title: bbs2_HO3

city: Cleveland

last: Perkins

address: 9500 Euclid Ave

institute: Cleveland Clinic

description: bbs2 -/- homozygote sample 3; mutant biological replicate

data_processing:
All reads were subject to quality control consisting of (1) trimming of exogenous adapter sequences, (2) removal of low quality bases from the end of reads, and (3) removal of whole reads if the average quality was too low. Most reads had Phred scores significantly greater than 30. Quality control was done using blinded data.
Reads were mapped to the zebrafish genome (D.rerio-ENSEMBL-grcz11.r104 : downloaded June 28, 2021) using the star version 2.7.5a aligner and gene abundance was estimated with star version 2.7.5a. Reads were also tested for rRNA, tRNA, mitochondrial, and mycoplasma sequences. Less than 1% of all reads were trimmed and more than 28% of all reads contributed to the final count tables. Raw counts appear in the sheet titled 'RawGeneCounts' of the 'bbs2-mapped-reads-and-pairwise-comparisons.xlsx' processed data file. Raw counts were established using blinded data.
DESeq2 (v1.30.1) and R (v4.0.4) were used to normalize counts using a regularized log (rlog) transformation of the raw counts and for transcripts per million (TPM) normalized counts. Rlog normalized counts appear in the sheet titled 'NormalizedGeneCounts' of the 'bbs2-mapped-reads-and-pairwise-comparisons.xlsx' processed data file. TPM normalized counts appear in the sheet titled 'TPMcounts' of the 'bbs2-mapped-reads-and-pairwise-comparisons.xlsx' processed data file. Both normalizations were done using blinded data.
Pairwise comparisons were made between the four bbs2 +/+ wild-type biological replicates and the four bbs2 -/- mutant biological replicates using DESeq2 (v1.30.1) and R (v4.0.4) to test for genes which were differentially expressed. A false discovery rate (FDR) was calculated and genes with a FDR < 0.05 were considered differentially expressed genes (DEGs). Pairwise comparisons appear in the sheet titled 'Bbs2_vs_Wildtype_FoldChanges' of the 'bbs2-mapped-reads-and-pairwise-comparisons.xlsx' processed data file. These pairwise comparisons were done using unblinded data.
Assembly: D.rerio-ENSEMBL-grcz11.r104 (downloaded June 28, 2021)
Supplementary files format and content: The 'bbs2-mapped-reads-and-pairwise-comparisons.xlsx' processed data file is an Excel file which contains aggregated data from all 8 libraries: four bbs2 +/+ wild-type biological replicates (bbs2_WT1, bbs2_WT2, bbs2_WT3, bbs2_WT4) and four bbs2 -/- homozygote mutant biological replicates (bbs2_HO1, bbs2_HO2, bbs2_HO3, bbs2_HO4). The Excel file contains 5 sheets: 'RawGeneCounts', 'NormalizedGeneCounts', 'TPMcounts', 'Bbs2_vs_Wildtype_FoldChanges', and 'SampleIDs'. The sheet titled 'RawGeneCounts' contains the raw, untransformed counts for each library and includes the GeneID and symbol. The sheet titled 'NormalizedGeneCounts' contains the gene counts for each library normalized using a regularized log (rlog) transformation and includes the GeneID and symbol. The sheet titled 'TPMcounts' contains the gene counts normalized as transcripts per million (TPM) for each library and includes the GeneID and symbol. The sheet titled 'Bbs2_vs_Wildtype_FoldChanges' contains data from the pairwise comparisons between wild-type and mutant libraries and includes the following columns: GeneID, symbol, baseMean (mean rlog normalized gene count across all 8 libraries), log2FoldChange (log2 transformation of the fold change in expression in bbs2 mutant samples versus wild-type samples), lfcSE (standard error of the log2FoldChange), stat (test statistic for the pairwise comparison), pvalue (the raw p-value), and FDR (false discovery rate adjusted p-value). The sheet titled 'SampleIDs' contains the library name and description of each of the 8 samples.

organism: Danio rerio

source_name: retina

growth_protocol: Adult zebrafish were maintained and housed in an Aquatic Habitats recirculating system (Pentair) with a 14/10 h light/dark cycle with ambient room lighting. Animals from heterozygous crosses of the bbs2 line were genotyped using high-resolution melt analysis (HRMA) as previously described. Experiments included animals of both sexes. The four bbs2 +/+ wild-type and four bbs2 -/- homozygote animals were 6 months post-fertilization at the time of the experiment.

extract_protocol:
Total RNA was purified using the standard Trizol (Thermofisher AM2238) protocol with Glycoblue (Thermofisher AM9515) used as a co-precipitant. Samples were Dnase treated (Turbo DNase, Thermofisher AM2238) and purified via lithium chloride precipitation. RNA concentration and purity was analyzed by Qubit Fluorometer (Invitrogen) and Agilent Bioanalyzer 2100. All samples had an RNA >= 8.8. 500ng of total RNA was used for quality control and the construction of sequencing libraries.
Libraries were prepared from total RNA using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit according to the manufacturer's protocol (Document #1000000124514 v02). Libraries were prepared by the Lerner Research Institute Genomics Core at the Cleveland Clinic.

treatment_protocol: Animals were dark-adapted overnight for 16-20 hours and euthanized in the dark. Eyes were ennucleated in the light after death and the retina dissected with minimal inclusion of the retinal pigmented epithelium.

value: retina


title: 2.5mM ALA treatment, harvest at 24h Replicate 2

status: Public on May 15 2023

type: RNA

city: São Paulo

first: Janice

last: Onuki

state: SP

address: Av. Vital Brasil, 1500 - Butantã

country: Brazil

institute: Butantan Institute

description: Biological replicate 2 of 4. treated with 2.5 mM ALA and harvested after 24 h.

hyb_protocol: RNA Spike-In Kit, two-color, was used as a positive hybridization control.

scan_protocol: Scanned on an Microarray Agilent SureScan scanner using AgilentG3_GX_2color protocol. Images were quantified Agilent Feture Extraction Software (version A.10.7.1.1).

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

molecule: total RNA

organism: Homo sapiens

source_name: HepG2 cell line (code 0103)

label_protocol: Double-stranded cDNA was generated from 100 ng total RNA using the Low Input Quick Amp Labeling Kit, two-color with Cyanine 3-CTP or Cyanine 5-CTP.

growth_protocol: The HepG2 cell line (code 0103), from Rio de Janeiro Cell Bank (BR), was cultivated in DMEM-low glucose with 100 IU/mL penicillin and 0.1 mg/mL streptomycin (Thermo Fisher, USA), supplemented with 10% fetal bovine serum (FBS) (Cultilab, BR), and maintained at 37° C in 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted using the RNAspin Mini RNA isolation kit (GE Healthcare, USA)

treatment_protocol: After reaching 80% confluence, the cells were treated or not with ALA 2.5 mM or 25 mM for 2 h or 24 h (identified as: Control, ‘2.5mM-2h’, ‘2.5mM-24h’, ‘25mM-2h’, ‘25mM-24h’)

tag: cell line

tag: time

tag: treatment

value: ALA 2.5 mM

source_name: Control

value: ALA 0 mM


title: C-enh-11d-Root-4

type: SRA

city: Richland

first: Hugh

middle: D

last: Mitchell

state: Washington

address: 902 Battelle Blvd, P.O. Box 999, MSIN J4-18

department: Computational Biology

country: USA

institute: Pacific Northwest National Laboratory

library_source: transcriptomic

data_processing:
Quality control was performed using FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read alignment to the genome was performed using the STAR software (https://github.com/alexdobin/STAR)
Read mapping/gene counting was performed using featureCounts (https://subread.sourceforge.net/).
Assembly: P. trichocarpa v3.1.1) available at Phytozome (https://phytozome.jgi.doe.gov)
Supplementary files format and content: For counts.txt files, columns are gene ID, chromosome, gene start(s), gene stop(s), strand orientation(s), gene length, gene counts

molecule: polyA RNA

organism: Populus tremula x Populus alba

source_name: root

growth_protocol: Populus tremula × Populus alba, clone INRA 717-1B4 one-year-old woody stem cuttings with 6-8 dormant buds were provided by Dr. Stephen DiFazio (West Virginia State University) and stored at -80℃ until use. One week before the start of planting, the woody cuttings were transferred to 4℃. Followed by that, the woody cuttings were planted in Pro-mix BX soil (Promix, PA, USA), and kept in a walk-in growth chamber with a temperature of 24 °C /18 °C (day/night), a light intensity of 400µM/sec and a photoperiod of 16h/18h (day/night). The poplar cuttings were fertilized once per week using 100 ppm of Jack’s professional fertilizer (Jr Peters Inc, PA, USA). After approximately one month, they were transplanted to bigger soil pots (4"x4"x9.5") to facilitate root growth and grown for an additional one month. Once shoots were formed on the main woody stems, leafy cuttings with 4-5 inches in size, were excised from the apical shoot tips and the internodes below apical tips. Each cutting had just one leaf left on them to reduce transpiration. The stem base of all cuttings was treated with commercially available rooting powder (Rhizopon AA#2, Hortus USA Corp., NY, USA) and planted in the Pro-mix BX soil in 4” square pots to enable the rooting process. The cuttings were grown under similar growth conditions as described above. After 21 days, the leafy cuttings were checked for newly formed roots and then transplanted onto 4"x4"x9.5" pots containing Pro-mix BX soil and fertilized. The cuttings were allowed to grow for an additional two weeks and the newly developed leaves in the 4-5 weeks old cuttings were used for auxin foliar spraying experiments.

extract_protocol:
The 11-day hormone-treated and control plant tissues were harvested between 10:00 am to 11:00 am (4-5 hours post-dawn). Stem and root samples were frozen in liquid nitrogen and ground into a fine powder using mortar and pestle. Total RNA was extracted from 100mgs of tissue powder using GeneJet Plant RNA purification mini kit (Thermo scientific, USA), and the concentration of RNA was measured using a nanodrop (Thermo scientific, USA). One microgram RNA was shipped to Genewiz (NJ, USA) on dry ice and used for polyA selection, and cDNA library was generated and sequenced using Illumina HiSeq 2x150 bp sequencing.
Library construction was performed by GENEWIZ corporation, using polyA selection.

treatment_protocol: For Auxin enhancers (AEs), 3 µM NAA (α143 Naphthalene Acetic Acid) and 4.5 µM IBA (Indole-3-Butyric Acid) were mixed and sprayed as an enhancer cocktail while for auxin inhibitors (AI), 100 µM NPA (Naphthylphthalamic Acid) was used. AE and AI were prepared in 1N KOH (control solution) as per manufacturer recommendation (Phytotechnology Laboratories Inc, KA, USA). Since there were no earlier reports of foliar spraying of these auxin modulators in poplar, we optimized the spraying concentration based on (i) our previous experiences in foliar spraying in other plant species like Petunia hybrida (Ahkami et al. 2013) which served as our base concentration, and (ii) published literatures on woody plants where NPA (auxin inhibitor) were directly sprayed at the root initiation site which served as our upper limit concentration 151 (Valladares et al. 2020). We were mindful of the fact that very high concentrations of these synthetic auxin modulators can result in chemical stresses on source leaves with potential reduction in plant biomass development, as reported in other studies (Nassef and El-aref 2018; Di Benedetto et al. 2015; 154 Rastogi et al. 2013). Based on these factors, in our pilot experiment, we optimized AE and AI concentrations that resulted in changes in root phenotype but not altered source leaf growth in terms of the number of leaves, leaf greenness, and dry weight. The control plants were sprayed with 1N KOH solution which grew normally and established leaf growth regularly at the end of the spraying experiment. Therefore, 1N KOH caused no negative phenotypic effects on leaves. The leaves of a minimum 6-8 rooted cuttings were sprayed between 10:00 AM and 11:00 AM, with AE and AI agents for a period of 11 days. We adopted 11 days as a treatment timeline for this study based on a pilot experiment, in which we determined that this duration resulted in a measurable difference in root phenotypes between AE and AI, without any detrimental effects on foliar tissues. For the foliar spraying, we used 8, 6, and 8 rooted cuttings for control, AE, and AI treatments, respectively. Each treated plant was sprayed with 5 mL of AE or AI reagents for the first 4 days, followed by 6.2 mL for the consecutive 2 days, and 7.4 mL until plant harvest. After 11 days of foliar spraying, plants were carefully uplifted, soil was removed by gentle washing in water, and stem and root tissues were harvested and flash-frozen in liquid nitrogen. The various tissue samples were kept at -80 °C until being processed for omics analyses. A separate batch of hormone-sprayed plants was harvested and dried at 60℃ for two days and used to measure dry biomass weights. All sample collections for downstream molecular works were performed between 10:00-11:00 AM (4-5 hours post dawn).

tag: tissue

value: root

value: control (1 N KOH)

tag: read depth

value: acceptable


title: C-enh-11d-Root-5


title: 2.5mM ALA treatment, harvest at 24h Replicate 4

description: Biological replicate 4 of 4. treated with 2.5 mM ALA and harvested after 24 h.


title: GCN-1(nc40)_D6_A, RNA-seq

city: Martinsried/Planegg

first: Martin

last: Mueller

address: Am Klopferspitz 18

country: Germany

institute: MPI of Biochemistry

description:
Counts_NC40_aged_mRNA.txt
GCN1A

data_processing:
Sequencing reads were demultiplexed and trimmed using a custom awk script. Barcodes used for Ribo-seq - replicate A: ATCGT; replicate B: AGCTA
The UMI were extracted using UMI-tools using the option ‘--extract-method=regex --bc-pattern="^(?P<umi_1>.{2}).+(?P<umi_2>.{6})$"’, which serves to remove duplicated reads arising from library amplification. The clipped reads were then mapped against ncRNA/rRNA indices using Bowtie2 (v2.4.2) with the parameters ‘-N 1 -L 15’. Unaligned reads were mapped against the genome using STAR (v2.7.10a) with parameters ‘--outFilterMismatchNmax 2 --quantMode TranscriptomeSAM GeneCounts --outSAMattributes MD NH --outFilterMultimapNmax 1’. The P-site offset and metagene plots were computed using the R package “riboWaltz” (Lauria, 2018). Transcript enrichment was calculated with the R package “DESeq2” (Love, 2014) or “DEBrowser” (Kucukural, 2019).
Assembly: hg38 and WBcel235(ce11)
Supplementary files format and content: tab-delimited text file with raw counts

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: The Bristol strain N2 was used as wild-type. Strains used in this study are listed in the Key Resource Table. Worms were grown on nematode growth medium (NGM) seeded with OP50 bacteria and maintained at 20°C unless otherwise indicated. For liquid culture, worm eggs were collected by bleaching and synchronized populations of L1 larvae were obtained by overnight growth in M9 medium. The L1 larvae were grown in S Basal in presence of OP50 bacteria.

extract_protocol:
C. elegans  Synchronized nematodes were transferred to 1 l S-Basal and grown in liquid culturentil D1 of adulthood or until D6, when indicated. FUdR (200 µM) was added when the culture had reached the L4/young adult stage. After thorough washing in M9, the nematodes were frozen in lysis buffer (25 mM Hepes-KOH pH 7.4, 100 mM KoAC, 10 mM MglCl2, 0.5 mM DTT, 2x EDTA free protease inhibitor, 0.1 U/μL SUPERase*In, 100 μg/mL cycloheximide) by dropwise transfer into liquid nitrogen. The nematodes were lysed with a Retsch Cryomill MM400 at 30 Hz for 3 times 90 s with cooling between cycles. The lysate was cleared for 10 min at 20,000 x g and 4oC. Ribosome protected fragments (RPFs) were recovered, and libraries were prepared as previously described {McGlincy, 2017 #78}.  HEK293T cells  HEK293T cells were seeded into 15 cm plates 24 h prior to treatment. The cells were treated with 10 nM CC-885 and 20 μg/ml G418 for 4 h. Ribosome protected fragments (RPFs) were recovered, and libraries were prepared as previously described {McGlincy, 2017 #78}.
C. elegans  The procedure for immunoprecipitation (IP) of GCN-1 bound ribosomes was adapted from {Matsuo, 2021 #75}. Nematodes were synchronized by bleaching. L1 larvae were transferred to 1 L S-Basal. The animals were harvested at D1 of adulthood. Bacteria were removed by repeated washes in M9. In the last washing step, M9 was replaced by lysis buffer (25 mM Hepes-KOH pH 7.4, 100 mM KoAC, 10 mM MglCl2, 0.5 mM DTT, 2x EDTA free protease inhibitor, 0.1 U/μL SUPERase*In, 100 μg/mL cycloheximide). After a quick spin, the worms were flash frozen in liquid nitrogen. The frozen worms were lysed with a Retsch cryomill MM400 at 30 Hz as above. The lysate was thawed on ice and clarified by centrifugation at 4,000 x g for 10 min at 4oC. Protein concentration was determined by Bradford assay. The supernatant fraction (80 mg of total protein) was partially digested with 3 units per 1 mg RNA RNase I (Epicenter) at 4oC for 1 h. Ribosomes were pelleted through a sucrose cushion (1 M, 20 U/mL SUPERase*In (Invitrogen)) at 55.000 rpm in a SW 55 Ti rotor (Beckman Coulter) for 2 h at 4oC and resuspended in lysis buffer supplemented with 10% glycerol. The IP was performed at 4oC for 1 h using M2 anti-FLAG magnetic agarose beads (Invitrogen). The beads were washed 10 times with lysis buffer and bound material was digested with 12.5 units of RNase I (Epicenter) at 23oC for 45 min (strong RNase I treatment). Ribosome protected mRNA fragments were eluted by adding TRIzol reagent (Invitrogen). Libraries were prepared as previously described (McGlincy, 2017 #78) and sequenced on an Illumina NextSeq 500 system.  HEK293T cells  Cells (treated with CC-885 or untreated) were harvested, washed with PBS and lysed by trituration through a 26 G needle for 10 times in lysis buffer (20 mM Tris, pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, 1 % Triton-X 100). The lysate was cleared at 4,000 x g for 10 min and an equivalent of 5 mg RNA input was digested with 15 units of RNAse I. The digested lysate was then layered over a sucrose cushion (1 M, 20 U/mL SUPERase*In (Invitrogen)) and centrifuged at 55.000 rpm in a SW 55 Ti rotor (Beckman Coulter) for 2 h at 4oC. The pelleted ribosomes were resuspended in lysis buffer supplemented with 10 % glycerol and incubated with GCN1 antibody (A301-843A, Thermo Fisher) coupled to protein G Dynabeads (10003D, Invitrogen) (5 µg antibody per 50 µl of protein G beads) for 2 h at 4oC. The beads were washed 10 times and digested with 4 units RNAse I for 45 min at 23oC. RPFs were isolated by TRIzol and libraries were prepared as previously described (McGlincy, 2017).

treatment_protocol: HEK293T cells were cultured in DMEM (Thermo Scientific, 11995073) supplemented with 10% FBS (Gibco, 10270106) at 5% CO2 and 37°C. Subsequently, cells were treated with 10 nM CC-885 and 20ug/ul G418 for 4 hours.

value: whole organism

tag: ip antibody

tag: genotype


title: 2.5mM ALA treatment, harvest at 24h Replicate 1

description: Biological replicate 1 of 4. treated with 2.5 mM ALA and harvested after 24 h.


title: bbs2_HO1

first: Brian

description: bbs2 -/- homozygote sample 1; mutant biological replicate


title: C-enh-11d-Root-2

value: low counts, not recommended for routine use


title: bbs2_WT4

description: bbs2 +/+ wild-type sample 4; wild-type biological replicate

value: wild-type


title: C-enh--11d-Root-3


title: Wild-type(N2)_D0_B, RNA-seq

description:
Counts_NC40_young_mRNA.txt
N2_B_mRNAseq


title: bbs2_HO2

description: bbs2 -/- homozygote sample 2; mutant biological replicate


title: bbs2_HO4

description: bbs2 -/- homozygote sample 4; mutant biological replicate


title: bbs2_WT1

description: bbs2 +/+ wild-type sample 1; wild-type biological replicate


title: bbs2_WT2

description: bbs2 +/+ wild-type sample 2; wild-type biological replicate


title: bbs2_WT3

description: bbs2 +/+ wild-type sample 3; wild-type biological replicate


title: GCN-1(nc40)_D0_B, RNA-seq

description:
Counts_NC40_young_mRNA.txt
GCN1_B_mRNAseq


title: zfish_nov2019_mcs_2

city: Columbus

first: Bradley

middle: Wayne

last: Blaser

state: OH

address: 400 W 12th Ave

department: Comprehensive Cancer Center

institute: Ohio State University

data_processing:
scRNA-seq data were processed from FASTQs to gene-cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome.
scATAC-seq data were processed from FASTQs to peak-cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome
RNA-seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome.
ATAC-seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome.
Genome_build: GRCz11, GRCh38
Supplementary_files_format_and_content: scRNAseq:  hdf5 file format containing gene-cell barcode matrices.  scATACseq:  hdf5 file format containing peak-cell barcode matrices.  RNA-seq:  Normalized abundance table from RSEM with TPM, FPKM and other metrics per gene.  ATAC-seq:  bigwig file with genome-weide accessibility tracks and narrowPeak files (standard BED6+4 format).

source_name: zebrafish kidney marrow

growth_protocol: Fish were maintained on a recirculating water system at 28C.

extract_protocol:
Fish were euthanized and kidney marrow was dissected, RBC lysis was performed and single cells were isolated using the 10X Chromium System.
Libraries were constructed using the 10X Single Cell 3' protocol.

treatment_protocol: No treatments

tag: Stage

value: adult

tag: class

value: mcs/control

value: kidney marrow


title: inhibitor-24h-Stem-3

source_name: stem

value: stem

value: Auxin inhibitor (100 uM naphthylphthalamic acid)


title: sele_mcs_scatac

library_source: genomic

molecule: genomic DNA


title: Wild-type(N2)_D0_A, RNA-seq

description:
Counts_NC40_young_mRNA.txt
N2_A_mRNAseq


title: GCN-1(nc40)_D0_A, RNA-seq

description:
Counts_NC40_young_mRNA.txt
GCN1_A_mRNAseq


title: inhibitor-24h-Stem-2


title: zfish_nov2019_mcs_1


title: zfish_nov2019_cxcl8_2


title: YFP-UTR_mRNA_B, RNA-seq

description:
Counts_YFP-UTR_mRNA.txt
279_B_mRNAseq

value: YFP-UTR


title: YFP-UTR_mRNA_A, RNA-seq

description:
Counts_YFP-UTR_mRNA.txt
279_A_mRNAseq


title: zfish_nov2019_cxcl8_1


title: inhibitor-24h-Stem-1


title: YFP-STOP_mRNA_B, RNA-seq

description:
Counts_YFP-UTR_mRNA.txt
277_B_mRNAseq

value: YFP-STOP


title: sele_prkcda_scatac

value: prkcda


title: siKRAS_A549_KK_11

type: genomic

city: San Francisco

first: Alex

middle: G

last: Lee

state: CA

address: 1550 4th Street

institute: UCSF

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

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

data_processing: R minfi ver 1.32.0

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: Cells were cultured in RPMI medium with 10% serum and passaged twice per week (1:10 for A549, 1:6 for H358).

extract_protocol: 72h post transfection genomic DNA was extracted using the AllPrep kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Cells were seeded into 6-well plates and 24h later transfected with siRNA (10nM) using Lipofectamine RNAiMAX (following manufacturer's instructions for forward transfection).

value: siKRAS

tag: disease

value: non-small cell lung cancer (NSCLC)

tag: mutation

value: KRAS G12S


title: inhibitor-11d-Stem-4


title: inhibitor-11d-Stem-5


title: YFP-STOP_mRNA_A, RNA-seq

description:
Counts_YFP-UTR_mRNA.txt
277_A_mRNAseq


title: M82 root, PEG treated, Replica 3

city: Milano

first: Raul

last: Pirona

address: Via Alfonso Corti 12

country: Italy

institute: IBBA-CNR

hyb_protocol: Each sample was hybridized to a custom NimbleGen microarray named 111012_Slyc_PT_expr (Roche, NimbleGen), which contains probes targeted to 28,191 tentative consensus sequences

scan_protocol: Scanning was performed with an Axon GenePix 4400A scanner (Molecular Devices, San Jose, CA). Scanner settings were set according to NimbleGen gene expression user guide.

data_processing: Gene calls were generated using the Robust Multichip Average (RMA)algorithm as described by Irizarry, et al. (Nucleic Acids Res. 2003; 31:e15 andBiostatistics2003; 4:249). Normalization was performed using quantile normalization as described by Bolstad, et al.(Bioinformatics2003; 19:185).

organism: Solanum lycopersicum

source_name: Treated

label_protocol: The cDNA synthesis, labeling and hybridization were performed according to NimbleGen Arrays User’s Guide: Gene Expression Analysis (Version 5.1) by the Functional Genomic Center of the University of Verona (Italy; http://ddlab.sci.univr.it/FunctionalGenomics/).

growth_protocol: The seeds were sterilized with 70 % ethanol for 5 min and subsequently with a solution of 10 % NaOCl and 0.1 % SDS for 10 min twice, thoroughly rinsed and then placed on dH2O-moistened Petri dishes at 26 °C in the dark. After 5 days, the germinated seedlings were inserted into holes of polystyrene foam sheets and transferred to plastic boxes containing the standard MS nutrient solution (Duchefa Biochemistry, Harlem, The Netherlands; Murashige and Skoog, 1962). To avoid hypoxia, continuous aeration of the medium was provided by an aquarium air pump via flexible plastic tubing. Nutrient solution was renewed every 2 days. To minimize any potential damage to the root system, plants were transferred into the new nutrient solution by moving the polystyrene foam sheets. All the hydroponic experiments were performed in a controlled growth chamber at 25 °C/21 °C under a 14 h light/10 h dark photoperiod with a light intensity of 200 µmol m-2 s-1 and 50 % relative humidity.

extract_protocol: Total RNA was extracted from leaves using the TRIzol® RNA Purification Kit (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions. RNA purity was checked spectrophotometrically (Nanodrop ND-1000 Spectrophotometer, Celbio, Italy) and only samples with absorbance reading ratio at 260 ⁄ 280 nm between 1.7 and 2.1 were used. The integrity of RNA was verified using the RNA 6000 Nano Labchip Kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, USA) following the manufacturer’s protocol. Only samples with a 28S ⁄ 18S ratio ≥ 2 were used for further experiments.

treatment_protocol: For the osmotic stress treatment, after 14 days of growth (third-leaf stage), half of the plants were transferred to a nutrient solution with 20 % PEG6000 (Duchefa Biochemistry, Harlem, The Netherlands) at 11.00 am (3 hours after the light onset). Leaves and roots from control and treated plants were separately collected after 24 h (11.00 am) in three biological replicates, each consisting of six plants.

tag: cultivar

value: root

value: PEG


title: M82 root, PEG treated, Replica 2


title: zfish_km_july2020_prkcda_2_gex


title: Input_mRNA_B(Cele), RNA-seq

description:
Counts_GCN1_Total_mRNA.txt
3xFLAG-GCN1_B_mRNAseq


title: siUHRF1_H358_KK_07

value: KRAS G12C


title: C-enh--11d-Root-1

value: control (1 N KOH)


title: inhibitor-11d-Stem-3

value: acceptable


title: M82 root, PEG treated, Replica 1


title: siKRAS_H358_KK_04


title: siKRAS_A549_KK_13


title: siUHRF1_H358_KK_06


title: siNeg_H358_KK_02

value: siNeg


title: zfish_km_july2020_mcs_2_gex

value: adult


title: Input_mRNA_A(Cele), RNA-seq

description:
Counts_GCN1_Total_mRNA.txt
3xFLAG-GCN1_A_mRNAseq

value: whole organism


title: M82 root, control, Replica 3

value: control


title: YFP-UTR_B, Ribo-seq

description:
Counts_YFP-UTR_ribo.txt
279B

data_processing:
Sequencing reads were demultiplexed and trimmed using a custom awk script. Barcodes used for Ribo-seq - replicate A: ATCGT; replicate B: AGCTA
The UMI were extracted using UMI-tools using the option ‘--extract-method=regex --bc-pattern="^(?P<umi_1>.{2}).+(?P<umi_2>.{6})$"’, which serves to remove duplicated reads arising from library amplification. The clipped reads were then mapped against ncRNA/rRNA indices using Bowtie2 (v2.4.2) with the parameters ‘-N 1 -L 15’. Unaligned reads were mapped against the genome using STAR (v2.7.10a) with parameters ‘--outFilterMismatchNmax 2 --quantMode TranscriptomeSAM GeneCounts --outSAMattributes MD NH --outFilterMultimapNmax 1’. The P-site offset and metagene plots were computed using the R package “riboWaltz” (Lauria, 2018). Transcript enrichment was calculated with the R package “DESeq2” (Love, 2014) or “DEBrowser” (Kucukural, 2019).
Assembly: hg38 and WBcel235(ce11)
Supplementary files format and content: tab-delimited text file with raw counts
Library strategy: Ribo-seq


title: siKRAS_H358_KK_03


title: zfish_km_july2020_mcs_1_gex

value: mcs/control

value: kidney marrow


title: siUHRF1_H358_KK_08


title: siUHRF1_A549_KK_16


title: inhibitor-11d-Stem-2

value: stem

value: Auxin inhibitor (100 uM naphthylphthalamic acid)

value: low counts, not recommended for routine use


title: siNeg_A549_KK_10


title: inhibitor-11d-Stem-1


title: rosa_brad_aug2019_zf_4E

source_name: dissociated zebrafish embryos

growth_protocol: Embryos were grown in E3. embryo medium at 28C.

extract_protocol:
Embryos were euthanized, minced and cells digested with Liberase before filtering and isolation using the 10X Chromium System.
Libraries were constructed using the 10X Single Cell 3' protocol.

value: 96 hpf

value: whole embryo


title: siKRAS_H358_KK_05

value: siKRAS

value: non-small cell lung cancer (NSCLC)


title: YFP-STOP_B, Ribo-seq

description:
Counts_YFP-UTR_ribo.txt
277B

value: YFP-STOP


title: siUHRF1_A549_KK_15

value: KRAS G12S


title: enhancer-24h-Stem-3

value: Auxin enhancer (3 uM alpha-naphthalene acetic acid and 4.5 uM indole-3-butyric acid)


title: rosa_brad_aug2019_zf_4C


title: siKRAS_A549_KK_12


title: YFP-UTR_A, Ribo-seq

description:
Counts_YFP-UTR_ribo.txt
279A

value: YFP-UTR


title: M82 root, control, Replica 2

value: root


title: enhancer-24h-Stem-1

value: acceptable


title: 2-runx-cxcl8-2a-mcherry


title: YFP-STOP_A, Ribo-seq

description:
Counts_YFP-UTR_ribo.txt
277A

value: whole organism


title: M82 root, control, Replica 1

value: control


title: siUHRF1_A549_KK_14


title: 1-runx-clover


title: siNeg_H358_KK_01

value: siNeg

value: KRAS G12C


title: Wild-type(N2)_D6_B, Ribo-seq

description:
Counts_NC40_aged_ribo.txt
WTB_old


title: enhancer-11d-Stem-6

value: stem


title: Wild-type(N2)_D6_A, Ribo-seq

description:
Counts_NC40_aged_ribo.txt
WTA_old


title: siNeg_A549_KK_09


title: enhancer-24h-Stem-2


title: enhancer-11d-Stem-5


title: Tondo root, PEG treated, Replica 3

value: Tondo

value: PEG


title: Caco2 BB02 biological replicate 3

city: Gentofte

first: Albin

last: Sandelin

address: Markvangen 26

country: Denmark

institute: University of Copenhagen

data_processing:
Basecalling done by Novogene as part of paid service.
Mapping done by Salmon vs gencode v32, standard settings

extract_protocol: Novogene paid service

value: WT


title: Caco2 LGG biological replicate 3

value: LGG


title: GCN-1(nc40)_D6_B, Ribo-seq

description:
Counts_NC40_aged_ribo.txt
NC40B_old


title: Tondo root, PEG treated, Replica 1


title: Tondo root, PEG treated, Replica 2


title: Tondo root tissue, control, Replica 2


title: Tondo root tissue, control, Replica 3


title: enhancer-11d-Stem-4


title: Caco2 BB12 biological replicate 3


title: Caco2 BIF195 biological replicate 3


title: GCN-1(nc40)_D6_A, Ribo-seq

description:
Counts_NC40_aged_ribo.txt
NC40A_old


title: enhancer-11d-Stem-3


title: enhancer-11d-Stem-2

value: low counts, not recommended for routine use


title: Caco2 Control biological replicate 3


title: Tondo root tissue, control, Replica 1


title: Wild-type(N2)_D0_A, Ribo-seq

description:
Counts_NC40_young_ribo.txt
WTA


title: GCN-1(nc40)_D0_B, Ribo-seq

description:
Counts_NC40_young_ribo.txt
NC40B


title: enhancer-11d-Stem-1


title: Caco2 LGG biological replicate 2


title: C-Inh-24h-Stem-3

value: control (1 N KOH)


title: Input(Cele)_B, Ribo-seq

description:
Counts_GCN1_IP_Cele.txt
TotalB

value: Input (Cele)


title: GCN-1(nc40)_D0_A, Ribo-seq

description:
Counts_NC40_young_ribo.txt
NC40A


title: Caco2 BIF195 biological replicate 2


title: Wild-type(N2)_D0_B, Ribo-seq

description:
Counts_NC40_young_ribo.txt
WTB


title: C-Inh-24h-Stem-2


title: Caco2 BB12 biological replicate 2


title: C-Inh-24h-Stem-1


title: Input(Cele)_A, Ribo-seq

description:
Counts_GCN1_IP_Cele.txt
TotalA


title: M82 leaf, PEG treated, Replica 1

value: leaf


title: Caco2 BB02 biological replicate 2


title: M82 leaf, PEG treated, Replica 2


title: C-Inh-11d-Stem-4


title: M82 leaf, control, Replica 1


title: M82 leaf, control, Replica 2


title: GCN-1-IP(Cele)_B, Ribo-seq

description:
Counts_GCN1_IP_Cele.txt
IPB

value: FLAG M2


title: Caco2 Control biological replicate 2


title: M82 leaf, control, Replica 3


title: GCN-1-IP(Cele)_A, Ribo-seq

description:
Counts_GCN1_IP_Cele.txt
IPA


title: Caco2 LGG biological replicate 1


title: C-Inh-11d-Stem-3


title: C-Inh-11d-Stem-2


title: Caco2 BB12 biological replicate 1


title: C-Inh-11d-Stem-1


title: Caco2 BIF195 biological replicate 1


title: zfish_km_july2020_prkcda_1_gex

value: adult

value: prkcda

value: kidney marrow


title: C-enh-24h-Stem-3

value: acceptable


title: Caco2 Control biological replicate 1


title: Caco2 BB02 biological replicate 1


title: WT MCF-7 H3K27me3 CUT&Tag repeat 1 experiment 2

city: Shenzhen

first: haiyun

last: gan

address: xueyuan lu 1068

country: China

institute: Shenzhen Institute of Advanced Technology

data_processing:
All CUT&Tag seq and ChIP-seq samples were pooled and sequenced with a paired-end (2×150 bp) sequencing on an Illumina NovaSeq 6000 platform. All raw data was trimmed by Trimmomatic (v.0.39), aligned to the reference genome hg38 and gene annotations from GENCODE.vM20 of Homo Sapiens, by using the STAR (v.2.7.7a) software with default settings. All RNA-seq samples were pooled and sequenced with a paired-end (2×150 bp) sequencing on an Illumina NovaSeq 6000 platform. All raw data was trimmed by Trimmomatic (v.0.39) and aligned to the reference genome hg38 using bowtie2 (v.2.4.2)
Peaks of H3K27me3 samples were detected using SICER software (v.1.0) (https://github.com/dariober/SICERpy) with false discovery rate (FDR) cut-off of 0.01, window size of 200bp and gap size of 600bp.
BigWig files and counting matrices in bins around peak summits were produced using bedtools (v.2.29.2) and bedGraphToBigWig (v.4) for visualization.
DiffBind R package (v.3.0) was used to filter differential peaks between WT and MCM2-2A samples, with P value cut-off of 0.01 and absolute log2(fold change) > 1. Principal component analysis of samples was implemented in R (v.4.03) and 3d-PCA plots were visualized by rgl R package (0.105.13). Homer suite (v.2.0) was used for peak annotations.
Assembly: hg38
Supplementary files format and content: bigwig files were generated.
Library strategy: CUT&Tag

source_name: Breast

growth_protocol: Regular MCF7 cell lines were obtained from ATCC. These cell lines were cultured using Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal calf serum (FBS) and 100 units/mL penicillin, and 100 mg/mL streptomycin, 2 mM l-glutamine.

extract_protocol:
CUT&Tag was performed as previously reported(Kaya-Okur HS et al., 2019)
CUT&Tag library PCR amplification was performed with NEBNext 2× PCR Master Mix and standard Illumina Nextera indexing primers. The libraries were purified with Ampure XP beads at a ratio of 1:1.

value: Breast

tag: cell type

value: human breast cancer

tag: media

value: DMEM

tag: cut&tag antibody

value: Anti-H3K27me3 Antibody (CST_9733)


title: C-enh-24h-Stem-2

value: stem


title: MCM2-2A MCF-7 H3K27me3 CUT&Tag repeat 1 experiment 2


title: MCM2-2A MCF-7 H3K27me3 CUT&Tag repeat 2 experiment 2


title: WT MCF-7 H3K27me3 CUT&Tag repeat 2 experiment 2


title: C-enh-24h-Stem-1


title: Spatial_10x_PCW4_20220122_slice7

city: Beijing

first: Zeyuan

last: Liu

address: 15 Datun Road, Chaoyang District, Beijing, 100101, China

institute: Institute of Biophysics,Chinese Academy of Sciences

library_source: transcriptomic single cell

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to hg19 human genome and mm10 mosue genome by Cellranger(v2.0.1 and v3.0.2) and Space Ranger (version 1.0.0)
Filtered count matrix was merged by Scanpy Package(v1.4.2)
Assembly: hg19, mm10
Supplementary files format and content: Filtered count matrix was formatted by mtx, and barcode and gene information was with tsv format

source_name: embryo

extract_protocol:
Human embryo samples were collected in ice-cold artificial cerebrospinal fluid (ACSF), single cell was selected by FACS
Chromium™ Single Cell 3’ Reagent Kits v2
Visium Spatial Gene Expression Slide & Reagent Kit
Chromium Single Cell 3ʹ Reagent Kits v3

value: embryo

tag: age

tag: region


title: C-enh-11d-Stem-5

tag: cell line


title: GFP-IP-1

city: Nanjing

first: Ruxu

last: Sun

state: Jiangsu

address: 140 Hanzhong Road

institute: Nanjing medical university

description: For Merip-Seq

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
MeRIPseq reads were aligned to the hg38 genome using STAR.
m6A Peaks were called uing MetPeak  with the significance cut-off p-value <=0.05
Assembly: hg38
Supplementary files format and content: BED (except for Input sample)
Library strategy: MeRIP-Seq

source_name: HUVEC

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells tranduced with L-EV or L-FTO were harvested for RNA extraction
further transcriptome-wide interrogation was pursued by deep sequencing using SMARTer Stranded Total RNA-Seq Kit version 2 (Pico Input Mammalian; 634413; Takara/Clontech, Japan) according to the manufacturer's protocol.

value: HUVEC

value: endothelial cells

tag: antibody


title: GFP-IP-2

description: For Merip-Seq


title: U2OS Cells, siKMT2A or KMT2A KD, replicate1

city: Hyderabad

first: Shweta

last: Tyagi

state: Telangana

address: Opp. to Metro Rail Pillar No.NUP-9, Inner Ring Road, Uppal

country: India

institute: Centre for DNA Fingerprinting and Diagnostics (CDFD)

data_processing:
The raw sequencing read pairs were trimmed by removing  adapters or low quality reads using TrimGalore
Trimmed sequencing reads were mapped to the human reference genome (GRCh38) using STAR
Read counts quantification was done using feature Counts
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file that include Raw readcounts for each Sample

growth_protocol: U-2OS cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was harvested using Trizol method. 1 ug of total RNA was used for the construction of sequencing libraries.
Libraries for RNA-Seq were prepared using NEB Ultra II RNA Directional Library kit. Paired-end sequencing was performed on  Illumina NextSeq 2000.

value: Osteosarcoma

value: KMT2A KnockDown

tag: treatment

value: KMT2A siRNA


title: U2OS Cells, siKMT2A or KMT2A KD, replicate2


title: Tondo leaf, PEG treated, Replica 1

value: Tondo

tag: tissue

value: leaf

value: PEG


title: U2OS Cells, siCtrl for KMT2A, replicate2

value: WT

value: Control siRNA


title: Tondo leaf tissue, control, Replica 3

value: control


title: M82 leaf, PEG treated, Replica 3


title: Tondo leaf tissue, control, Replica 1


title: C-enh-11d-Stem-4

value: control (1 N KOH)

tag: read depth

value: acceptable


title: Tondo leaf tissue, control, Replica 2


title: Tondo leaf, PEG treated, Replica 3


title: Spatial_10x_PCW4_20220122_slice6


title: U2OS Cells, siCtrl for KMT2A, replicate1


title: Tondo leaf, PEG treated, Replica 2


title: Spatial_10x_PCW4_20220122_slice8


title: U2OS Cells, siKMT2F or KMT2F KD, replicate2

value: KMT2F KnockDown

value: KMT2F siRNA


title: C-enh-11d-Stem-2

value: stem


title: Spatial_10x_PCW4_20220122_slice5

value: embryo


title: C-enh-11d-Stem-3

value: low counts, not recommended for routine use


title: Spatial_10x_PCW4_20220122_slice4


title: FTO-IP-2

description: For Merip-Seq

value: HUVEC

value: endothelial cells


title: Spatial_10x_PCW4_20220122_slice3


title: C-enh-11d-Stem-1


title: U2OS Cells, siKMT2F or KMT2F KD, replicate1

value: Osteosarcoma


title: Spatial_10x_PCW4_20220122_slice2


title: U2OS Cells, siCtrl for KMT2F, replicate1


title: FTO-IP-1

description: For Merip-Seq


title: FTO-Input-2

description: For Merip-Seq


title: 2_xlg_24h rep3

city: Sinagpore

first: Daisuke

last: Urano

address: 1 Research Link

country: Singapore

institute: Temasek Life Science Laboratory

data_processing:
1-4: STAR for genome mapping
Assembly: Arabidopisis: TAIR10; Marantia v3.1, v5.1; Rice: IRGSP 1.0
Supplementary files format and content: 1-4: raw counts

organism: Marchantia polymorpha

source_name: Gemmalings

growth_protocol: 1: 7-day-old arabidopsis seedlings liquid grown in 1/2 MS, continuous light; 2-3: 7-day-old marchantia gemma liquid grown in 1/2 B5, continuous light;  4: 7-day-old NB seedlings grwon on 1/2 MS plates, 16/8 Light/Dark cycle

extract_protocol:
1-4: Plant samples were frozen in liquid nitrogen, and followed by RNA extraction using Rneasy Plant Mini Kit (Qiagen)
1-4: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1/2 Ms + 100 mM NaCl treatment for 0, 2 and 24 hr, 1/2 MS + 0.3 ug/ mL tunicamycin for 4 hr

value: Gemmalings


title: U2OS Cells, siCtrl for KMT2F, replicate2


title: THP1_IFNg_Hyp_3

city: SAN DIEGO

first: Stephan

last: Spangenberg

address: 10550 N Torrey Pines Rd, La Jolla, CA 92037

department: Chemistry

institute: The Scripps Research Institute

data_processing:
Raw basecall (or BCL) files from the NextSeq2000 sequencer were converted to sample fastqs using an in-house custom-built wrapper around Illumina’s bcl2fastq conversion software v2.19.0
100bp long single-end reads were generated and checked for data quality using FastQC (Babraham Institute, Cambridge, UK)
Samples were analyzed using nf-core/RNA-seq pipeline v1.4.2 (implemented on Nextflow v20.07.1), which is an open-source and available at https://github.com/nf-core/rnaseq as part of the nf-core project (Ewels et al., 2020)
reads were trimmed for adapters using trimGalore! V0.6.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the human reference genome (ENSEMBL build GRCh38 r98) using STAR v2.6.1d (Dobin et al., 2012)
Gene-level assignment was then performed using featureCounts v1.6.4 (Liao et al., 2014)
Assembly: ENSEMBL build GRCh38
Supplementary files format and content: Tab-delimited file that includes tpm value for each sample

source_name: peripheral blood

growth_protocol: THP-1 cells were grown in RPMI (ATCC) modification with 10% heat inactivated FBS, and 1X Anti-Anti, in a 37C, 5% CO2, humidified incubator

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
Library was constructed using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit (FWD)

treatment_protocol: THP-1 cells were teated with either a vehicle control (DPBS, added to 2% v/v), IFN-g (50 ng/ml) and vehicle, or IFN-g and hydroxyproline (40 mM final concentration, trans-4-hydroxy-L-proline). Cells were then incubated for 72 hours.

value: peripheral blood

value: acute monocytic leukemia

value: wild type

value: trans-4-hydroxy-L-proline 40 mM, IFN-gamma (50 ng/ml)


title: GFP-Input-2

description: For Merip-Seq


title: FTO-Input-1

description: For Merip-Seq


title: 2_gpb_24h rep3


title: PCW12-01_whole_brain_20190603

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to hg19 human genome by Cellranger(v2.0.1 and v3.0.2)
Filtered count matrix was merged by Scanpy Package(v1.4.2)
Genome_build: hg19, mm10
Supplementary_files_format_and_content: Filtered count matrix was formatted by mtx, and barcode and gene information was with tsv format

source_name: human embryo

extract_protocol:
Human embryo samples were collected in ice-cold artificial cerebrospinal fluid (ACSF), single cell was selected by FACS
Chromium™ Single Cell 3’ Reagent Kits v2

value: brain tissue

value: whole brain tissue


title: PCW9-02_whole_brain_20190423


title: THP1_IFNg_Hyp_2


title: THP1_IFNg_Hyp_1


title: 2_gpb_24h rep2


title: 2_xlg_24h rep2


title: Spatial_10x_PCW4_20220122_slice1


title: THP1_IFNg_3

value: PBS, 2% (v/v), IFN-gamma (50 ng/ml)


title: U2OS with mCherry-EWS(YS37)-FLI1 untreated biol rep2

first: Chunyu

last: Yu

address: Xueyuan Road 38#

institute: Peking University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using kallisto 0.46
Assembly: hg38
Supplementary files format and content: Abundance table with raw counts and TPM values for each transcript and sample

source_name: U2OS cell line

growth_protocol: Wild type U2OS, U2OS integrated with mCherry-EWS-FLI1, and A673 cell lines were cultured in DMEM (HyClone) supplemented with 10% FBS (Gibco) and 100 units/mL penicillin and 100 μg/mL streptomycin (HyClone) at 37℃ with 5% CO2 in a humidified incubator (Above 10^7 cells in 10cm dish).

extract_protocol:
RNA was harvested using Trizol reagent. Sequenceing library were generated using Illumina VAHTS Universial V6 RNA-seq library Kit (Cat#NR604-01/02) following the manafacturer's recommendations.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Each replicate was treated with 7.5μM LY2835219 for 0(untreated), 3 and 6 hours.

value: U2OS cell line

value: U2OS with mCherry-EWS(YS37)-FLI1

value: Untreated


title: PCW9-01_whole_brain_20181126


title: 2_xlg_24h rep1


title: U2OS with mCherry untreated biol rep3

value: U2OS with mCherry


title: PCW8-01_whole_head_20190619

value: head

value: whole head


title: U2OS with mCherry-EWS(YS37)-FLI1 untreated biol rep3


title: 2_gpb_24h rep1


title: U2OS with mCherry-EWS(YS37)-FLI1 untreated biol rep1


title: THP1_IFNg_2


title: PCW7-01_whole_head_20190619


title: U2OS with mCherry untreated biol rep2


title: 2_gpa_24h rep2


title: THP1_IFNg_1


title: PCW6-01_whole_head_20190906


title: THP1_vehicle_3


title: GFP-Input-1

description: For Merip-Seq

value: HUVEC


title: U2OS with mCherry-EWS-FLI1mut untreated biol rep3

value: U2OS with mCherry-EWS-FLI1mut


title: 2_gpa_24h rep1


title: U2OS with mCherry untreated biol rep1

value: Osteosarcoma


title: THP1_vehicle_2


title: PCW5-03_whole_head_20190614


title: PCW5-02_whole_head_20190911


title: THP1_vehicle_1


title: 2_tak-1_24h rep2

value: Gemmalings

value: Tak1, WT


title: PCW5-01_whole_body_20190703

value: embryo

value: whole embryo


title: 2_gpa_24h rep3


title: 2_xlg_2h rep3


title: U2OS with mCherry-EWS-FLI1mut untreated biol rep1


title: Baboon37979

city: San Antonio

middle: P.

last: Hermann

state: TX

address: 1 UTSA Circle

department: Department of Biology

institute: University of Texas at San Antonio

data_processing:
Illumina base-calling and demultiplexing with BCL-2-Fastq.
Trimmed FASTQ files were generated using the Cell Ranger v3.1.0 (10x Genomics) mkfastq command using default parameters. Alignment of trimmed reads, filtering, and UMI counting were performed using CellRanger v3.1.0 count function using mouse GRCm38 (mm10), human GRCh38 (hg38), Papio anubis (olive baboon) Panubis1.0 (Ensemble GCA_008728515.1) and rhesus macaque Mmul_10 (Ensemble GCA_003339765.3) references.
Gene expression matrices for each dataset were imported into Seurat (v3.2.3) and merged by species to produce aggregated gene-barcode matrices which were subsequently filtered, normalized and used for cell clustering.
Assembly: Papio anubis (olive baboon) Panubis1.0 (Ensemble GCA_008728515.1) and rhesus macaque Mmul_10 (Ensemble GCA_003339765.3)
Supplementary files format and content: A single gene-barcode matrix file (MTX). Each sparse matrix is stored in Market Exchange Format (MEX), which contains TSV files with features (genes) and barcode sequences corresponding to row and column indices, respectively.

organism: Papio anubis

source_name: Testis

extract_protocol:
Donor cells were recovered from olive baboon and rhesus macaque testes using  two-step enzymatic digestion approach.  Briefly, testicular parenchyma were digested with 1mg/ml Collagenase Type IV (Worthington Biochemicals) for 2-3 minutes at 37°C, washed with Hank’s Buffered Salt Solution (HBSS) to remove interstitial cells, digested with 0.25% trypsin/EDTA containing 1.4mg/ml DNase I (Sigma) for 7-9 minutes at 37°C, and quenched with 10% FBS. Testis cell suspensions were filtered through a nylon mesh to generate a single-cell suspension.  Single-cell transcriptomes were generated using the 10x Genomics Chromium Cell Gene Expression kit (v2 chemistry) per manufacturer recommendations (Zheng et al., 2017) at the UTSA Genomics Core as previously described (Hermann et al., 2018). For each replicate, we targeted collection of 5,000 single-cell gelbead emulsions (GEMs) containing single cells and generated libraries as per manufacturer recommendations (Zheng et al., 2017). Libraries were sequenced at the Genome Sequencing Facility (GSF) at Greehey Children’s Cancer Research Institute at UT Health San Antonio (UTHSA) on a HiSeq2500 (Illumina) instrument.
10x Genomics Single-cell 3' libraries were prepared according to manufacturer recommendations (Single Cell 3' v3 chemistry for 37979, Single Cell 3' v2 chemistry for all others).

treatment_protocol: Animal were untreated and testes obtained at necropsy for another purpose

value: Testis

value: Testicular cells

tag: library type

value: 10x Genomics 3' single-cell Gene Expression


title: U2OS with mCherry-EWS-FLI1 treated 24h biol rep3

tag: genotype

value: U2OS with mCherry-EWS-FLI1

tag: time


title: 2_xlg_2h rep2


title: PCW4-02_whole_head_20190702


title: PCW4-01_whole_body_20190920


title: U2OS with mCherry-EWS-FLI1 treated 24h biol rep2

value: U2OS cell line


title: Baboon36506A


title: 2_tak-1_24h rep3


title: U2OS with mCherry-EWS-FLI1mut untreated biol rep2


title: U2OS with mCherry-EWS-FLI1 treated 24h biol rep1


title: U2OS with mCherry-EWS-FLI1 treated 6h biol rep3


title: 2_xlg_2h rep1


title: 2_gpb_2h rep3


title: U2OS with mCherry-EWS-FLI1 treated 6h biol rep2


title: PCW3-01_whole_body_20190614

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to hg19 human genome by Cellranger(v2.0.1)
Filtered count matrix was merged by Scanpy Package(v1.4.2)
Genome_build: hg19
Supplementary_files_format_and_content: Filtered count matrix was formatted by mtx, and barcode and gene information was with tsv format


title: 2_tak-1_24h rep1


title: Baboon36506B


title: 2_gpb_2h rep2


title: ACME fixed NPC sample, biological replicate 1

city: L'Hospitalet de Llobregat

first: Mireya

last: Plass

state: Barcelona

address: Feixa Llarga s/n, Pavelló de Govern,

country: Spain

institute: IDIBELL

data_processing:
data were processed with Drop-seq tools to generate Digital Gene Expression (DGE) matrices using default parameters. DGE matrices include reads overlapping exonic, intronic and intergenic regions and were enereated using the parameters LOCUS_FUNCTION_LIST=INTRONIC LOCUS_FUNCTION_LIST=INTERGENIC.
Assembly: hg38
Supplementary files format and content: Matrix files with the number of UMIs assigned to each gene in ach cell

extract_protocol:
Cells were dissociated into a single-cell suspension following a previously described protocol optimized for scRNA-seq techniques28. In summary, cells were enzymatically dissociated for 35 min at 37ºC using papain-accutase dissociation buffer (1:1) , and quenched with DMEM/F-12 GlutaMAX supplemented with 10 µM of ROCK inhibitor and 0.033 mg/ml of DNase . Cell suspension was filtered through a 40 µm strainer  and then centrifuged at 150 g for 3 min at RT. After 3 washes with 0.4 mg/ml BSA in DPBS, cells were counted, and viability recorded. Only samples with cell viability higher than 80% were included in the study.
For a single-cell encapsulation in NADIA instrument we loaded 75.000 cells in a volume of 250 µl (300.000 cells/ml) and 150.000 Macosko oligodT beads in 250 µl (600 beads/µl) previously washed and resuspended in lysis buffer (6% w/v Ficoll PM-400, 0.2% v/v Sarkosyl , 0.02M EDTA, 0.2 M Tris pH 7.5, 0.05 M DTT in nuclease-free water). Cells and beads co-flowed in the microfluidic chip of the device with a capture efficiency of 5-7%.  Immediately after the droplet emulsion breakage, the RNAs captured by the oligodT are reverse transcribed. Collected single-cell transcriptomes attached to microparticles (STAMPS) were then splitted in pools of 4000 and amplified for 9 or 11 PCR cycles depending on the bead batch used for the encapsulation (01 and 02 respectively). After cDNA purification with AMPure XP Beads, quantification and fragment size check-up using a 4200 TapeStation System, Nextera XT DNA Library Prep Kit was used for the tagmentation of 600 pg of cDNA, illumina adaptor tagging and amplification. The size of Nextera libraries after being purified with AMPure XP Beads was determined using a 4200 TapeStation System and quantified with Qubit dsDNA HS Assay (Thermo, #Q32851).

value: NPC


title: VivoPHIX fixed NPC sample, biological replicate 2


title: 2_gpb_2h rep1


title: VivoPHIX fixed NPC sample, biological replicate 1


title: U2OS with mCherry-EWS-FLI1 untreated biol rep3

value: Untreated


title: 2_gpa_2h rep3


title: 2_gpa_2h rep2


title: DMSO cryopreserved NPC sample, biological replicate 2


title: DMSO cryopreserved NPC sample, biological replicate 3


title: ACME fixed NPC sample, biological replicate 2


title: U2OS with mCherry-EWS-FLI1 untreated biol rep2


title: methanol fixed NPC sample, biological replicate 4


title: DMSO cryopreserved NPC sample, biological replicate 1


title: U2OS with mCherry-EWS-FLI1 treated 6h biol rep1


title: U2OS with mCherry-EWS-FLI1 untreated biol rep1


title: 2_gpa_2h rep1


title: methanol fixed NPC sample, biological replicate 3


title: 2_tak-1_2h rep3


title: 2_tak-1_2h rep2


title: KO oleic acid rep3

city: New York

first: Michael

last: Gildea

state: New York

address: 550 1st avenue

institute: NYU Langone Health

data_processing:
Read quality assessment (Fastqc)
Adapter sequence and low-quality base trimming (fastp)
Alignment (STAR)
Assigment of alignments to genic features (featurecounts)
Assembly: GRCh38
Supplementary files format and content: counts

source_name: Liver

growth_protocol: HepG2 cells were obtained from American Type Culture Collection. Cells were maintained in Dulbecco’s modification of Eagle’s medium (DMEM) (Thermo Fisher) containing GlutaMAX supplement (Thermo Fisher), 10% fetal bovine serum (FBS), 100 units ml-1 penicillin, and 100 g/ml streptomycin in 5% CO2 at 37°C. The medium was changed every 2-3 days.

extract_protocol:
Following incubation with 200 µM OA (or vehicle control) overnight for 12 hr, total RNA was purified from cells using the RNeasy Mini Kit (#NC9677589, Qiagen). High-Capacity cDNA Reverse Transcription Kit (#4368814, Thermo Fisher) with random priming was used to obtain full-length reverse transcripts.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.  Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: Wild type (WT) and ANGPTL3-knockout (KO) HepG2 cells were exposed to either vehicle control (fatty acid-free BSA) or 200uM oleic acid (conjugated to fatty acid-free BSA) in serum-free media for 12hr before sample collection.

value: Liver

value: Hepatocyte

value: ANGPTL3 KO

value: 200uM oleic acid (12hr)


title: KO oleic acid rep1


title: KO oleic acid rep2


title: methanol fixed NPC sample, biological replicate 2


title: 2_tak-1_2h rep1


title: 2_xlg_0h rep3


title: WT oleic acid rep3

value: WT


title: PCW4-03_whole_head_20190613

value: head

value: whole head


title: methanol fixed NPC sample, biological replicate 1


title: WT oleic acid rep2


title: 2_xlg_0h rep2

value: Gemmalings


title: WT oleic acid rep1


title: B15_RTu9B3

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

hyb_protocol: Arrays were washed, stained, and scanned as described in the Affymetrix GeneChip expression analysis technical manual

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Background adjustment, normalization, and median polish summarization of CEL files were performed with the robust multichip average (RMA) algorithm using the “affy” Bioconductor package

label: biotin

organism: Macaca mulatta

source_name: sorted lymphocyte

label_protocol: Five micrograms of the amplified cDNA was fragmented, bio- tinylated, and hybridized to arrays using the NuGEN Ovation Encore biotin module according to kit instruc- tions.

extract_protocol: Total RNA extraction was performed using the RNeasy minikit (Qiagen, Hilden, Germany). The integrity and quantity of the extracted RNA were assessed with an Agilent bioanalyzer (Agilent Technologies, Santa Clara, CA) and NanoDrop 2000 spectrophotometer (Thermo Scientific, Inc., Wilmington, DE).

treatment_protocol: brief PMA/ionomycin stimulation

value: sorted lymphocyte

tag: subset

value: DP

tag: stimulation

value: Unstim


title: 2_xlg_0h rep1


title: B13_RTu9B1


title: fresh NPC sample, biological replicate 1


title: B9_REi7B3


title: B12_RLv12B3


title: B10_RLv12B1


title: B8_REi7B2

value: TFH


title: B14_RTu9B2_2


title: KO vehicle rep3

value: Vehicle (fatty acid-free BSA) (12hr)


title: B6_RCj13B3


title: KO vehicle rep1


title: KO vehicle rep2


title: 2_gpb_0h rep1


title: 2_gpb_0h rep2


title: WT vehicle rep3


title: B11_RLv12B2


title: 2_gpa_0h rep3


title: WT vehicle rep2


title: B7_REi7B1


title: 2_gpa_0h rep2


title: B5_RCj13B2


title: B4_RCj13B1


title: WT vehicle rep1


title: 2_tak-1_0h rep3

value: Tak1, WT


title: 2_gpb_0h rep3


title: fresh NPC sample, biological replicate 2


title: 2_tak-1_0h rep2


title: POLE3-KO MCF-7 RNA-seq 3D repeat 2

data_processing:
All ATAC-seq, CUT&Tag seq and ChIP-seq samples were pooled and sequenced with a paired-end (2×150 bp) sequencing on an Illumina NovaSeq 6000 platform. All raw data was trimmed by Trimmomatic (v.0.39), aligned to the reference genome hg38 and gene annotations from GENCODE.vM20 of Homo Sapiens, by using the STAR (v.2.7.7a) software with default settings. All RNA-seq samples were pooled and sequenced with a paired-end (2×150 bp) sequencing on an Illumina NovaSeq 6000 platform. All raw data was trimmed by Trimmomatic (v.0.39) and aligned to the reference genome hg38 using bowtie2 (v.2.4.2)
Peaks of H3K27me3, H3K9me3, H3K36me3, H3K36me2 and H2AK119ub samples were detected using SICER software (v.1.0) (https://github.com/dariober/SICERpy) with false discovery rate (FDR) cut-off of 0.01, window size of 200bp and gap size of 600bp. Peaks of H3K4me3, H3K4me1, H3K27ac, H3.3, EZH2, SUZ12 and RING1B samples were detected using MACS2 software (v.2.2.7.1) with P value cut-off of 0.01. BigWig files and counting matrices in bins around peak summits were produced using bedtools (v.2.29.2) and bedGraphToBigWig (v.4) for visualization. DiffBind R package (v.3.0) was used to filter differential peaks between WT and MCM2-2A samples, with P value cut-off of 0.01 and absolute log2(fold change) > 1. Principal component analysis of samples was implemented in R (v.4.03) and 3d-PCA plots were visualized by rgl R package (0.105.13). Homer suite (v.2.0) was used for peak annotations.
Single-cell RNA sequencing was implemented on an Illumina NovaSeq 6000 platform. Raw data was processed by Kallisto-bustools workflow (v.0.46.0), including steps of associating reads with cells, collapsing reads based on unique molecular identifiers (UMIs), and generating gene counts in cells. For data quality control, genes detected in less than three cells and cells with less than 200 genes captured were removed. Furthermore, cells with extremely high (> 8000) or low (< 2000) numbers of detected UMIs and cells with more than 5 % mitochondrial gene expressions were filtered out to avoid multiplets, broken droplets and apoptosis influences. After quality control, data was imported into Seurat (v.4.0.3)
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
Assembly: hg38
Supplementary files format and content: bigwig files were generated(ATAC-seq, CUT&Tag-seq, ChIP-seq and RNA-seq), and gz files are the outputs of kallisto workflow (scRNA-seq)

source_name: whole cell

extract_protocol:
CUT&Tag was performed as previously reported(Kaya-Okur HS et al., 2019)
CUT&Tag library PCR amplification was performed with NEBNext 2× PCR Master Mix and standard Illumina Nextera indexing primers. The libraries were purified with Ampure XP beads at a ratio of 1:1. ChIP-seq libraries were prepared from 10 ng EZH2 ChIP, 100 ng H3K36me2 ChIP and input DNA using the KAPA Hyper prep kit (KAPA).

value: DMEM

tag: chip antibody


title: MCM2-2A MCF-7 RNA-seq 3D repeat 4


title: 2_tak-1_0h rep1


title: MCM2-2A MCF-7 RNA-seq 3D repeat 3


title: 2_gpa_0h rep1


title: MCM2-2A MCF-7 RNA-seq 3D repeat 2


title: MCM2-2A MCF-7 RNA-seq 3D repeat 1


title: WT MCF-7 RNA-seq 3D repeat 2


title: POLE3-KO MCF-7 RNA-seq 3D repeat 1


title: B1_RBK10B1


title: B3_RBK10B3


title: A35_RMq13A4

value: Stim


title: A34_RMq13A3


title: MCM2-2A ESC Sox1 CUT&RUN repeat 1

data_processing:
Sequence reads were mapped back to the mouse reference genome (mm10) using Bowtie2 software (version 1.3.0). Only consistent pair-end reads were chosen for further analysis.
Uniquely aligned reads were extracted using SAMtools (Version 1.7). Peaks were called using MACS2 (version 2.2.7.1) and SICER (version 1.0). For each data source, peaks were called using all samples from all replicates combined. For visualization, bigWig files and count matrices in bins around peak summits were produced using deepTools (version 3.5.1).
scCUT&Tag data was analysis by cellranger-atac (version 2.0.0) and custom python scripts. scRNA-seq data was preprocessed by kallisto-bustools (version 0.46.0) workflow, and further analysed by Seurat (version 4.0.3) and monocle (version 2.18.0) R packages.
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
MINCE-seq, Repli-ATAC-seq and CUT&RUN, data processing steps were similar as CUT&Tag data analysis. The signal profile densities were normalized and calculated using a custom Perl (v.5.26.2) script with scan bin size of 50 bp or 100 bp.
Assembly: mm10
Supplementary files format and content: bigwig files were generated, and gz files are the outputs of cellranger (scCUT&Tag) or kallisto workflow (scRNA-seq)
Library strategy: CUT&Tag

organism: Mus musculus

source_name: MCM2-2A ESC

growth_protocol: Mouse embryonic stem cell (ESC) E14TG2a (kind gift from Bing Zhu lab, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China) were cultured on gelatin coated dishes in DMEM/F-12 (Gibco) supplemented with 15% (v/v) fetal bovine serum (Gibco), 1% penicillin/streptomycin (Gibco), 1 mM sodium pyruvate (Gibco), 2 mM GlutaMAX (Gibco), 1% MEM nonessential amino acids (Gibco), 55 μM β-mercaptoethanol (Sigma-Aldrich), and 10 ng/ml mouse leukemia inhibitory factor (Millipore) in a 37°C incubator with a humidified, 5% CO2 atmosphere. Cells were passaged using Trypsin-EDTA (Gibco) and routinely tested for mycoplasma contamination. ESCs were differentiated into Neuronal precursor cell (NPC) as previous described with modifications3. Briefly, ESCs were grown on gelatin coated dishes in N2B27 medium that 1:1 mixed of DMEM/F-12 (Gibco) and Neurobasal media (Gibco) and supplemented with 2 mM GlutaMAX (Gibco), 100 μM β-mercaptoethanol (Sigma-Aldrich), 1× N-2 and 0.5× B-27 supplements (Gibco). After 7 days, ESCs were re-plated in suspension using nonadherent plates to promote the formation of cellular aggregates for 3 additional days. Cellular aggregates were harvested and plated on gelatin coated dishes in N2B27 medium supplemented with 10 ng/ml EGF and FGF, respectively. The aggregates will attach and NPCs will grow out of the attached aggregates on differentiation day 11. Medium was changed every 2 days without exposing the NPC culture to air and passaged using Accutase (Sigma-Aldrich).

extract_protocol:
CUT&Tag was performed as previously reported with modifications4,5. Cells (1-2×105) were washed twice in 1 mL Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1×Protease inhibitor cocktail) at room temperature. Concanavalin-coated magnetic beads (Bangs Laboratories) were washed twice in 1 mL Binding Buffer (20 mM HEPES pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). Cells were resuspended in 1 mL Wash Buffer and incubated with 10 μL pre-washed Concanavalin-coated magnetic beads at room temperature for 15 min. Beads (bound to cells) were incubated in Antibody Buffer (Wash Buffer, 0.08% Digitonin for ESCs/0.05% Digitonin for other cells, 2 mM EDTA, 0.1% BSA, 1:100 dilution of the appropriate primary antibody) on a rotating platform overnight at 4°C. Prepare mixture of 1 μg appropriate secondary antibody (Table S1) and pAG-Tn5 adapter complex (Novoprotein) at 1:2 molar ratio at room temperature for 1 hour. Beads were washed once with 1 mL Dig-wash Buffer (Wash Buffer, 0.08% Digitonin for ESCs/0.05% Digitonin for other cells) and nutated in 100 μL Dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl, 0.5mM Spermidine, 1×Protease inhibitor cocktail, 0.01% Digitonin) added the secondary antibody bound pAG-Tn5 complex at room temperature for 1 hour. Beads were washed 3 times with 1 mL Dig-300 buffer and resuspended in Tagmentation Buffer (Dig-300 buffer, 10 mM MgCl2) at 37°C for 1 hour. Beads were washed once with 1 mL TAPS Wash Buffer (10mM TAPS, pH 7.5, 0.4 mM EDTA) and incubated in 250 µL Dig-300 buffer containing 15 mM EDTA, 0.1% SDS and 100 µg/mL Proteinase K at 37°C for 1 hour with shaking of 900rpm. Then CUT&Tag DNA was extracted by phenol-chloroform-isoamyl alcohol and purified again by DNA Clean & Concentrator-5 Kit (Zymo Research) to 20 µL EB buffer. CUT&Tag DNA was Incubated by RNase A (1/400) at 37°C for 10 min. To amplify libraries, 10 μL CUT&Tag DNA was mixed with 1 μL of a uniquely barcoded i5, 1 μL a uniquely barcoded i7 primer, using a different barcode for each sample, and 12 μL NEBNext 2× PCR mix, and run the following cycling conditions with lid heat on: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 10 s; final extension at 72 °C for 1 min and hold at 10 °C. Post-PCR clean-up was performed by adding 1× volume of Ampure XP beads (24 μL) (Beckman Counter), and libraries were incubated with beads for 10 min at RT, washed twice gently in 80% ethanol, and eluted in 20 μL EB buffer. The libraries were used for paired-end (2×150 bp) sequencing on an Illumina Novaseq or HiSeq Xten platform by Annoroad Gene Technology Co. Ltd.
RNA-seq library preparation and deep sequencing were performed by Annoroad Gene Technology Co. Ltd.. Cell suspensions were barcoded through the 10x Chromium Single Cell platform using Chromium Single Cell 3′ Library, Gel Bead and Multiplex Kit (10x Genomics).

value: MCM2-2A ESC

value: Ant-Sox1 Antibody(CST_4194)


title: B2_RBK10B2


title: WT ESC Sox1 CUT&RUN repeat 1

source_name: WT ESC

value: WT ESC


title: A33_RMq13A2


title: A31_RPg14A4


title: A30_RPg14A3


title: A29_RPg14A1


title: MCM2-2A ESC Olig2 CUT&RUN repeat 1

value: Ant-Olig2 Antibody(Proteintech_133999)


title: A32_RMq13A1


title: A28_RGd14A4


title: HCT116 cells, NC

city: Nanchang

first: Yi

last: Sang

state: Jiangxi

address: No.128,Xiangshan North Road

institute: Nanchang University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

source_name: HCT116 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: 37℃，5% CO2, 10%FBS in DMEM

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: Knockdwon of SUN2 or not

value: Scr

value: control


title: A27_RGd14A3


title: MCM2-90A T47D RNA-seq repeat 1


title: A26_RGd14A2


title: WT ESC Olig2 CUT&RUN repeat 1


title: WT T47D RNA-seq repeat 2

value: WT


title: MCM2-90A T47D RNA-seq repeat 2


title: WT MCF-7 RNA-seq 3D repeat 1


title: WT T47D RNA-seq repeat 1


title: MCM2-2A 293T RNA-seq repeat 2


title: WT NPC 7D Pax6 CUT&RUN repeat 1

source_name: WT NPC

value: WT NPC

value: DMEM/F12：Neurobasal 1：1+N2+B27

value: Ant-Pax6 Antibody(Biolengend_12323)


title: MCM2-2A 293T RNA-seq repeat 1


title: MCM2-2A NPC 3D Pax6 CUT&RUN repeat 1

source_name: MCM2-2A NPC

value: MCM2-2A NPC


title: MCM2-2A NPC 7D Pax6 CUT&RUN repeat 1


title: WT NPC 3D Pax6 CUT&RUN repeat 1


title: WT 293T RNA-seq repeat 2


title: MCM2-2A ESC Pax6 CUT&RUN repeat 1


title: WT 293T RNA-seq repeat 1


title: MCM2-90A T47D Brdu-IP

value: anti-BRDU


title: HCT116 cells, shSUN2-1

value: SUN2 knockdown


title: WT T47D Brdu-IP


title: MCM2-2A ESC Sox2 CUT&RUN repeat 1

value: Ant-Sox2 Antibody(Abcam_ab92494)


title: MCM2-90A T47D H3K36me3 espan

value: Anti-H3K36me3 Antibody (Active Motif_61021)


title: MCM2-2A ESC MINCE-seq input repeat 1

data_processing:
Sequence reads were mapped back to the mouse reference genome (mm10) using Bowtie2 software (version 1.3.0). Only consistent pair-end reads were chosen for further analysis.
Uniquely aligned reads were extracted using SAMtools (Version 1.7). Peaks were called using MACS2 (version 2.2.7.1) and SICER (version 1.0). For each data source, peaks were called using all samples from all replicates combined. For visualization, bigWig files and count matrices in bins around peak summits were produced using deepTools (version 3.5.1).
scCUT&Tag data was analysis by cellranger-atac (version 2.0.0) and custom python scripts. scRNA-seq data was preprocessed by kallisto-bustools (version 0.46.0) workflow, and further analysed by Seurat (version 4.0.3) and monocle (version 2.18.0) R packages.
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
MINCE-seq, Repli-ATAC-seq and CUT&RUN, data processing steps were similar as CUT&Tag data analysis. The signal profile densities were normalized and calculated using a custom Perl (v.5.26.2) script with scan bin size of 50 bp or 100 bp.
Assembly: mm10
Supplementary files format and content: bigwig files were generated, and gz files are the outputs of cellranger (scCUT&Tag) or kallisto workflow (scRNA-seq)
Library strategy: MINCE-seq


title: wild type Rabbit, replicate 2 [TD-3]

city: Shanghai

first: hu

last: xiaolin

state: Shanghai

address: south congqing road 227#

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Adapters, low-quality reads (percentages of base quality lower than 15 higher than 20%), reads with unknown base higher than 5% were removed with SOAPnuke V1.5.2
Clean reads were mapped to reference genome with HISAT2 V2.0.4  with default parameters. Then, gene expressions were quantified by RSEM V1.1.17  and HTSeq V1.99.2
Supplementary files format and content: GCA_000003625.1
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Oryctolagus cuniculus

source_name: femoral head

extract_protocol:
5 μg RNA of each sample were utilized with ribosomal RNA removed by Epicentre Ribo-zeroTM rRNA Removal Kit (Epicentre, United States)
NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (NEB, United States)

value: femoral head


title: WT T47D H3K36me3 espan

value: DMEM


title: wild type Rabbit, replicate 2 [TD-2]


title: MCM2-2A 293T Brdu-IP


title: WT ESC Pax6 CUT&RUN repeat 1


title: A25_RGd14A1

value: sorted lymphocyte

value: Stim


title: WT ESC MINCE-seq input repeat 1

value: WT ESC


title: A22_RTu9A2

value: TFH


title: A24_RTu9A4


title: A21_RTu9A1


title: A23_RTu9A3


title: MCM2-2A D0 ESC total RNA-seq repeat 2

data_processing:
Sequence reads were mapped back to the mouse reference genome (mm10) using Bowtie2 software (version 1.3.0). Only consistent pair-end reads were chosen for further analysis.
Uniquely aligned reads were extracted using SAMtools (Version 1.7). Peaks were called using MACS2 (version 2.2.7.1) and SICER (version 1.0). For each data source, peaks were called using all samples from all replicates combined. For visualization, bigWig files and count matrices in bins around peak summits were produced using deepTools (version 3.5.1).
scCUT&Tag data was analysis by cellranger-atac (version 2.0.0) and custom python scripts. scRNA-seq data was preprocessed by kallisto-bustools (version 0.46.0) workflow, and further analysed by Seurat (version 4.0.3) and monocle (version 2.18.0) R packages.
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
MINCE-seq, Repli-ATAC-seq and CUT&RUN, data processing steps were similar as CUT&Tag data analysis. The signal profile densities were normalized and calculated using a custom Perl (v.5.26.2) script with scan bin size of 50 bp or 100 bp.
Assembly: mm10
Supplementary files format and content: bigwig files were generated, and gz files are the outputs of cellranger (scCUT&Tag) or kallisto workflow (scRNA-seq)

source_name: D0 ESC

value: D0 ESC


title: A20_RLv12A4


title: MCM2-2A D0 ESC total RNA-seq repeat 1


title: A18_RLv12A2


title: MCM2-2A 293T H3K36me3 espan


title: WT ESC Sox2 CUT&RUN repeat 1


title: Perthes' disease Rabbit, replicate 5 [TB-5]

value: Perthes' disease


title: A19_RLv12A3


title: A15_RJq12A3


title: WT D0 ESC total RNA-seq repeat 2


title: A16_RJq12A4


title: A17_RLv12A1


title: A14_RJq12A2


title: A13_RJq12A1


title: Perthes' disease Rabbit, replicate 4 [TB-4]


title: Perthes' disease Rabbit, replicate 3 [TB-3]


title: wild type Rabbit, replicate 1 [TD-1]

value: WT


title: WT 293T H3K36me3 espan


title: WT 293T Brdu-IP


title: MCM2-2A MCF-7 Brdu-IP


title: POLE3-KO MCF-7 Brdu-IP


title: POLE3-/- H3.3 D0 ESC CUT&Tag repeat 2

value: DMEM/F12 _serum


title: WT D0 ESC total RNA-seq repeat 1


title: A12_REi7A4


title: POLE3-/- H3.3 D0 ESC CUT&Tag repeat 1


title: WT MCF-7 Brdu-IP


title: MCM2-90A T47D H3.3 CUT&Tag repeat 1

data_processing:
All ATAC-seq, CUT&Tag seq and ChIP-seq samples were pooled and sequenced with a paired-end (2×150 bp) sequencing on an Illumina NovaSeq 6000 platform. All raw data was trimmed by Trimmomatic (v.0.39), aligned to the reference genome hg38 and gene annotations from GENCODE.vM20 of Homo Sapiens, by using the STAR (v.2.7.7a) software with default settings. All RNA-seq samples were pooled and sequenced with a paired-end (2×150 bp) sequencing on an Illumina NovaSeq 6000 platform. All raw data was trimmed by Trimmomatic (v.0.39) and aligned to the reference genome hg38 using bowtie2 (v.2.4.2)
Peaks of H3K27me3, H3K9me3, H3K36me3, H3K36me2 and H2AK119ub samples were detected using SICER software (v.1.0) (https://github.com/dariober/SICERpy) with false discovery rate (FDR) cut-off of 0.01, window size of 200bp and gap size of 600bp. Peaks of H3K4me3, H3K4me1, H3K27ac, H3.3, EZH2, SUZ12 and RING1B samples were detected using MACS2 software (v.2.2.7.1) with P value cut-off of 0.01. BigWig files and counting matrices in bins around peak summits were produced using bedtools (v.2.29.2) and bedGraphToBigWig (v.4) for visualization. DiffBind R package (v.3.0) was used to filter differential peaks between WT and MCM2-2A samples, with P value cut-off of 0.01 and absolute log2(fold change) > 1. Principal component analysis of samples was implemented in R (v.4.03) and 3d-PCA plots were visualized by rgl R package (0.105.13). Homer suite (v.2.0) was used for peak annotations.
Single-cell RNA sequencing was implemented on an Illumina NovaSeq 6000 platform. Raw data was processed by Kallisto-bustools workflow (v.0.46.0), including steps of associating reads with cells, collapsing reads based on unique molecular identifiers (UMIs), and generating gene counts in cells. For data quality control, genes detected in less than three cells and cells with less than 200 genes captured were removed. Furthermore, cells with extremely high (> 8000) or low (< 2000) numbers of detected UMIs and cells with more than 5 % mitochondrial gene expressions were filtered out to avoid multiplets, broken droplets and apoptosis influences. After quality control, data was imported into Seurat (v.4.0.3)
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
Assembly: hg38
Supplementary files format and content: bigwig files were generated(ATAC-seq, CUT&Tag-seq, ChIP-seq and RNA-seq), and gz files are the outputs of kallisto workflow (scRNA-seq)
Library strategy: CUT&TAG

value: Anti-H3 Antibody (ab1791)


title: SH-SY5Y_sORF1

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

description: Gene expression after stable transfection of sORF1

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample.

source_name: SH-SY5Y stably transfected with sORF1

growth_protocol: Human neuroblastoma cell line SH-SY5Y was grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The sORF1 expression or empty vectors were transfected into tumor cells, and stable cell lines were screened by administration of puromycin.

value: neuroblastoma

tag: passages


title: MCM2-2A H3.3 D0 ESC CUT&Tag repeat 2

tag: cell type


title: WT T47D H3.3 CUT&Tag repeat 1

tag: media


title: A10_REi7A2


title: A11_REi7A3


title: WT H3.3 D0 ESC CUT&Tag repeat 1


title: WT H3.3 D0 ESC CUT&Tag repeat 2


title: MCM2-2A H3.3 D0 ESC CUT&Tag repeat 1


title: A8_RCj13A4


title: MCM2-2A H3K27me3 D0 ESC CUT&Tag related to scCUT&Tag repeat 3

value: Anti-H3K27me3 Antibody (CST_9733)


title: MCM2-90A T47D H3K27me3 CUT&Tag repeat 1


title: MCM2-2A H3K27me3 D0 ESC CUT&Tag related to scCUT&Tag repeat 2


title: Perthes' disease Rabbit, replicate 1 [TB-1]


title: WT H3K27me3 D0 ESC CUT&Tag related to scCUT&Tag


title: A9_REi7A1


title: WT T47D H3K27me3 CUT&Tag repeat 1


title: SH-SY5Y_mock empty vector

description: Gene expression after stable transfection of empty vector

source_name: SH-SY5Y stably transfected with empty vector


title: WT T47D H3K27me3 CUT&Tag repeat 2


title: MCM2-90A T47D H3K27me3 CUT&Tag repeat 2


title: MCM2-90A T47D H3K4me3 CUT&Tag repeat 2

value: Anti-H3K4me3 Antibody (Active Motif_39159)


title: A5_RCj13A1


title: MCM2-2A (MCM2-AID) IAA H3K27me3 D0 ESC CUT&Tag 5d repeat 2


title: A6_RCj13A2


title: A4_RBK10A4


title: A2_RBK10A2


title: A3_RBK10A3


title: A1_RBK10A1


title: A7_RCj13A3


title: MCM2-2A (MCM2-AID) IAA H3K27me3 D0 ESC CUT&Tag 24h repeat 2


title: First RNAseq dataset: PR8-infected WT mouse #M2

city: Bethesda

first: Matthew

last: Chung

state: MD

address: 50 South Dr

institute: NIAID (National Institute of Allergy and Infectious Diseases)

data_processing:
For the RNA-seq dataset, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.7.3a) was used for the alignment. featureCounts in the subread package (v.1.5.1) was used for gene counting.
Assembly: GRCm38.99 and influenza A/Puerto Rico/8/34/Mount Sinai (H1N1) were used for RNA-seq
Supplementary files format and content: For the RNA-seq dataset, a tab-delimited text file containing the raw gene counts for all the samples was provided.

source_name: Lung

extract_protocol:
Whole lungs were homogenized in QIAzol. The total RNA was extracted using miRNeasy Mini Kit (Qiagen) with on-column DNA digestion using RNase-free DNase (Qiagen), followed by poly(A) mRNA enrichment.
The enriched poly(A) mRNAs were subject to RNA-seq library preparatin with NEBNext Ultra II RNA library prep kit for Illumina following the manufacturer’s protocol.

value: Lung

tag: mouse strain

value: PR8-only infection


title: MCM2-2A (MCM2-AID) IAA H3K27me3 D0 ESC CUT&Tag 0h repeat 2


title: First RNAseq dataset: PR8-infected WT mouse #M1


title: WT (MCM2-AID) IAA H3K27me3 D0 ESC CUT&Tag 5d repeat 2


title: combination, biological replicate 2

city: Memphis

first: Gintvile

last: Valinciute

state: TN

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

description:
Gene expression from combination treated cells
4_combo_2

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix CEL files were GCRMA normalized1 and log2-transformed. Differentially expressed probesets due to treatment were identified using the empirical Bayes approach2 based on moderated t-statistics as implemented in the Bioconductor package limma3 accounting for paired samples. Probesets showing an over-additive effect for treatment combination were identified by testing the interaction effect between treatments. Gene set enrichment analysis was performed using the camera test4. In case a gene was represented by multiple probesets, the probeset with the strongest effect was selected for GSEA. p-values were adjusted for multiple testing using the Benjamini-Hochberg correction to control the false discovery rate. All analyses were performed with statistical software R 3.65.

source_name: HD-MB03 cells treated with combination

label_protocol: standard Affymetrix protocol

growth_protocol: RPMI medium, 37C, adherent

extract_protocol: RNA extracted with Qiagen RNA extraction kit according to manufacturer's instructions

treatment_protocol: Treated once with vehicle, 5 uM entnostat, 1 uM volasertib or their combination, collected after 6 hours

tag: timepoint

value: combination


title: First RNAseq dataset: PR8-infected WT mouse #F2


title: MCM2-2A 293T H3.3 CUT&Tag repeat 1


title: WT (MCM2-AID) IAA H3K27me3 D0 ESC CUT&Tag 24h repeat 2


title: WT T47D H3K4me3 CUT&Tag repeat 1


title: First RNAseq dataset: mock-infected WT mouse #M2

value: Mock infection


title: WT 293T H3.3 CUT&Tag repeat 1

value: DMEM


title: WT T47D H3K4me3 CUT&Tag repeat 2


title: Perthes' disease Rabbit, replicate 2 [TB-2]

value: femoral head


title: WT (MCM2-AID) IAA H3K27me3 D0 ESC CUT&Tag 0h repeat 2


title: volasertib, biological replicate 1

description:
Gene expression from volasertib treated cells
3_vola_1

source_name: HD-MB03 cells treated with volasertib

value: volasertib


title: volasertib, biological replicate 3

description:
Gene expression from volasertib treated cells
3_vola_3


title: MCM2-2A 293T H3K27me3 CUT&Tag repeat 2


title: volasertib, biological replicate 2

description:
Gene expression from volasertib treated cells
3_vola_2


title: First RNAseq dataset: mock-infected WT mouse #M1


title: combination, biological replicate 1

description:
Gene expression from combination treated cells
4_combo_1


title: MCM2-2A (MCM2-AID) IAA H3K27me3 D0 ESC CUT&Tag 5d repeat 1


title: First RNAseq dataset: mock-infected WT mouse #F2


title: combination, biological replicate 3

description:
Gene expression from combination treated cells
4_combo_3


title: MCM2-2A (MCM2-AID) IAA H3K27me3 D0 ESC CUT&Tag 24h repeat 1


title: MCM2-2A 293T H3K27me3 CUT&Tag repeat 1


title: First RNAseq dataset: mock-infected WT mouse #F1


title: WT 293T H3K27me3 CUT&Tag repeat 2


title: MCM2-90A T47D H3K4me3 CUT&Tag repeat 1


title: First RNAseq dataset: DI244-treated WT mouse #M2

value: DI244 co-treatment


title: WT 293T H3K27me3 CUT&Tag repeat 1


title: MCM2-2A 293T H3K4me3 CUT&Tag repeat 2


title: First RNAseq dataset: DI244-treated WT mouse #M1


title: MCM2-2A (MCM2-AID) IAA H3K27me3 D0 ESC CUT&Tag 0h repeat 1


title: WT (MCM2-AID) IAA H3K27me3 D0 ESC CUT&Tag 5d repeat 1


title: entinostat, biological replicate 3

description:
Gene expression from entinostat treated cells
2_ms275_3

source_name: HD-MB03 cells treated with entinostat

value: entinostat


title: MCM2-2A 293T H3K4me3 CUT&Tag repeat 1


title: First RNAseq dataset: DI244-treated WT mouse #F2


title: 4_xlg_24h rep3

data_processing:
1-4: STAR for genome mapping
Assembly: Arabidopisis: TAIR10; Marantia v3.1, v5.1; Rice: IRGSP 1.0
Supplementary files format and content: 1-4: raw counts

organism: Oryza sativa Japonica Group

source_name: Seedlings

value: Seedlings

tag: age


title: First RNAseq dataset: DI244-treated WT mouse #F1


title: WT (MCM2-AID) IAA H3K27me3 D0 ESC CUT&Tag 24h repeat 1

value: D0 ESC


title: WT 293T H3K4me3 CUT&Tag repeat 2

tag: cell line

value: WT


title: 4_xlg_24h rep2


title: WT (MCM2-AID) IAA H3K27me3 D0 ESC CUT&Tag 0h repeat 1

value: DMEM/F12 _serum


title: entinostat, biological replicate 1

description:
Gene expression from entinostat treated cells
2_ms275_1


title: WT 293T H3K4me3 CUT&Tag repeat 1


title: First RNAseq dataset: DI222-treated WT mouse #M2

value: DI222 co-treatment


title: HIRA-/- H3K27me3 D0 ESC CUT&Tag repeat 1


title: HIRA-/-; MCM2-2A H3K27me3 D0 ESC CUT&Tag repeat 1


title: 4_xlg_24h rep1


title: vehicle, biological replicate 2

description:
Gene expression from vehicle treated cells
1_dmso_2

source_name: HD-MB03 cells treated with vehicle

value: vehicle


title: entinostat, biological replicate 2

description:
Gene expression from entinostat treated cells
2_ms275_2


title: vehicle, biological replicate 1

description:
Gene expression from vehicle treated cells
1_dmso_1


title: GCN1_8h_C

city: Martinsried/Planegg

first: Martin

last: Mueller

address: Am Klopferspitz 18

institute: MPI of Biochemistry

data_processing:
Sequencing reads were demultiplexed and trimmed using a custom awk script. Barcodes used for Ribo-seq - replicate A: ATCGT; replicate B: AGCTA
The UMI were extracted using UMI-tools using the option ‘--extract-method=regex --bc-pattern="^(?P<umi_1>.{2}).+(?P<umi_2>.{6})$"’, which serves to remove duplicated reads arising from library amplification. The clipped reads were then mapped against ncRNA/rRNA indices using Bowtie2 (v2.4.2) with the parameters ‘-N 1 -L 15’. Unaligned reads were mapped against the genome using STAR (v2.7.10a) with parameters ‘--outFilterMismatchNmax 2 --quantMode TranscriptomeSAM GeneCounts --outSAMattributes MD NH --outFilterMultimapNmax 1’. The P-site offset and metagene plots were computed using the R package “riboWaltz” (Lauria, 2018). Transcript enrichment was calculated with the R package “DESeq2” (Love, 2014) or “DEBrowser” (Kucukural, 2019).
Assembly: hg38 and WBcel235(ce11)
Supplementary files format and content: tab-delimited text file with raw counts or comma-delimited text file with half-lives and CPM

extract_protocol:
C. elegans  Synchronized nematodes were transferred to 1 l S-Basal and grown in liquid culturentil D1 of adulthood or until D6, when indicated. FUdR (200 µM) was added when the culture had reached the L4/young adult stage. After thorough washing in M9, the nematodes were frozen in lysis buffer (25 mM Hepes-KOH pH 7.4, 100 mM KoAC, 10 mM MglCl2, 0.5 mM DTT, 2x EDTA free protease inhibitor, 0.1 U/μL SUPERase*In, 100 μg/mL cycloheximide) by dropwise transfer into liquid nitrogen. The nematodes were lysed with a Retsch Cryomill MM400 at 30 Hz for 3 times 90 s with cooling between cycles. The lysate was cleared for 10 min at 20,000 x g and 4oC. Ribosome protected fragments (RPFs) were recovered, and libraries were prepared as previously described {McGlincy, 2017 #78}.  HEK293T cells  HEK293T cells were seeded into 15 cm plates 24 h prior to treatment. The cells were treated with 10 nM CC-885 and 20 μg/ml G418 for 4 h. Ribosome protected fragments (RPFs) were recovered, and libraries were prepared as previously described {McGlincy, 2017 #78}.
C. elegans  The procedure for immunoprecipitation (IP) of GCN-1 bound ribosomes was adapted from {Matsuo, 2021 #75}. Nematodes were synchronized by bleaching. L1 larvae were transferred to 1 L S-Basal. The animals were harvested at D1 of adulthood. Bacteria were removed by repeated washes in M9. In the last washing step, M9 was replaced by lysis buffer (25 mM Hepes-KOH pH 7.4, 100 mM KoAC, 10 mM MglCl2, 0.5 mM DTT, 2x EDTA free protease inhibitor, 0.1 U/μL SUPERase*In, 100 μg/mL cycloheximide). After a quick spin, the worms were flash frozen in liquid nitrogen. The frozen worms were lysed with a Retsch cryomill MM400 at 30 Hz as above. The lysate was thawed on ice and clarified by centrifugation at 4,000 x g for 10 min at 4oC. Protein concentration was determined by Bradford assay. The supernatant fraction (80 mg of total protein) was partially digested with 3 units per 1 mg RNA RNase I (Epicenter) at 4oC for 1 h. Ribosomes were pelleted through a sucrose cushion (1 M, 20 U/mL SUPERase*In (Invitrogen)) at 55.000 rpm in a SW 55 Ti rotor (Beckman Coulter) for 2 h at 4oC and resuspended in lysis buffer supplemented with 10% glycerol. The IP was performed at 4oC for 1 h using M2 anti-FLAG magnetic agarose beads (Invitrogen). The beads were washed 10 times with lysis buffer and bound material was digested with 12.5 units of RNase I (Epicenter) at 23oC for 45 min (strong RNase I treatment). Ribosome protected mRNA fragments were eluted by adding TRIzol reagent (Invitrogen). Libraries were prepared as previously described (McGlincy, 2017 #78) and sequenced on an Illumina NextSeq 500 system.  HEK293T cells  SLAM-seq was performed using the Lexogen SLAM-seq kinetics kit following the manufacturer's instructions.
Ribo-seq (disome) and mRNAseq (SLAMseq)

treatment_protocol: HEK293T cells were cultured in DMEM (Thermo Scientific, 11995073) supplemented with 10% FBS (Gibco, 10270106) at 5% CO2 and 37°C.

value: embryonic kidney

value: 100uM 4sU fed for 24h, then washed out for chase over 8h


title: First RNAseq dataset: DI222-treated WT mouse #M1

value: Lung


title: MCM2-2A H3K27me3 D0 ESC CUT&Tag repeat 4

last: gan

address: xueyuan lu 1068

institute: Shenzhen Institute of Advanced Technology

value: Anti-H3K27me3 Antibody (CST_9733)


title: vehicle, biological replicate 3

description:
Gene expression from vehicle treated cells
1_dmso_3


title: 4_xlg_2h rep3


title: WT H3K27me3 D0 ESC CUT&Tag repeat 4


title: GCN1_8h_B


title: 4_xlg_2h rep2


title: GCN1_8h_A


title: First RNAseq dataset: DI222-treated WT mouse #F1


title: First RNAseq dataset: DI222-treated WT mouse #F2


title: POLE3-/- H3K27me3 D0 ESC CUT&Tag repeat 3


title: 4_xlg_2h rep1


title: First RNAseq dataset: PR8-infected IFNAR-/- mouse #M2

value: IFNAR-/-

value: PR8-only infection


title: GCN1_4h_C


title: GCN1_4h_B


title: POLE3-/- H3K27me3 D0 ESC CUT&Tag repeat 2


title: First RNAseq dataset: PR8-infected IFNAR-/- mouse #M1


title: 4_xlg_0h rep2


title: 4_xlg_0h rep3


title: POLE3-/- H3K27me3 D0 ESC CUT&Tag repeat 1


title: GCN1_4h_A


title: First RNAseq dataset: PR8-infected IFNAR-/- mouse #F2


title: GCN1_2h_C


title: First RNAseq dataset: PR8-infected IFNAR-/- mouse #F1


title: GCN1_2h_B


title: First RNAseq dataset: mock-infected IFNAR-/- mouse #M2

value: Mock infection


title: 4_nb_24h rep2

value: NB, WT


title: LT-HSC, WT-1-2nd

first: Shaoqin

last: Rong

address: 138 Yi Xue Yuan Road

institute: Fudan University

description:
WT-1-LT
4LT_counts.txt

data_processing:
For RNA data, the raw data were trimmed by Trim Galore (v0.6.7) with default settings.
Then, the clean RNA-seq FASTQ data were mapped to mm10 using Hisat2 (v7.5.0) with default parameters.
DEG analysis was performed by using DESeq2 package with the raw count. Only genes with padj less than 0.05 and at least 2-fold-change were considered to be differentially expressed.
Assembly: mm9
Supplementary files format and content: raw count

source_name: Bone marrow

extract_protocol:
Different populations of hematopoietic stem/progenitor cells (LT-HSC, ST-HSC, CMP, GMP, MEP, CLP) from bone marrow cells of different genotypes of mice (WT, Sting-KO, Tet2-KO, Tet2/Sting-dKO) were sorted by  FACS with a number of 200 cells. The sorted cells were lysed with the lysis buffer obtained by SMART-seq construction Kit (Cat. N712, Vazyme) immediately and followed the library construction protocol from the Kit to generate cell full length mRNA library.
RNA libraries of pre-malignant cells were constructed by Smart-seq2 protocol, Nat. Methods 10, 1096–1098 (2013). RNA libraries of mouse hematopoietic cells were constructed by kit (Vazyme, NR611)

value: Bone marrow

value: LT-HSC

value: Hematopoietic stem/progenitor cells


title: 4_nb_24h rep3

extract_protocol:
1-4: Plant samples were frozen in liquid nitrogen, and followed by RNA extraction using Rneasy Plant Mini Kit (Qiagen)
1-4: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Seedlings


title: 4_xlg_0h rep1


title: GCN1_2h_A


title: LT-HSC, StingKO-3

description:
StingKO3-LT
4LT_counts.txt

value: Sting knockout


title: 4_nb_24h rep1


title: GCN1_0h_C


title: First RNAseq dataset: mock-infected IFNAR-/- mouse #F2


title: LT-HSC, StingKO-2

description:
StingKO2-LT
4LT_counts.txt


title: MCM2-2A H3K27me3 D0 ESC CUT&Tag related to scCUT&Tag repeat 1

first: haiyun

value: D0 ESC


title: 4_nb_2h rep3


title: GCN1_0h_B


title: First RNAseq dataset: mock-infected IFNAR-/- mouse #F1


title: 4_nb_2h rep2


title: LT-HSC, StingKO-1

description:
StingKO1-LT
4LT_counts.txt


title: GCN1_0h_A


title: LT-HSC, DKO-3

description:
DKO3-LT
4LT_counts.txt

value: Tet2/Sting double knockout


title: LT-HSC, WT-3-2nd

description:
WT-3-LT
4LT_counts.txt

value: WT


title: LT-HSC, WT-2-2nd

description:
WT-2-LT
4LT_counts.txt


title: 4_nb_2h rep1


title: First RNAseq dataset: DI244-treated IFNAR-/- mouse #M1

value: DI244 co-treatment


title: WT_8h_C

value: embryonic kidney


title: First RNAseq dataset: DI244-treated IFNAR-/- mouse #M2


title: LT-HSC, DKO-2

description:
DKO2-LT
4LT_counts.txt


title: WT_8h_B

value: 100uM 4sU fed for 24h, then washed out for chase over 8h


title: 4_nb_0h rep3


title: First RNAseq dataset: DI244-treated IFNAR-/- mouse #F2

value: Lung


title: 4_nb_0h rep2


title: First RNAseq dataset: mock-infected IFNAR-/- mouse #M1


title: LT-HSC, DKO-1

description:
DKO1-LT
4LT_counts.txt


title: First RNAseq dataset: DI244-treated IFNAR-/- mouse #F1


title: WT_8h_A


title: 4_nb_0h rep1


title: MEP, KO5

description:
T2KO5-MEP
TET2_project_counts.csv

value: MEP

value: Tet2 knockout


title: First RNAseq dataset: DI222-treated IFNAR-/- mouse #M1

value: IFNAR-/-

value: DI222 co-treatment