet, rep 2

description:
L15EP
D_CHFvsD_CND_deg.txt
D_PHFvsD_CHF_deg.txt

value: Female


title: Suv39h1_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_Suv39h1_DBA_Lamin_Zygote.bedgraph
Suv39h1_DBA_Lamin_Zygote_LAD_coordinates.bed


title: E16.5 Placenta, control, normal diet, rep 3

description:
L12CP
D_CHFvsD_CND_deg.txt
D_PNDvsD_CND_deg.txt
D_PHFvsD_CND_deg.txt

value: WT


title: p2019-006_IFNg_Pos

value: AA


title: Setdb2_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID

value: 700 ng/μL Setdb2


title: p2019-006_IFNg_Neg


title: E16.5 Placenta, control, HF diet, rep 3

description:
L20IP
D_CHFvsD_CND_deg.txt
D_PHFvsD_CHF_deg.txt

value: Pregnancy


title: K562_treated_with_DMSO_RNAPIIS5P_CUTnTAG_(20240408_WW1108_240329)

description: CUT&Tag targeting RNAPIIS5P in K562 in DMSO, 1000DMSO,1h,P51,RNAPIIS5P


title: p2018-106_IFNg_Pos

value: GG

value: Healthy Control


title: K562_RNAPIIS2P_CUTnRUN_rep2_(20240515_WW1140_240416)

description: CUT&RUN targeting RNAPIIS2P in K562, 625K,P72,RNAPIIS2P

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads. 2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the repeat-masked hg19 Homo sapiens reference sequence obtained from UCSC. 3. We used samtools 1.14 "view" to extract properly paired reads from the hg19 alignments. 4. We used bedtools 2.30.0 "genomecov" to make a normalized count hg19 track which is the fraction of counts at each base pair scaled by the size of the hg19 reference sequence (3095693983) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .hg19.bw)
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

value: Cell Signaling Technology, 13499S


title: E16.5 Placenta, control, normal diet, rep 1

description:
L1FP
D_CHFvsD_CND_deg.txt
D_PNDvsD_CND_deg.txt
D_PHFvsD_CND_deg.txt


title: Ehmt1_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID

value: 2-cell embryo


title: p2018-106_IFNg_Neg


title: E16.5 Placenta, control, HF diet, rep 1

description:
L14EP
D_CHFvsD_CND_deg.txt
D_PHFvsD_CHF_deg.txt


title: Setdb2_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_Setdb2_DBA_Lamin_Zygote.bedgraph
Setdb2_DBA_Lamin_Zygote_LAD_coordinates.bed

value: Zygote

value: (C57BL/6J xCBA) x DBA/2J


title: K562_treated_with_Flavopiridol_RNAPIIS5P_CUTnTAG_(20240408_WW1115_240329)

description: CUT&Tag targeting RNAPIIS5P in K562 in Flavopiridol, 1uMFla,1h,P51,RNAPIIS5P


title: p2018-098_IFNg_Pos

value: Parkinson's Disease


title: K562_RNAPIIS2P_CUTnRUN_rep1_(20240515_WW1139_240416)


title: Uterus, PNA, HF diet, unstimulated, rep 4

description:
PH31W
PHXvsPHW_deg.txt
PHWvsPNW_deg.txt
PHWvsCHW_deg.txt

source_name: Uterus

value: Uterus


title: Uterus, PNA, HF diet, stimulated, rep 4

description:
PH32X
PHXvsPHW_deg.txt
PHXvsPNX_deg.txt
PHXvsCHX_deg.txt

value: Artificial decidualization, stimulated


title: K562_H3K36me3_CUTnRUN_rep2_(20240515_WW1138_240416)

description: CUT&RUN targeting H3K36me3 in K562, 625K,H152,H3K36me3

value: Epicypher, SKU:13-0058


title: Setdb1_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID

value: 1200 ng/μL Setdb1


title: Uterus, PNA, HF diet, stimulated, rep 3

description:
PH30X
PHXvsPHW_deg.txt
PHXvsPNX_deg.txt
PHXvsCHX_deg.txt


title: p2018-019_IFNg_Neg

value: PBMC

value: Monocytes

value: Neg


title: K562_H3K36me3_CUTnRUN_rep1_(20240515_WW1137_240416)


title: K562_RNAPIIS2P_CUTnTAG_(20240319_WW1026_240312)

description: CUT&Tag targeting RNAPIIS2P in K562, 50K,P72,RNAPIIS2P,CUTTag


title: p2018-019_IFNg_Pos

value: Pos

value: AA


title: K562_treated_with_EPZ719_U2AF2_CUTnRUN_rep2_(20240408_WW1122_240402)

description: CUT&RUN targeting U2AF2 in K562 in EPZ719, 2uLP372,U2AF2,100nMEPZ719,24h

value: Abcam, ab37530


title: Setdb1_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_Setdb1_DBA_Lamin_Zygote.bedgraph
Setdb1_DBA_Lamin_Zygote_LAD_coordinates.bed


title: p2018-101_IFNg_Neg


title: K562_treated_with_DMSO_U2AF2_CUTnRUN_4_(20240408_WW1126_240402)

description: CUT&RUN targeting U2AF2 in K562 in DMSO, 2uLP372,U2AF2,10000DMSO,24h


title: T cells of donor CF-018

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

data_processing:
Sequencing libraries for gene expression and TCR was jointly processed using cellranger multi (v7.1.0) and the GRCh38 genome annotation
Assembly: GRCh38
Supplementary files format and content: cellranger h5 output (gene expression), contig tables (VDJ)
Library strategy: 10X immune profiling

source_name: blood

extract_protocol:
To isolate peripheral blood mononuclear cells (PBMCs), peripheral blood was diluted 1:1 in 1x PBS and subjected to density gradient centrifugation using Pancoll human (PAN-Biotech, P06-1391500) at 800g for 20 minutes at room temperature. T cells were then isolated from PBMCs using the EasySep Human T cell Isolation Kit (Stemcell Technologies, 17951). The T cell fraction was then resuspended in a freezing medium composed of 90% FCS and 10% DMSO. Subsequently, the PBMCs were frozen using a Cryo-freezing container (Nalgene) and stored in liquid nitrogen for long-term preservation.  Thawed T cells underwent sorting using the FACS Aria III sorter, employing a 85-micron nozzle. DAPI-negative cells were sorted.
According to the manufacturer's instructions, single-cell RNA-seq libraries were generated using the Chromium Next GEM Single Cell 5' Reagent Kits v2 by 10x Genomics (CG000330 Rev D). Briefly, a droplet emulsion was generated in a microfluidic chip, followed by barcoded cDNA and surface tag generation inside the droplets. Purified and amplified cDNA and surface tags were then subjected to NGS library preparation. The manufacturer's instructions generated T cell receptor sequencing libraries from amplified cDNA. Sequencing was performed on a NovaSeq 6000 instrument (Illumina). The read depth aimed for 30K reads per cell for GEX and ~20K for TCR libraries.

value: blood

tag: donor

value: post-therapy


title: Uterus, PNA, HF diet, stimulated, rep 2

description:
PH28X
PHXvsPHW_deg.txt
PHXvsPNX_deg.txt
PHXvsCHX_deg.txt

value: Female

value: WT


title: K562_treated_with_EPZ719_U2AF2_CUTnRUN_rep1_(20240408_WW1121_240402)


title: Uterus, PNA, HF diet, stimulated, rep 1

description:
PH26X
PHXvsPHW_deg.txt
PHXvsPNX_deg.txt
PHXvsCHX_deg.txt


title: T cells of donor CF-023


title: Uterus, PNA, HF diet, unstimulated, rep 2

description:
PH27W
PHXvsPHW_deg.txt
PHWvsPNW_deg.txt
PHWvsCHW_deg.txt


title: K562_treated_with_DMSO_U2AF2_CUTnRUN_3_(20240408_WW1125_240402)


title: p2018-101_IFNg_Pos


title: Uterus, PNA, HF diet, unstimulated, rep 1

description:
PH25W
PHXvsPHW_deg.txt
PHWvsPNW_deg.txt
PHWvsCHW_deg.txt


title: Lsd1_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID

value: Zygote

value: 800 ng/μL Lsd1


title: Lsd1_DBA_Lamin_Zygote_rep4

description: Low-input LaminB1 DamID

value: (C57BL/6J xCBA) x DBA/2J


title: Lsd1_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: T cells of donor CF-027


title: Setdb1_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: K562_treated_with_ActinomycinD_U2AF2_CUTnRUN_1_(20240401_WW1045_240315)

description: CUT&RUN targeting U2AF2 in K562 in ActinomycinD, 5uLP372,U2AF2,5ugmLActino,1h,EpiStop


title: Uterus, PNA, HF diet, unstimulated, rep 3

description:
PH29W
PHXvsPHW_deg.txt
PHWvsPNW_deg.txt
PHWvsCHW_deg.txt

value: Uterus


title: Setdb2_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID

value: 700 ng/μL Setdb2


title: Uterus, PNA, normal diet, stimulated, rep 4

description:
PN24X
PNXvsPNW_deg.txt
PHXvsPNX_deg.txt
PNXvsCNX_deg.txt

value: Artificial decidualization, stimulated


title: Kdm7c_DBA_Lamin_Zygote_rep4

description: Low-input LaminB1 DamID

value: 1000 ng/μL Kdm7c


title: T cells of donor CF-042


title: E16.5 Placenta, control, normal diet, rep 2

description:
L27FP
D_CHFvsD_CND_deg.txt
D_PNDvsD_CND_deg.txt
D_PHFvsD_CND_deg.txt

value: Placenta

value: Pregnancy


title: T cells of donor CF-005


title: K562_treated_with_Flavopiridol_U2AF2_CUTnRUN_2_(20240401_WW1040_240315)

description: CUT&RUN targeting U2AF2 in K562 in Flavopiridol, 5uLP372,U2AF2,1uMFlavo,1h,HomeStop


title: T cells of donor CF-031


title: K562_treated_with_Flavopiridol_U2AF2_CUTnRUN_1_(20240401_WW1039_240315)

description: CUT&RUN targeting U2AF2 in K562 in Flavopiridol, 5uLP372,U2AF2,1uMFlavo,1h,EpiStop


title: Kdm7c_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID


title: Kdm7c_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: Uterus, PNA, normal diet, unstimulated, rep 3

description:
PN21W
PNXvsPNW_deg.txt
PHWvsPNW_deg.txt
PNWvsCNW_deg.txt


title: T cells of donor TC-48

value: pre-therapy


title: K562_treated_with_ActinomycinD_U2AF2_CUTnRUN_2_(20240401_WW1046_240315)

description: CUT&RUN targeting U2AF2 in K562 in ActinomycinD, 5uLP372,U2AF2,5ugmLActino,1h,HomeStop


title: Kdm7c_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_Kdm7c_DBA_Lamin_Zygote.bedgraph
Kdm7c_DBA_Lamin_Zygote_LAD_coordinates.bed


title: K562_treated_with_Triptolide_U2AF2_CUTnRUN_2_(20240401_WW1034_240315)

description: CUT&RUN targeting U2AF2 in K562 in Triptolide, 5uLP372,U2AF2,10uMTrip,1h,HomeStop


title: T cells of donor CF-036


title: Uterus, PNA, normal diet, stimulated, rep 2

description:
PN20X
PNXvsPNW_deg.txt
PHXvsPNX_deg.txt
PNXvsCNX_deg.txt


title: K562_treated_with_DMSO_U2AF2_CUTnRUN_2_(20240401_WW1028_240315)

description: CUT&RUN targeting U2AF2 in K562 in DMSO, 5uLP372,U2AF2,001DMSO,1h,HomeStop


title: T cells of donor CF-019


title: Uterus, PNA, normal diet, unstimulated, rep 2

description:
PN19W
PNXvsPNW_deg.txt
PHWvsPNW_deg.txt
PNWvsCNW_deg.txt


title: Kdm7a_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID

value: 800 ng/μL Kdm7a


title: Uterus, PNA, normal diet, unstimulated, rep 4

description:
PN23W
PNXvsPNW_deg.txt
PHWvsPNW_deg.txt
PNWvsCNW_deg.txt


title: Uterus, PNA, normal diet, stimulated, rep 1

description:
PN18X
PNXvsPNW_deg.txt
PHXvsPNX_deg.txt
PNXvsCNX_deg.txt


title: Uterus, PNA, normal diet, unstimulated, rep 1

description:
PN17W
PNXvsPNW_deg.txt
PHWvsPNW_deg.txt
PNWvsCNW_deg.txt


title: Uterus, PNA, normal diet, stimulated, rep 3

description:
PN22X
PNXvsPNW_deg.txt
PHXvsPNX_deg.txt
PNXvsCNX_deg.txt


title: K562_U2AF2_CUTnRUN_5_(20240302_WW950_240216)

description: CUT&RUN targeting U2AF2 in K562, 5uLP372,U2AF65,homeMNase,ice2h


title: Uterus, control, HF diet, stimulated, rep 4

description:
CH16X
PNXvsPNW_deg.txt
CHXvsCNX_deg.txt
PHXvsCHX_deg.txt


title: T cells of donor CF-033


title: Kdm7a_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: Kdm7a_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_Kdm7a_DBA_Lamin_Zygote.bedgraph
Kdm7a_DBA_Lamin_Zygote_LAD_coordinates.bed


title: K562_U2AF2_CUTnRUN_4_(20240302_WW946_240216)

description: CUT&RUN targeting U2AF2 in K562, 5uLP372,U2AF65,homeMNase,4C2h


title: T cells of donor CF-028


title: K562_treated_with_Triptolide_U2AF2_CUTnRUN_1_(20240401_WW1033_240315)

description: CUT&RUN targeting U2AF2 in K562 in Triptolide, 5uLP372,U2AF2,10uMTrip,1h,EpiStop


title: Lsd1_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_Lsd1_DBA_Lamin_Zygote.bedgraph
Lsd1_DBA_Lamin_Zygote_LAD_coordinates.bed


title: THP-1 cells, WT, no treatment, n=3

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

data_processing:
QC and metric calculation of all fastq files were done with fastQC version v0.11.6. Compilation for inspection of all fastQC reports was done using multiQC version 1.13. Adapter trimming was performed using fastp version 0.23.2. Alignments of the reads into the reference genome hg38.bwa was performed using STAR version 2.7.10b using the following parameters: --twopassMode Basic --readFilesCommand zcat --outSAMstrandField intronMotif --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66. PCR Duplicates were removed from aligned BAM files with picard version 2.27.5 using the MarkDuplicates command with the following arguments: REMOVE_DUPLICATES=true. Reads for analysed features were assigned and counted from the processed BAM files using SubRead's FeatureCounts version v2.0.3  with the following arguments: -p --primary -C -t exon -g gene_id.
Assembly: hg38
Supplementary files format and content: Tab separated raw reads values

growth_protocol: THP-1 cells were grown in RPMI 1640 GlutaMAX supplemented with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA kit. 1 ug of total RNA was used foas input for the construction of the sequencing libraries.
Sequencing libraries were prepared following “TruSeq Stranded mRNA Sample Preparation Guide (Part # 15031058 Rev. E)” using the “TruSeq® Stranded mRNA Library Prep” kit  (Illumina Inc. Cat. # 20020594) and TruSeq RNA CD Index Plate (96 Indexes, 96 Samples) (Illumina Inc. Cat. # 20019792).

treatment_protocol: THP-1 cells were differentiated with 20 ng/ml of phorbol 12-myristate 13-acetate (PMA) for 24 h in 6-well plates. After 24 h, the medium was changed. The following day, differentiated THP-1 macrophages were polarized adding recombinant human IFN-gamma.

value: human monocytic cells

value: PMA


title: K562_U2AF2_CUTnRUN_3_(20240302_WW945_240216)

description: CUT&RUN targeting U2AF2 in K562, 1uLP372,U2AF65,homeMNase,4C2h

value: Abcam, ab37530


title: Kdm7a_DBA_Lamin_Zygote_rep4

description: Low-input LaminB1 DamID


title: Hp1g_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID

value: 300 ng/μL Hp1g


title: Hp1g_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID


title: Uterus, control, HF diet, unstimulated, rep 3

description:
CH13W
CHXvsCHW_deg.txt
CHWvsCNW_deg.txt
PHWvsCHW_deg.txt

value: Female


title: K562_treated_with_DMSO_U2AF2_CUTnRUN_1_(20240401_WW1027_240315)

description: CUT&RUN targeting U2AF2 in K562 in DMSO, 5uLP372,U2AF2,001DMSO,1h,EpiStop


title: THP-1 cells, WT, no treatment, n=1

value: WT


title: Uterus, control, HF diet, stimulated, rep 2

description:
CH12X
CHXvsCHW_deg.txt
CHXvsCNX_deg.txt
PHXvsCHX_deg.txt


title: K562_U2AF2_CUTnRUN_2_(20240302_WW944_240216)

description: CUT&RUN targeting U2AF2 in K562, 5uLP331,U2AF65,homeMNase,4C2h


title: K562_U2AF2_Plus_RNAseA_CUTnRUN_rep3_(20240302_WW962_240219)

description: CUT&RUN targeting U2AF2 in K562 ( RNAseA plus), 5uLP372,U2AF65,3uLRNAseA,homeMNase,4C2h


title: THP-1 cells, WT, IFN-gamma treatment, n=3

value: PMA + IFN-gamma


title: Hp1a_DBA_Lamin_Zygote_rep4

description: Low-input LaminB1 DamID

value: Zygote

value: 300 ng/μL Hp1a


title: T cells of donor CF-021

value: blood


title: Hp1g_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_Hp1g_DBA_Lamin_Zygote.bedgraph
Hp1g_DBA_Lamin_Zygote_LAD_coordinates.bed

value: (C57BL/6J xCBA) x DBA/2J


title: THP-1 cells, WT, IFN-gamma treatment, n=2


title: Uterus, control, HF diet, unstimulated, rep 4

description:
CH15W
CHXvsCHW_deg.txt
CHWvsCNW_deg.txt
PHWvsCHW_deg.txt

value: Uterus


title: K562_U2AF2_Plus_RNAseA_CUTnRUN_rep2_(20240302_WW961_240219)


title: Hp1a_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID


title: K562_U2AF2_Plus_RNAseA_CUTnRUN_rep1_(20240302_WW960_240219)


title: THP-1 cells, WT, IFN-gamma treatment, n=1


title: THP-1 cells, SDC3-KO, no treatment, n=3


title: K562_U2AF2_Minus_RNAseA_CUTnRUN_rep3_(20240302_WW959_240219)

description: CUT&RUN targeting U2AF2 in K562 ( RNAseA minus), 5uLP372,U2AF65,0uLRNAseA,homeMNase,4C2h


title: Uterus, control, HF diet, unstimulated, rep 1

description:
CH9W
CHXvsCHW_deg.txt
CHWvsCNW_deg.txt
PHWvsCHW_deg.txt


title: Hp1g_DBA_Lamin_Zygote_rep4

description: Low-input LaminB1 DamID


title: K562_U2AF2_Minus_RNAseA_CUTnRUN_rep2_(20240302_WW958_240219)


title: THP-1 cells, SDC3-KO, no treatment, n=2


title: Ehmt2_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID

value: 1200 ng/μL Ehmt2


title: Uterus, control, normal diet, unstimulated, rep 4

description:
CN7W
CNXvsCNW_deg.txt
CHWvsCNW_deg.txt
PNWvsCNW_deg.txt


title: Uterus, control, HF diet, stimulated, rep 3

description:
CH14X
CHXvsCHW_deg.txt
CHXvsCNX_deg.txt
PHXvsCHX_deg.txt

value: Artificial decidualization, stimulated


title: Uterus, control, HF diet, unstimulated, rep 2

description:
CH11W
CHXvsCHW_deg.txt
CHWvsCNW_deg.txt
PHWvsCHW_deg.txt


title: Ehmt2_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: Uterus, control, normal diet, stimulated, rep 3

description:
CN6X
CNXvsCNW_deg.txt
CHXvsCNX_deg.txt
PNXvsCNX_deg.txt


title: K562_U2AF1_Plus_RNAseA_CUTnRUN_rep2_(20240302_WW982_240221)

description: CUT&RUN targeting U2AF1 in K562 ( RNAseA plus), 5uLP374,U2AF1,3uLRNAseA,homeMNase,4C2h

value: Bethyl Laboratories, A302-079A


title: THP-1 cells, SDC3-KO, IFN-gamma treatment, n=3


title: K562_U2AF2_CUTnRUN_1_(20230621_WW313_230606)

description: CUT&RUN targeting U2AF2 in K562, P331,U2AF65,500K,CUTRUN


title: THP-1 cells, WT, no treatment, n=2


title: Ehmt2_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_Ehmt2_DBA_Lamin_Zygote.bedgraph
Ehmt2_DBA_Lamin_Zygote_LAD_coordinates.bed


title: Uterus, control, normal diet, unstimulated, rep 3

description:
CN5W
CNXvsCNW_deg.txt
CHWvsCNW_deg.txt
PNWvsCNW_deg.txt


title: Hp1a_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: Ehmt1_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID

value: 1200 ng/μL Ehmt1


title: Uterus, control, HF diet, stimulated, rep 1

description:
CH10X
CHXvsCHW_deg.txt
CHXvsCNX_deg.txt
PHXvsCHX_deg.txt


title: K562_U2AF1_Plus_RNAseA_CUTnRUN_rep1_(20240302_WW981_240221)


title: K562_U2AF2_Minus_RNAseA_CUTnRUN_rep1_(20240302_WW957_240219)


title: THP-1 cells, SDC3-KO, IFN-gamma treatment, n=2


title: Uterus, control, normal diet, stimulated, rep 2

description:
CN4X
CNXvsCNW_deg.txt
CHXvsCNX_deg.txt
PNXvsCNX_deg.txt


title: THP-1 cells, SDC3-KO, IFN-gamma treatment, n=1


title: Uterus, control, normal diet, stimulated, rep 4

description:
CN8X
CNXvsCNW_deg.txt
CHXvsCNX_deg.txt
PNXvsCNX_deg.txt


title: Hp1a_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_Hp1a_DBA_Lamin_Zygote.bedgraph
Hp1a_DBA_Lamin_Zygote_LAD_coordinates.bed


title: Uterus, control, normal diet, unstimulated, rep 2

description:
CN3W
CNXvsCNW_deg.txt
CHWvsCNW_deg.txt
PNWvsCNW_deg.txt


title: Ehmt1_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: K562_U2AF1_Minus_RNAseA_CUTnRUN_rep2_(20240302_WW980_240221)

description: CUT&RUN targeting U2AF1 in K562 ( RNAseA minus), 5uLP374,U2AF1,0uLRNAseA,homeMNase,4C2h


title: BLT, IP, Rep3

city: Ann Arbor

first: Kin Fai

last: Au

state: MI

address: 100 Washtenaw Avenue

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

description: Raw data (Fastq format) was generated in Norway, and is not allowed to upload to GEO per Norway policy.

data_processing:
*library strategy: meRIP-seq
The quality of the raw sequencing reads for both Input and IP samples was evaluated using FastQC (v0.11.8) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and sequencing adapters were trimmed using Cutadapt (v1.8.1) with settings “-m 20 --max-n 0.01 --trim-n”.
The trimmed reads were aligned to the human reference genome (hg38) using HISAT2 (v2.1.0) with the parameter “-5 8 --no-mixed --no-discordant”.
We retained only those read pairs aligning uniquely to one genomic location, as indicated by HISAT2. PCR duplicates were removed using SAMtools (v1.9) fixmate & markdup, and the read pairs aligning to ribosomal RNAs (per GENCODE v39 annotation) were filtered out using BEDTools (v2.28.0) intersect function.
The genome coverage bigWig files with a resolution of 10 bp (i.e., bin szie = 10 bp) and normalization accordiing to RPKM (reads per kilobase per million reads) were generated by deepTools (v3.2.0).
MACS2 (v2.1.2) callpeak with the parameter “-g 421727543 --keep-dup all -B --nomodel --call-summits” was used identify m6A peaks (q value <0.05), with the IP sample and the corresponding Input sample.
Assembly: hg38
Supplementary files format and content: The bigWig files are generated by deepTools (v3.2.0) bamCoverage with the bin size=10bp and normalized by RPKM.
Supplementary files format and content: The bed files are m6A peaks (q value <0.05), generated by MACS2 (v2.1.2) callpeak.

source_name: Blastocyst embryo

growth_protocol: Human embryonic stem cells (H1-hESC cell line) obtained from ATCC were cultured in feeder-free conditions. Patients undergoing treatment at the Department of Reproductive Medicine, Oslo University Hospital (OUH) underwent controlled ovarian stimulation. Initially, pituitary function was suppressed using a GnRH analogue, followed by follicle stimulation using recombinant or urine-derived FSH. Final follicular maturation was induced by administering human chorionic gonadotropin (hCG) upon observation of ≥ 3 follicles with a diameter of ≥ 17mm via ultrasound monitoring. Oocyte retrieval was performed 36 h (±2h) after hCG administration under transvaginal ultrasound guidance. Retrieved embryos were cultured in Vitrolife G1, G2, or G-TL media under controlled conditions of 6% CO2 and 37°C, in accordance with standard clinical protocols at the Department of Reproductive Medicine, OUH. Healthy sperm samples were cryopreserved in liquid nitrogen using cryoprotectants. Immature oocytes, identified by the presence of a germinal vesicle (GV), were selected for analysis. Single matured (MII) oocytes from fertile, healthy donors were included for single-cell analysis. These oocytes underwent vitrification and warming using RapidVit and RapidWarm oocyte kits (Vitrolife, Sweden). Intra cytoplasmic sperm injection (ICSI) was employed for fertilization. Fertilization was assessed post-ICSI, and embryo cleavage was monitored every 12 h. Suboptimal grade embryos, deemed unsuitable for cryopreservation, were donated to the project with patient consent.

extract_protocol:
Step 1. DNA and ribosomal RNA were depleted using the NEBNext rRNA depletion kit (NEB).
Step 2. RNA samples were fragmented by sonication.
Step 3. Anti-m6A antibody (Millipore, ABE572) was used to pull-down RNA fragments with m6A, followed by washes.
Step 4. RNA samples were precipitated by ethanol.
SMART-Seq stranded kit (Takara, 634442) was used to construct sequencing libraries.

treatment_protocol: For METTL3 inhibition experiments in H1-hESC, STM2457 (MCE, HY-134836) was added into the medium at a final concentration of 5 μM for 2 days

value: Blastocyst embryo


title: K562_U2AF1_Minus_RNAseA_CUTnRUN_rep1_(20240302_WW979_240221)


title: Uterus, control, normal diet, stimulated, rep 1

description:
CN2X
CNXvsCNW_deg.txt
CHXvsCNX_deg.txt
PNXvsCNX_deg.txt


title: BLT, IP, Rep2


title: THP-1 cells, SDC3-KO, no treatment, n=1

value: human monocytic cells


title: Ehmt1_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_Ehmt1_DBA_Lamin_Zygote.bedgraph
Ehmt1_DBA_Lamin_Zygote_LAD_coordinates.bed


title: Uterus, control, normal diet, unstimulated, rep 1

description:
CN1W
CNXvsCNW_deg.txt
CHWvsCNW_deg.txt
PNWvsCNW_deg.txt


title: BLT, IP, Rep1


title: K562_SF3B1_Plus_RNAseA_CUTnRUN_rep1_(20240302_WW975_240221)

description: CUT&RUN targeting SF3B1 in K562 ( RNAseA plus), 5uLP373,SF3B1,3uLRNAseA,homeMNase,4C2h

value: Cell Signaling Technology, 14434S


title: Uterus, control, normal diet, rep 4

description:
CN16
CHvsCN_deg.txt
PNvsCN_deg.txt

value: WOI


title: BLT, Input


title: PoolN_DBA_Lamin_TwoCell_rep4

description: Low-input LaminB1 DamID

value: 2-cell embryo

value: 1200 ng/μL Ehmt1, 1200 ng/μL Ehmt2, 1200 ng/μL Setdb1, 700 ng/μL Setdb2


title: PoolN_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID


title: K562_SF3B1_Minus_RNAseA_CUTnRUN_rep2_(20240302_WW974_240221)

description: CUT&RUN targeting SF3B1 in K562 ( RNAseA minus), 5uLP373,SF3B1,0uLRNAseA,homeMNase,4C2h


title: PoolN_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID


title: 8C, IP, Rep2

source_name: Eight-cell embryo

value: Eight-cell embryo


title: RiboPro_EIF3D_3

data_processing:
Illumina bcl2fastq (v2.20.0.422) were performed for converting fastq files and separation by samples with default setting
Fastp were executed for quality control and removing adapter sequence from each read and reads over 42 nt insert.
For demultiplexing with inner index sequences, fastx-split were perfomed.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.2.5), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.7.10b).
fp-framing and fp-count were perfomed for setting A-site and counting reads with GENCODE annotation file (v35).
To normalized read counts and calculate translational efficiency (TE), R (v4.1) and its package DESeq2 (v1.26.0) were performed with RNA-seq data.
To analyze non-canonical ORFs, the reads were counted with our original bed file, which were detected by ORF-RATER using WTB6 hiPSCs.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including DESeq2 nomalized counts and TE for each sample.
Library strategy: Ribosome Profiling

extract_protocol:
RNA was prepared using the Direct-zol RNA micoprep kit or Direct-zol RNA miniprep kit (Zymo Research) for ribosome profiling. RNA was quantified with Qubit RNA BR (Thermo Fisher Scientific).
Ribosome profiling libraries were constructed by the protocol of Dr. Shintaro Iwasaki (RIKEN, Japan).

tag: time

value: Day 3

value: Primed iPSC


title: PoolN_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolN_DBA_Lamin_TwoCell.bedgraph
PoolN_DBA_Lamin_TwoCell_LAD_coordinates.bed


title: 8C, IP, Rep1


title: K562_SF3B1_Minus_RNAseA_CUTnRUN_rep1_(20240302_WW973_240221)


title: PoolM_DBA_Lamin_TwoCell_rep4

description: Low-input LaminB1 DamID


title: 8C, Input


title: RiboPro_Control_3


title: Uterus, control, HF diet, rep 4

description:
CH12
CHvsCN_deg.txt
PHvsCH_deg.txt

value: Female

value: WT


title: RiboPro_EIF3D_2


title: Uterus, control, normal diet, rep 1

description:
CN13
CHvsCN_deg.txt
PNvsCN_deg.txt


title: K562_SF3B1_Plus_RNAseA_CUTnRUN_rep2_(20240302_WW976_240221)


title: PoolM_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID

value: (C57BL/6J xCBA) x DBA/2J


title: 2C, IP, Rep2

source_name: Two-cell embryo

value: Two-cell embryo


title: 2C, IP, Rep1


title: RiboPro_Control_2


title: PoolM_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID


title: Uterus, control, HF diet, rep 3

description:
CH11
CHvsCN_deg.txt
PHvsCH_deg.txt

value: Uterus


title: Uterus, control, HF diet, rep 2

description:
CH10
CHvsCN_deg.txt
PHvsCH_deg.txt


title: PoolM_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolM_DBA_Lamin_TwoCell.bedgraph
PoolM_DBA_Lamin_TwoCell_LAD_coordinates.bed


title: RiboPro_EIF3D_1


title: 1C, IP, Rep3

source_name: Zygote embryo

value: Zygote embryo


title: 2C, Input


title: Uterus, control, HF diet, rep 1

description:
CH9
CHvsCN_deg.txt
PHvsCH_deg.txt


title: RiboPro_Control_1


title: PoolL_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID

value: 500 ng/μL Hdac1, 1000 ng/μL Hdac6, 800 ng/μL Sirt1


title: Uterus, control, normal diet, rep 2

description:
CN14
CHvsCN_deg.txt
PNvsCN_deg.txt


title: Uterus, control, normal diet, rep 3

description:
CN15
CHvsCN_deg.txt
PNvsCN_deg.txt


title: 1C, IP, Rep2


title: Uterus, PNA, normal diet, rep 3

description:
PN7
PHvsPN_deg.txt
PNvsCN_deg.txt


title: Uterus, PNA, normal diet, rep 4

description:
PN8
PHvsPN_deg.txt
PNvsCN_deg.txt


title: RNAseq_EIF3D_3

data_processing:
Illumina bcl2fastq (v2.20.0.422) were performed for converting fastq files and separation by samples with default setting
Illumina bcl2fastq (v2.20.0.422) were performed for converting fastq files and separation by samples with default setting
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v1.12) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.2.5), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.7.10b)
fp-count were perfomed for counting reads with GENCODE annotation file (v35).
To normalized read counts and calculate translational efficiency (TE), R (v4.1) and its package DESeq2 (v1.26.0) were performed with Ribosome Profiling data.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including DESeq2 nomalized counts and TE for each sample.

extract_protocol:
RNA was prepared using the Direct-zol RNA micoprep kit or Direct-zol RNA miniprep kit (Zymo Research) and quantified with Qubit RNA BR (Thermo Fisher Scientific).
RNA-seq libraries were constructed by using Illumina Stranded Total RNA Library Prep (Illumina) with ribosomal RNA removal by using riboPOOLs (siTOOLs Biotech).


title: PoolL_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID


title: PoolL_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolL_DBA_Lamin_TwoCell.bedgraph
PoolL_DBA_Lamin_TwoCell_LAD_coordinates.bed


title: RNAseq_Control_3


title: 1C, IP, Rep1


title: RNAseq_Control_2


title: 1C, Input


title: Uterus, PNA, normal diet, rep 1

description:
PN5
PHvsPN_deg.txt
PNvsCN_deg.txt


title: MII, IP, Rep3

source_name: MII oocyte

value: MII oocyte


title: RNAseq_EIF3D_2


title: Uterus, PNA, normal diet, rep 2

description:
PN6
PHvsPN_deg.txt
PNvsCN_deg.txt


title: Uterus, PNA, HF diet, rep 4

description:
PH4
PHvsPN_deg.txt
PHvsCH_deg.txt


title: PoolK_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID

value: 800 ng/μL G2e3, 800 ng/μL Phf19, 800 ng/μL Dhx33


title: PoolK_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID


title: MII, IP, Rep2


title: RNAseq_EIF3D_1


title: PoolK_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolK_DBA_Lamin_TwoCell.bedgraph
PoolK_DBA_Lamin_TwoCell_LAD_coordinates.bed


title: Uterus, PNA, HF diet, rep 3

description:
PH3
PHvsPN_deg.txt
PHvsCH_deg.txt


title: Uterus, PNA, HF diet, rep 2

description:
PH2
PHvsPN_deg.txt
PHvsCH_deg.txt


title: PoolL_DBA_Lamin_TwoCell_rep4

description: Low-input LaminB1 DamID


title: MII, Input


title: MII, IP, Rep1


title: Uterus, PNA, HF diet, rep 1

description:
PH1
PHvsPN_deg.txt
PHvsCH_deg.txt


title: RNAseq_Control_1


title: PoolJ_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID

value: 600 ng/μL Suv39h1, 300 ng/μL Hp1a, 300 ng/μL Hp1g


title: Ox-mtDNA_3_scRNAseq

city: La Jolla

first: Masafumi

last: Ohira

state: California

address: 9500 Gilman Drive

department: Department of Pharmacology

institute: University of California San Diego

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw fastq files were aligned to the mouse mm10 reference genome using 10x Genomics Cell Ranger 7.1.0 with 10x Genomics Cloud Analysis.
Assembly: GRCm39
Supplementary files format and content: comma-separated text file includes raw counts for each sample

source_name: peritoneal cells

extract_protocol:
Live freshly collected peritoneal cells was determined and 10,000 cells per sample were run on the 10x Chromium platform (10x Genomics).
Library preparation were performed using the Chromium Next GEM Single Cell 3' Kit v3.1 according to manufacturer's instructions.

tag: strain

value: peritoneal cells

value: Ox-mtDNA


title: GV, IP, Rep4

source_name: GV oocyte

value: GV oocyte


title: d16_2

source_name: Primed iPSC

value: Day 16

tag: library type

value: Set B


title: PoolJ_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID

value: 2-cell embryo


title: d16_3

value: Primed iPSC


title: d0_3

value: Day 0


title: PoolJ_DBA_Lamin_TwoCell_rep4

description: Low-input LaminB1 DamID


title: PoolJ_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolJ_DBA_Lamin_TwoCell.bedgraph
PoolJ_DBA_Lamin_TwoCell_LAD_coordinates.bed


title: GV, IP, Rep2


title: Ox-mtDNA_2_scRNAseq

description: 10x Genomics


title: PoolI_DBA_Lamin_TwoCell_rep4

description: Low-input LaminB1 DamID

value: 800 ng/μL Lsd1, 800 ng/μL Kdm7a, 1000 ng/μL Kdm7c


title: GV, IP, Rep3


title: GV, IP, Rep1


title: Ox-mtDNA_1_scRNAseq

description: 10x Genomics


title: PoolI_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID

value: (C57BL/6J xCBA) x DBA/2J


title: PoolI_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID


title: mtDNA_3_scRNAseq

description: 10x Genomics

value: mtDNA


title: d0_1

value: Set A


title: Inhibitors_d5_Nut6inhibitors_3

description:
Inhibitors_d5_Nut6inhibitors_3
RNAseq_DESeq2_Normalized_2.csv

data_processing:
Illumina bcl2fastq (v2.20.0.422) were performed for converting fastq files and separation by samples with default setting
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v1.12) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.2.5), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.7.10b)
HTSeq (v0.13.5) were perfomed for counting reads with the GENCODE (version 35) annotation gtf file.
To normalized read counts, R (v4.1) and its package DESeq2 (v1.26.0) were performed.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including DESeq2 nomalized count values for each sample.

growth_protocol: Primed human pluripotent stem cells (hPSCs) were maintained in StemFiT AK02N media (Ajinomoto) on iMatrix-511-coated plates at 37 ºC in a humidified incubator with 20% O2 and 5% CO2. Naive hiPSCs were maintained media consisting of NDiff227 supplemented with 1 μM PD325901, 2 μM XAV939 (WAKO), 2 μM Gö6983 (Sigma-Aldrich), 10 ng/mL of LIF, 1/30 volume of Geltrex (Thermo Fisher Scientific) in a humidified incubator with 5% O2 and 5% CO2.

extract_protocol:
RNA was prepared using the Direct-zol RNA miniprep kit (Zymo Research) following the manufacturer's recommendations. RNA was quantified with the Agilent 2100 Bioanalyzer (Agilent Technologies) and Qubit RNA (Thermo).
Illumina Stranded Total RNA Library Prep

treatment_protocol: For inducing the knockdown, 1 μg/mL of DOX were added. For endoderm differentiation, the primed hiPSCs were treated with differentiation media 1 (DM1), which consisted of DMEM/F-12 (Thermo Fisher Scientific), 2% B27 supplement (Thermo Fisher Scientific), 1% MEM Non-Essential Amino Acids (NEAA, Thermo Fisher Scientific) and 0.1 mM 2-mercaptoethanol (2-ME, Thermo Fisher Scientific) supplemented with 100 ng/mL Activin A (Nacalai tesque), 3 μM CHIR99021 (Nacalai tesque), 20 ng/mL bFGF (Nacalai tesque) and 50 nM PI-103 (Cayman Chemical). Twenty-four hours later, after washing with DMEM/F-12, the media was replaced with DM1 supplemented with 100 ng/mL Activin A and 250 nM LDN193189 (Stemgent). Two days later, after washing with DMEM/F-12, the media was replaced with DM1 containing 100 ng/mL Activin A until another 48 hours passed. For mesoderm differentiation, primed hiPSCs were cultured in DM1 containing 30 ng/mL Activin A, 40 ng/mL BMP4 (Peprotech), 6 μM CHIR99021, 20 ng/mL bFGF and 100 nM PIK-90 (MedChemExpress) for 24 hours. Then, after washing with DMEM/F-12, the media was replaced with DM1 supplemented with 40 ng/mL BMP4, 1 μM A83-01, and 4 μM CHIR99021, and the cells were maintained for 48 hours. Two days later, the cells were washed once with DMEM/F-12 and then cultured in DM1 supplemented with 40 ng/mL BMP4 for 48 hours. For neuroectoderm differentiation, primed iPSCs were cultured in Glasgow's MEM (WAKO) containing 8% Knockout serum replacement (KSR, Thermo Fisher Scientific), 1 mM sodium pyruvate (Sigma-Aldrich), 1% NEAA and 0.1 mM 2-ME, 1 μM A83-01 and 250 nM LDN193189 for 5 days. For the last disrupting the homeostasis of EIF3D’s target pathways, we replaced the media with StemFit AK02N containing (1) six factors consisting of 10 μM SC79 (Sigma-Aldrich), 10 μM MHY1485 (MedChemExpress), 1 μM A83-01, 2 μM CHIR99021, 50 ng/mL EGF (WAKO), and 1 μM Nutlin-3a (Sigma-Aldrich), (2) five factors (excluding Nutlin-3a from six factors) or (3) 1 μM Nutlin-3a alone.

value: Day 5

value: WT

value: Control


title: PoolH_DBA_Lamin_TwoCell_rep4

description: Low-input LaminB1 DamID

value: 1200 ng/μL Kdm3a, 1500 ng/μL Kdm3b


title: mtDNA_2_scRNAseq

description: 10x Genomics


title: Alum_3_scRNAseq

description: 10x Genomics

value: Alum


title: Inhibitors_d5_6inhibitors_3

description:
Inhibitors_d5_6inhibitors_3
RNAseq_DESeq2_Normalized_2.csv

value: Nutlin3a to 6 inhibitors treatment


title: PoolI_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolI_DBA_Lamin_TwoCell.bedgraph
PoolI_DBA_Lamin_TwoCell_LAD_coordinates.bed


title: ESC, STM2457, IP, Rep1

value: Human embryonic stem cells


title: ESC, STM2457, Input, Rep2


title: Inhibitors_d5_Nutlin3a_3

description:
Inhibitors_d5_Nutlin3a_3
RNAseq_DESeq2_Normalized_2.csv

value: 6 inhibitors treatment


title: PoolH_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID


title: d0_2


title: Alum_1_scRNAseq

description: 10x Genomics

value: peritoneal cells


title: Alum_2_scRNAseq

description: 10x Genomics


title: ESC, STM2457, Input, Rep1


title: Inhibitors_d5_Nut5inhibitors_3

description:
Inhibitors_d5_Nut5inhibitors_3
RNAseq_DESeq2_Normalized_2.csv

value: Nutlin3a to 5 inhibitors treatment


title: PoolH_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID

value: 2-cell embryo


title: d16_1

value: Day 16

value: Primed iPSC


title: Inhibitors_d5_Control_3

description:
Inhibitors_d5_Control_3
RNAseq_DESeq2_Normalized_2.csv

value: Nutlin3a treatment


title: GV, Input

description: Raw data (Fastq format) was generated in Norway, and is not allowed to upload to GEO per Norway policy.

value: GV oocyte


title: PoolH_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolH_DBA_Lamin_TwoCell.bedgraph
PoolH_DBA_Lamin_TwoCell_LAD_coordinates.bed

value: (C57BL/6J xCBA) x DBA/2J


title: PBS_3_scRNAseq

description: 10x Genomics

value: PBS


title: ESC, DMSO, IP, Rep2

value: DMSO


title: ESC, STM2457, IP, Rep2


title: PoolG_DBA_Lamin_TwoCell_rep4

description: Low-input LaminB1 DamID


title: ESC, DMSO, Input, Rep2


title: PoolG_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID


title: PBS_1_scRNAseq

description: 10x Genomics


title: Ox-mtDNA_3_RNAseq [A9]

data_processing:
Raw fastq format data were quality checked and trimmed using fastp 0.23.4 with its default parameters, except that automatic adapter detection for pair-end data was enabled with detect_adapter_for_pe.
Reads were mapped using STAR 2.7.11b with its default parameters except that outFilterMultimapNmax was set to 1. GRCm39 was used as a reference genome.
Aligned reads were counted using featureCounts v2.0.1 with its default parameters.
Assembly: GRCm39
Supplementary files format and content: comma-separated text file includes raw counts for each sample

source_name: pDC

extract_protocol:
Total RNA was isolated from FACS-sorted pDC treated as indicated. Cells were homogenized with TRIzol reagent and purified using RNeasy Mini Kit (Qiagen).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP.

value: pDC

value: Ox-mtDNA


title: Inhibitors_d5_Nut6inhibitors_2

description:
Inhibitors_d5_Nut6inhibitors_2
RNAseq_DESeq2_Normalized_2.csv

value: Day 5

value: WT

value: Control


title: mtDNA_1_scRNAseq

description: 10x Genomics

value: mtDNA


title: Inhibitors_d5_Nutlin3a_2

description:
Inhibitors_d5_Nutlin3a_2
RNAseq_DESeq2_Normalized_2.csv

value: 6 inhibitors treatment


title: Inhibitors_d5_6inhibitors_2

description:
Inhibitors_d5_6inhibitors_2
RNAseq_DESeq2_Normalized_2.csv

value: Nutlin3a to 6 inhibitors treatment


title: ESC, 10cells, IP, Rep2

value: Human embryonic stem cells


title: PoolG_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolG_DBA_Lamin_TwoCell.bedgraph
PoolG_DBA_Lamin_TwoCell_LAD_coordinates.bed

value: 2-cell embryo


title: Inhibitors_d5_5inhibitors_3

description:
Inhibitors_d5_5inhibitors_3
RNAseq_DESeq2_Normalized_2.csv

value: 5 inhibitors treatment


title: mtDNA_3_RNAseq [A8]


title: PBS_2_scRNAseq

description: 10x Genomics

value: peritoneal cells


title: ESC, 10cells, IP, Rep1


title: Inhibitors_d5_5inhibitors_2

description:
Inhibitors_d5_5inhibitors_2
RNAseq_DESeq2_Normalized_2.csv

value: Primed iPSC


title: ESC, DMSO, IP, Rep1


title: Inhibitors_d5_Nut5inhibitors_2

description:
Inhibitors_d5_Nut5inhibitors_2
RNAseq_DESeq2_Normalized_2.csv

value: Nutlin3a to 5 inhibitors treatment


title: Ox-mtDNA_2_RNAseq [A6]


title: PBS_3_RNAseq [A7]


title: PoolF_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID

value: (C57BL/6J xCBA) x DBA/2J

value: 1200 ng/μL Kdm6a, 800 ng/μL Kdm6b


title: PoolF_DBA_Lamin_TwoCell_rep4

description: Low-input LaminB1 DamID


title: ESC, 100cells, IP, Rep1


title: PoolG_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID


title: ESC, 1000cells, IP, Rep2


title: Inhibitors_d5_Control_2

description:
Inhibitors_d5_Control_2
RNAseq_DESeq2_Normalized_2.csv

value: Nutlin3a treatment


title: Inhibitors_d5_Nut6inhibitors_1

description:
Inhibitors_d5_Nut6inhibitors_1
RNAseq_DESeq2_Normalized_2.csv


title: PoolF_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolF_DBA_Lamin_TwoCell.bedgraph
PoolF_DBA_Lamin_TwoCell_LAD_coordinates.bed


title: PoolF_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID


title: Inhibitors_d5_6inhibitors_1

description:
Inhibitors_d5_6inhibitors_1
RNAseq_DESeq2_Normalized_2.csv


title: Ox-mtDNA_1_RNAseq [A3]

value: pDC


title: PoolE_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID

value: 600 ng/μL NLS Actin R62D, 600 ng/μL Hdac3


title: ESC, 1000cells, IP, Rep1


title: Inhibitors_d5_Nutlin3a_1

description:
Inhibitors_d5_Nutlin3a_1
RNAseq_DESeq2_Normalized_2.csv

value: Day 5


title: ESC, Input


title: PoolE_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID


title: Inhibitors_d5_Nut5inhibitors_1

description:
Inhibitors_d5_Nut5inhibitors_1
RNAseq_DESeq2_Normalized_2.csv

value: WT


title: ESC, 100cells, IP, Rep2


title: P3 Tumor, snRNAseq

city: Daejeon

first: Jeong Ho

last: Lee

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description:
10x Genomics
Sample_Tu

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

source_name: Tumor

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

value: Tumor

value: brain cells

tag: age

value: 56 years old

tag: Sex

value: F


title: PBS_1_RNAseq [A1]

value: PBS


title: PoolE_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolE_DBA_Lamin_TwoCell.bedgraph
PoolE_DBA_Lamin_TwoCell_LAD_coordinates.bed

source_name: 2-cell embryo

value: 2-cell embryo


title: Inhibitors_d5_5inhibitors_1

description:
Inhibitors_d5_5inhibitors_1
RNAseq_DESeq2_Normalized_2.csv

tag: cell line

value: 5 inhibitors treatment


title: P2 Tumor, snRNAseq

description:
10x Genomics
1932Tu

value: 42 years old

value: M


title: PoolD_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID

value: 1200 ng/μL DN NM1, 1200 ng/μL DN MyosinVb


title: mtDNA_2_RNAseq [A5]

value: mtDNA


title: C2C12, 37C, mock, 24h, rep4

city: Princeton

first: Aaron

middle: E

last: Lin

state: NJ

address: Washington Road

department: Molecular Biology

institute: Princeton University

data_processing:
Reads were demultiplexed using Picard v2.25.6, from within viral-ngs v2.1.33 with the read structure ‘5S8B15M8B101T’ and Q20M1 mismatch tolerance.
Demultiplexed reads were mapped to the mouse genome mm39 using STAR v2.7.10a.
Uniquely mapped reads were counted based on the GENCODE comprehensive gene annotation on the primary assembly using htseq-count v1.99.2.
Assembly: mm39, GENCODE release M28
Supplementary files format and content: Counts matrix of genes (mm39, M28) x all 45 samples

growth_protocol: C2C12 mouse myoblast cells were maintained in DMEM supplemented with 20% heat-inactivated fetal bovine serum (FBS) and penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen) and phenol-chloroform purification.
Starting from 50 ng total RNA per sample, we performed bulk RNA barcoding and sequencing (BRB-Seq) with minor modifications. We performed reverse transcription with SuperScript IV (Invitrogen) and a uniquely barcoded oligo(dT)30 primer for each sample, modified to use Illumina TruSeq Read 1 priming site instead of Nextera Read 1. Following the remainder of the standard BRB-Seq protocol, we pooled up to 24 barcoded first-strand cDNAs into a single tube, synthesized second-strand cDNA with Gubler-Hoffman nick translation, and tagmented cDNA pools with Tn5 produced in-house. We performed 14 cycles of PCR using a P5-containing primer and a unique multiplexed i7 indexing primer (Chromium i7 Multiplex Kit, 10X Genomics). We purified and size-selected libraries with 0.65X SPRIselect (Beckman Coulter) and then 0.7X SPRIselect. We sequenced all pools on a NovaSeq SP v1.5 flowcell (Illumina) with 28 cycles of Read 1, 8 cycles of Read i7, and 101 cycles of Read 2.

treatment_protocol: C2C12 mouse myoblast cells were plated at 50,000 cells/well in 24-well plates and cultured at 37 °C overnight. The following day, cells were transfected with either 250 ng of CHIKV-D-SGR WT or GAA using Lipofectamine 2000 (1:2, Invitrogen), or mock treated (Lipofectamine 2000 only). Cells were then inucbated at 37 °C or 28 °C, for 12 h or 24 h.

value: myoblast

tag: temperature

tag: chikv

value: mock

tag: replicate


title: Inhibitors_d5_Control_1

description:
Inhibitors_d5_Control_1
RNAseq_DESeq2_Normalized_2.csv

value: Primed iPSC

value: Nutlin3a treatment


title: C2C12, 37C, mock, 24h, rep3


title: PoolD_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID

value: (C57BL/6J xCBA) x DBA/2J


title: P1 Tumor, snRNAseq

description:
10x Genomics
Sample_2011T

value: 74 years old


title: Inhibitors_d3_5inhibitors_3

description:
Inhibitors_d3_5inhibitors_3
RNAseq_DESeq2_Normalized_2.csv

value: Day 3

value: WT

value: 6 inhibitors treatment


title: PBS_2_RNAseq [A4]

value: pDC


title: P3 SVZ, snRNAseq

description:
10x Genomics
Sample_V

source_name: SVZ

value: SVZ

value: brain cells

value: 56 years old

value: F


title: PoolD_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolD_DBA_Lamin_TwoCell.bedgraph
PoolD_DBA_Lamin_TwoCell_LAD_coordinates.bed

value: 2-cell embryo


title: C2C12, 37C, GAA, 24h, rep3

value: GAA


title: Inhibitors_d3_Nutlin3a_3

description:
Inhibitors_d3_Nutlin3a_3
RNAseq_DESeq2_Normalized_2.csv

value: Control treatment


title: P2 SVZ, snRNAseq

description:
10x Genomics
1932V

value: 42 years old

value: M


title: PoolC_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID

value: 2500 ng/μL Tpr, 600 ng/μL DN Nup98


title: mtDNA_1_RNAseq [A2]

value: mtDNA


title: C2C12, 37C, WT, 24h, rep3

value: myoblast


title: P1 SVZ, snRNAseq

description:
10x Genomics
Sample_2011V

value: 74 years old


title: Inhibitors_d3_6inhibitors_3

description:
Inhibitors_d3_6inhibitors_3
RNAseq_DESeq2_Normalized_2.csv

value: Day 3

value: Primed iPSC

value: 5 inhibitors treatment


title: Inhibitors_d3_Control_3

description:
Inhibitors_d3_Control_3
RNAseq_DESeq2_Normalized_2.csv

value: WT

value: Nutlin3a treatment


title: A375_DFFB_KO_DTEPs

first: August

last: Williams

state: CA

address: 9500 Gilman Dr.

department: Dermatology

institute: UC San Diego

data_processing:
Reads were aligned, samples aggregated, and expression quantified using 10X pipeline cellranger-3.1.0.
Assembly: GRCh38
Supplementary files format and content: raw counts

source_name: A375 human cancer cell line

growth_protocol: A375 cells were cultured in DMEM with 10% fetal bovine serum (FBS) and 1% Antimycotic/Antibiotic (AA). PC9 cells were cultured in RPMI with 5% FBS with 1% AA. Cell lines were split with 0.25% trypsin. All cell lines were maintained in 5% CO2 atmosphere at 37 degrees Celsius.

extract_protocol:
Cells were washed with PBS, trypsinized, centrifuged at 300xg, then resuspended at 1,000 cells per μL in PBS.
Single cells were processed with 10X Chromium Single Cell 3' Reagents Kits v3 with all steps performed as recommended by the manufacturer.

treatment_protocol: A375 cells were treated with 250 nM dabrafenib and 25 nM trametinib for 14 days to derive persister cells, and for 9 weeks to derive DTEPs. PC9 cells were treated with 2.5 mM erlotinib for 14 days to derive persister cells. Fresh drug media was replenished every 3-4 days.

value: melanoma cell line

value: DFFB KO

value: 250 nM dabrafenib + 25 nM trametinib (9 weeks)


title: C2C12, 37C, mock, 12h, rep3

value: mock


title: PoolC_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID

value: 2-cell embryo

value: (C57BL/6J xCBA) x DBA/2J


title: ESC, DMSO, Input, Rep1

value: Human embryonic stem cells

value: DMSO


title: PoolC_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolC_DBA_Lamin_TwoCell.bedgraph
PoolC_DBA_Lamin_TwoCell_LAD_coordinates.bed

value: 2500 ng/μL Tpr, 600 ng/μL DN Nup98


title: C2C12, 37C, GAA, 12h, rep3

value: GAA


title: Inhibitors_d3_5inhibitors_2

description:
Inhibitors_d3_5inhibitors_2
RNAseq_DESeq2_Normalized_2.csv

value: 6 inhibitors treatment


title: C2C12, 37C, WT, 12h, rep3

value: myoblast


title: PoolA_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID

value: 100 ng/μL DN Baf, 800 ng/μL DN Prr14, 400 ng/μL DN Syne1


title: PC9_WT_persister

data_processing:
Reads were aligned, samples aggregated, and expression quantified using 10X pipeline cellranger-3.1.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_counts_matrix.csv: Comma-separated text files include raw counts.

source_name: PC9 human cancer cell line

value: lung cancer cell line

value: 2.5 uM erlotinib


title: A375_WT_DTEPs

value: WT


title: Inhibitors_d3_Nutlin3a_2

description:
Inhibitors_d3_Nutlin3a_2
RNAseq_DESeq2_Normalized_2.csv

value: Day 3

value: Primed iPSC

value: Control treatment


title: PoolA_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolA_DBA_Lamin_TwoCell.bedgraph
PoolA_DBA_Lamin_TwoCell_LAD_coordinates.bed

data_processing:
Samples were sequenced using Illumina HiSeq4000 or HiSeq2500 platforms in 150 bp PE mode but only read1 was used for downstream analysis. For pre-processing of reads, first 6 random bases were discarded using trimmomatic (version 0.39). Subsequently, the reads were demultiplexed according to DamID indexes using fastx barcode splitter and the additional 15 bp of adaptors were trimmed using trimmomatic. The pre-processed reads starting with GATC were then mapped to the mm10 using bowtie2 (version 2.5.1) with default parameters. Reads aligning to the genome with quality score below 30 were discarded using samtools (version 1.17). Duplicates were removed using picard (version 3.0.0) to finally obtain unique GATC reads.
The computation of OE (Observed/Expected) values were performed in 100-kb genomic bins. To distinguish LAD domains from inter-LADs, a two-state hidden Markov model (HMM) was applied to non-zero OE mean values.
Assembly: mm10
Supplementary files format and content: Dam-LaminB1 observed over expected (OE) values calculated in 100-kb genomic bins provided in bedgraph files and LAD domain coordinates are provided in bed files.
Supplementary files format and content: Mean OE and LAD coordinates files are available on Rep 1 samples.
Library strategy: DamID-seq


title: PC9_WT_parental

value: untreated


title: PoolA_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID


title: Inhibitors_d3_6inhibitors_2

description:
Inhibitors_d3_6inhibitors_2
RNAseq_DESeq2_Normalized_2.csv

value: 5 inhibitors treatment


title: C2C12, 28C, GAA, 24h, rep3


title: Control_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID

value: 2-cell embryo


title: A375_DFFB_KO_persister

value: melanoma cell line

value: DFFB KO

value: 250 nM dabrafenib + 25 nM trametinib


title: Inhibitors_d3_Control_2

description:
Inhibitors_d3_Control_2
RNAseq_DESeq2_Normalized_2.csv

value: Nutlin3a treatment


title: C2C12, 28C, WT, 24h, rep3


title: A375_DFFB_KO_parental


title: Control_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID

value: (C57BL/6J xCBA) x DBA/2J


title: Inhibitors_d3_Nutlin3a_1

description:
Inhibitors_d3_Nutlin3a_1
RNAseq_DESeq2_Normalized_2.csv


title: Inhibitors_d3_5inhibitors_1

description:
Inhibitors_d3_5inhibitors_1
RNAseq_DESeq2_Normalized_2.csv

value: 6 inhibitors treatment


title: A375_WT_persister


title: C2C12, 28C, mock, 12h, rep3

value: myoblast

value: mock


title: Inhibitors_d3_6inhibitors_1

description:
Inhibitors_d3_6inhibitors_1
RNAseq_DESeq2_Normalized_2.csv


title: A375_WT_parental


title: PoolN_DBA_Lamin_Zygote_rep4

description: Low-input LaminB1 DamID

source_name: Zygote

value: Zygote

value: 1200 ng/μL Ehmt1, 1200 ng/μL Ehmt2, 1200 ng/μL Setdb1, 700 ng/μL Setdb2


title: C2C12, 28C, WT, 12h, rep3

value: WT


title: PoolN_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID


title: C2C12, 28C, mock, 24h, rep3


title: P6-N3

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on a MGI DNBSEQ-G400 platform in a 100+100-base paired-end mode.
The DNBSEQ control software operated base calling analysis software and delivered raw sequencing data.
Generated reads were mapped to the Human herpesvirus 1 genome (GU734771.1) using hisat2 v2.1.0.
Mapped read counts were calculated using featureCounts (in subread-2.0.0) with option -M -O --fraction.
Assembly: Human herpesvirus 1 strain F, complete genome (GU734771.1)
Supplementary files format and content: tab-delimited text files include mapped read counts for each sample

organism: Human alphaherpesvirus 1

extract_protocol:
HeLa cells were infected with the YK410 strain at a multiplicity of infection (MOI) of 5 by incubating for 24 h. The cells were then washed with phosphate-buffered saline (PBS) and detached with 0.25% trypsin/EDTA solution (Wako). Then, 5 x 10^5 cells from the f1–f6 subpopulations were sorted in PBS using a BD FACSMelodyTM Cell Sorter (Becton Dickinson). Following centrifugation, the total RNA was isolated from the fractionated cells with a High Pure RNA Isolation kit (Roche).
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan) according to the manufacturer's instructions. According to the SMARTer kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

tag: host

value: HeLa cells

tag: population


title: C2C12, 28C, GAA, 12h, rep3

value: GAA


title: Naïve_set2_D5_sgEIF3D_3

description:
Naïve_set2_D5_sgEIF3D_3
RNAseq_DESeq2_Normalized_1.csv

value: Day 5

value: Naive iPSC

tag: genotype

value: EIF3D knockdown

value: DOX+


title: C2C12, 37C, GAA, 24h, rep4


title: C2C12, 37C, WT, 24h, rep5


title: P6-N2


title: Inhibitors_d3_Control_1

description:
Inhibitors_d3_Control_1
RNAseq_DESeq2_Normalized_2.csv

value: Day 3

value: Primed iPSC

tag: treatment


title: PoolN_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID

tag: tissue


title: Naïve_set2_D5_sgEIF3D_2

description:
Naïve_set2_D5_sgEIF3D_2
RNAseq_DESeq2_Normalized_1.csv

tag: cell type


title: P6-N1


title: PoolN_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolN_DBA_Lamin_Zygote.bedgraph
PoolN_DBA_Lamin_Zygote_LAD_coordinates.bed

tag: mrna injected


title: C2C12, 37C, mock, 24h, rep2


title: P5-N3


title: C2C12, 37C, GAA, 24h, rep2


title: Naïve_set2_D5_sgControl_3

description:
Naïve_set2_D5_sgControl_3
RNAseq_DESeq2_Normalized_1.csv

value: Control knockdown


title: PoolM_DBA_Lamin_Zygote_rep4

description: Low-input LaminB1 DamID


title: P5-N2


title: Naïve_set2_D5_sgControl_2

description:
Naïve_set2_D5_sgControl_2
RNAseq_DESeq2_Normalized_1.csv


title: C2C12, 37C, WT, 24h, rep2


title: Control_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_Control_DBA_Lamin_TwoCell.bedgraph
Control_DBA_Lamin_TwoCell_LAD_coordinates.bed

value: 2-cell embryo


title: P5-N1


title: C2C12, 37C, mock, 12h, rep2


title: Naïve_set2_D5_sgControl_1

description:
Naïve_set2_D5_sgControl_1
RNAseq_DESeq2_Normalized_1.csv


title: PoolM_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolM_DBA_Lamin_Zygote.bedgraph
PoolM_DBA_Lamin_Zygote_LAD_coordinates.bed

value: (C57BL/6J xCBA) x DBA/2J


title: P4-N3


title: PoolM_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: Primed_KD_D5_sgEIF3D_3

description:
Primed_KD_D5_sgEIF3D_3
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: PoolL_DBA_Lamin_Zygote_rep4

description: Low-input LaminB1 DamID

value: 500 ng/μL Hdac1, 1000 ng/μL Hdac6, 800 ng/μL Sirt1


title: P4-N2


title: C2C12, 37C, WT, 12h, rep2

value: myoblast


title: PoolL_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID


title: C2C12, 37C, mock, 12h, rep4

value: mock


title: Primed_KD_D5_sgEIF3D_2

description:
Primed_KD_D5_sgEIF3D_2
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: PoolL_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID

value: Zygote


title: P3-N3


title: Naïve_set2_D5_sgEIF3D_1

description:
Naïve_set2_D5_sgEIF3D_1
RNAseq_DESeq2_Normalized_1.csv


title: C2C12, 37C, GAA, 12h, rep4


title: Primed_KD_D5_sgEIF3D_1

description:
Primed_KD_D5_sgEIF3D_1
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: Primed_KD_D5_sgControl_3

description:
Primed_KD_D5_sgControl_3
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: C2C12, 28C, mock, 24h, rep2


title: P3-N2


title: P3-N1


title: PoolM_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID


title: PoolL_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolL_DBA_Lamin_Zygote.bedgraph
PoolL_DBA_Lamin_Zygote_LAD_coordinates.bed


title: C2C12, 28C, GAA, 24h, rep2


title: Primed_KD_D5_sgControl_1

description:
Primed_KD_D5_sgControl_1
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: PoolK_DBA_Lamin_Zygote_rep4

description: Low-input LaminB1 DamID

value: 800 ng/μL G2e3, 800 ng/μL Phf19, 800 ng/μL Dhx33


title: P2-N3


title: PoolK_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID


title: C2C12, 37C, GAA, 12h, rep2


title: Primed_KD_D3_sgEIF3D_3

description:
Primed_KD_D3_sgEIF3D_3
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: P4-N1


title: PoolK_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: C2C12, 28C, mock, 12h, rep2


title: P2-N1


title: C2C12, 28C, GAA, 12h, rep2


title: P2-N2


title: Primed_KD_D3_sgEIF3D_1

description:
Primed_KD_D3_sgEIF3D_1
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: P1-N3


title: Primed_KD_D5_sgControl_2

description:
Primed_KD_D5_sgControl_2
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: PoolJ_DBA_Lamin_Zygote_rep4

description: Low-input LaminB1 DamID

value: 600 ng/μL Suv39h1, 300 ng/μL Hp1a, 300 ng/μL Hp1g


title: C2C12, 28C, WT, 12h, rep2

value: WT


title: Primed_KD_D3_sgControl_3

description:
Primed_KD_D3_sgControl_3
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: P1-N2

value: HeLa cells


title: C2C12, 37C, WT, 24h, rep4


title: Primed_KD_D3_sgControl_2

description:
Primed_KD_D3_sgControl_2
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: PoolJ_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: P1-N1


title: Primed_KD_D3_sgControl_1

description:
Primed_KD_D3_sgControl_1
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: CB_MYC_3

first: Sriram

last: Venneti

state: Michigan

address: 1500 E Medical Center Dr

department: Pathology

description: Illumina NovaSeqX 10B Paired-end 150bp (Illumina 20085594)

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files
Assembly: Reads were mapped to the reference genome GRCh38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq
Supplementary files format and content: .xls file for the counts for each of the samples

source_name: cerebellum

growth_protocol:
D283 cells were mantained in MEM medium supplimented with 10%FBS
CB Myc, and CBSV40 cells were grown in 70% Gibco DMEM (ThermoFisher 11960) and 30% GibcoHam’s F12 Nutrient Mix (ThermoFisher 11765054) with 1x Glutamine, 2% B27 without Vitamin A (ThermoFisher 12587010), 20ng/mL EGF (Peprotech AF-100-15), 20ng/mLFGF (Peprotech 100-18B), and 5ug/ML heparin (Stemcell Technologies 07980).

extract_protocol:
RNA was isolated using Trizol (Invitrogen 15596-026)
Libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490), NEBNext UltraExpress RNALibrary Prep Kit for Illumina (NEB E3330L), and NEBNext Multiplex Oligos for Illumina Unique dual (NEB E6440L).

treatment_protocol:
10uM IDH inhibitor
12.5nM Elesclomol

value: cerebellum


title: C2C12, 28C, WT, 24h, rep2


title: C2C12, 37C, WT, 12h, rep4


title: CB_MYC_2


title: Primed_KD_D0_sgEIF3D_3

description:
Primed_KD_D0_sgEIF3D_3
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv

value: Day 0


title: Primed_KD_D3_sgEIF3D_2

description:
Primed_KD_D3_sgEIF3D_2
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv

value: EIF3D knockdown


title: PoolJ_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolJ_DBA_Lamin_Zygote.bedgraph
PoolJ_DBA_Lamin_Zygote_LAD_coordinates.bed


title: PoolI_DBA_Lamin_Zygote_rep4

description: Low-input LaminB1 DamID

value: 800 ng/μL Lsd1, 800 ng/μL Kdm7a, 1000 ng/μL Kdm7c


title: C2C12, 37C, mock, 24h, rep1


title: C2C12, 37C, GAA, 24h, rep1

value: GAA


title: CB_MYC_1


title: PoolI_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID


title: PoolK_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolK_DBA_Lamin_Zygote.bedgraph
PoolK_DBA_Lamin_Zygote_LAD_coordinates.bed


title: Primed_KD_D0_sgEIF3D_1

description:
Primed_KD_D0_sgEIF3D_1
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv

value: Primed iPSC

value: DOX+


title: CB_SV40_3


title: Primed_KD_D0_sgEIF3D_2

description:
Primed_KD_D0_sgEIF3D_2
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: PoolI_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: C2C12, 37C, mock, 12h, rep1


title: C2C12, 37C, GAA, 12h, rep1


title: PoolI_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_PoolI_DBA_Lamin_Zygote.bedgraph
PoolI_DBA_Lamin_Zygote_LAD_coordinates.bed


title: CB_SV40_2


title: Primed_KD_D0_sgControl_3

description:
Primed_KD_D0_sgControl_3
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv

value: Control knockdown


title: CB_SV40_1


title: PoolH_DBA_Lamin_Zygote_rep4

description: Low-input LaminB1 DamID

value: (C57BL/6J xCBA) x DBA/2J

value: 1200 ng/μL Kdm3a, 1500 ng/μL Kdm3b


title: PoolJ_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID


title: Primed_KD_D0_sgControl_1

description:
Primed_KD_D0_sgControl_1
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: D283_Elesclomol_3

value: Elesclomol


title: PoolH_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID


title: C2C12, 28C, WT, 24h, rep4

value: myoblast


title: Primed_KD_D5_sgNANOG_3

description:
Primed_KD_D5_sgNANOG_3
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv

value: Day 5

value: NANOG knockdown


title: PoolH_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID

value: Zygote


title: D283_Elesclomol_2


title: C2C12, 28C, WT, 12h, rep4

value: WT


title: Primed_KD_D5_sgNANOG_2

description:
Primed_KD_D5_sgNANOG_2
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: D283_Parental_DMSO_3

value: DMSO


title: D283_Elesclomol_1


title: Primed_KD_D5_sgNANOG_1

description:
Primed_KD_D5_sgNANOG_1
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv


title: C2C12, 37C, WT, 24h, rep1


title: C2C12, 28C, GAA, 24h, rep1


title: D283_Parental_DMSO_2


title: Primed_KD_D5_sgSOX2_3

description:
Primed_KD_D5_sgSOX2_3
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv

value: SOX2 knockdown


title: Primed_KD_D0_sgControl_2

description:
Primed_KD_D0_sgControl_2
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv

value: Day 0


title: PoolG_DBA_Lamin_Zygote_rep4

description: Low-input LaminB1 DamID


title: C2C12, 28C, WT, 24h, rep1


title: D283_Parental_DMSO_1


title: PoolG_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID


title: C2C12, 37C, WT, 12h, rep1


title: C2C12, 28C, mock, 12h, rep1

value: mock


title: Primed_KD_D5_sgSOX2_2

description:
Primed_KD_D5_sgSOX2_2
RNAseq_DESeq2_Normalized_1.csv
RNAseq_DESeq2_Normalized_2.csv