title: C7H8_Ctrl_Rep3

description:
Library name: iXist-chrX_DMSO_Rep3
RNA type: Chromatin-associated RNA (ChrRNA)

data_processing:
The ChrRNA-seq data mapping pipeline used in this study was similar to our previous work (Pintacuda et al 2017; Nesterova et al 2019). Briefly, the raw fastq files of read pairs were first mapped to an rRNA build by bowtie2 and rRNA-mapped reads discarded. The remaining unmapped reads were aligned to the ‘N-masked’ genome (mm10) with STAR using parameters (--twopassMode Basic --outSAMstrandField intronMotif --outFilterMismatchNoverReadLmax 0.06 --outFilterMultimapNmax 1 --alignEndsType EndToEnd) for all the sequencing libraries. Unique alignments were retained for further analysis. We made use of SNPs between Cast and 129S genomes and employed SNPsplit (v0.4.0dev, Babraham Institute, Cambridge, UK) to split the alignment into distinct alleles (Cast and 129S) using the parameter “--paired”. The (allelic) read numbers were counted by the program featureCounts (-t transcript -g gene_id -s 2) and the alignments were sorted by Samtools. Files of bigWig were generated by Bedtools and visualized by IGV or UCSC Genome Browser. Metagene profile and heatmap were generated by deepTools, as well as custom python scripts. For biallelic analysis, counts were normalized to 1 million mapped read pairs (as CPM) by the R package of edgeR. Genes with at least 10 SNP-covering reads across all the samples were further taken to calculate the allelic ratio of Xi/(Xi+Xa) where Xi and Xa indicate inactive and active allele, respectively. Principal components analysis (PCA) was done using the prcomp function in R and plotted using the ggplot2 package. Allelic ratio of samples derived from SPEN KO or deletion of Xist B/C-repeat were taken from the previous studies, gene categories including initial X-linked gene expression level and promoter chromatin landscape were taken from Nesterova et al, 2019 and Pintacuda et al 2017, gene silencing kinetics data were taken from Bowness et al, 2022.
Assembly: mm10
Supplementary files format and content: text file with allelic ratio called for each X-linked genes (note: replicate3 was performed together with METTL3i 20uM and 30uM)
Supplementary files format and content: text file with gene expression value for each X-linked genes (note: replicate3 was performed together with METTL3i 20uM and 30uM)

growth_protocol: ES cells were grown in DMEM media supplemented with 10% Fetal Calf Serum (ThermoFisher), 0.1mM non-essential amino acids, 2mM L-glutamine, 50μM β-mercaptoethanol, 100 U/ml Penicillin/100 μg/ml Streptomycin (all from Life Technologies) and 1000U/mL Leukemia Inhibitory Factor (LIF) (made in-house). Mitomycin-inactivated mouse fibroblasts were used as feeders. All ES cells were grown in feeder-dependent conditions on gelatinised plates at 37°C with 5% CO2.

extract_protocol:
Chromatin RNA was extracted from one confluent T25 plates of mESCs. Briefly, cells were trypsinised and washed in PBS. Cells were lysed on ice in RLB (10 mM Tris pH 7.5, 10 mM KCl, 1.5 mM MgCl2, and 0.1% NP40), and nuclei were purified by centrifugation through a sucrose cushion (24% sucrose in RLB). The nuclei pellet was resuspended in NUN1 (20 mM Tris pH 7.5, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol), then lysed with NUN2 (20 mM Hepes pH 7.9, 300 mM, 7.5 mM MgCl2, 0.2 mM EDTA, 1 M Urea). Samples were incubated for 15 minutes on ice then centrifuged at 2800 g to isolate the insoluble chromatin fraction. The chromatin pellet was resuspended in TRIzol by passing multiple times through a 23 gauge needle. Finally chromatin-associated RNA was purified through standard TRIzol/chloroform extraction followed by isopropanol precipitation. Samples were then treated with Turbo DNAse.
Approximal 100 - 500 ng of RNA was used for library preparation using the Illumina TruSeq stranded total RNA kit. Libraries were quantified by Qubit. The libraries were pooled and 2X 81 paired end sequencing was performed using Illumina NextSeq 500/550.

treatment_protocol: Inducible Xist expression was driven by a TetOn promoter induced by addition of 1.0 µg/mL of doxycycline for 24 hours.

value: DMSO 6 h, DMSO+Dox 24 h


title: Raw LPS rep2

status: Public on Jun 19 2025

type: SRA

city: Yayoi, Bunkyo-ku

first: Tomoatsu

last: Hayashi

state: Tokyo

country: Japan

institute: The University of Tokyo

library_source: transcriptomic

data_processing:
BAM-formatted map files were generated using STAR version 2.7.10a with default parameters.
The gene-level expression values (counts and TPM) were estimated by RSEM version 1.3.1 with default paramters.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw read counts per gene
Supplementary files format and content: tab-delimited text files include transcripts per kilobase million (TPM)

molecule: total RNA

organism: Mus musculus

source_name: Macrophage

growth_protocol: Raw-Blue (InvivoGen) mouse macrophage cells were cultured in DMEM supplemented with 10% FBS, 100 μg/ml Normocin (InvivoGen), 200 μg/ml Zeocin (InvivoGen), and Pen-Strep (100 U/ml) at 37°C in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted using RNA Clean & Concentrator (ZYMO RESEARCH) according to the manufacturer’s instructions.
Library construction, and sequencing (PE100) were performed by Beijing Genomic Institution (BGI, https://www.bgi.com/jp/home). The Raw data with adapter sequences or low-quality sequences was filtered using SOAPnuke software (BGI).

treatment_protocol: The cells were cultured in regular medium for an additional 24 hours. To assess the effect of ELNs, they were added to the medium at a final concentration of 1x10^10 particles/ml, and the cells were incubated for 16 hours. The cells were then stimulated with LPS (Wako) at a final concentration of 1 μg/ml for 24 hours to induce an inflammatory response.

tag: tissue

value: Macrophage

tag: cell line

value: RAW-Blue

tag: cell type

value: cultured cell

tag: treatment

value: LPS


title: C7H8_METTL3i-30uM

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

description:
Library name: iXist-chrX_METTL3i-30uM
RNA type: Chromatin-associated RNA (ChrRNA)

library_source: other

molecule: other

source_name: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

tag: strain background

value: Cast x 129S

value: mESC

tag: xist type

value: Endogenous Xist

value: METTL3i (STM2457; 30uM) 6 h,  METTL3i + Dox 24 h


title: C7H8_METTL3i-10uM_Rep2

description:
Library name: iXist-chrX_METTL3i-10uM_Rep2
RNA type: Chromatin-associated RNA (ChrRNA)

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: METTL3i (STM2457; 10uM) 6 h,  METTL3i + Dox 24 h


title: KD_3´IMP1_PBS_PeMPs_3

city: Leioa

first: Jimena

last: Baleriola

address: Science Park UPV/EHU. Sede Building, 3rd Floor

country: Spain

institute: Achucarro Basque Center for Neuroscience

description: Library name: S23

data_processing:
Reads were aligned to the rat refence genome (mRatBN7.2) using HISAT2 and differential localization to PeMPs was analyzed with DESeq2. Clustering of RNAs of interest was performed with Metascape and STRING.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited file includes normalized counts for each sample by Deseq2

organism: Rattus norvegicus

source_name: Primary cortical microglial culture

growth_protocol: Cortical microglial cells were isolated from mixed glial cultures. Briefly, brain hemispheres were dissected from postnatal Sprague Dawley rats (P0-P2) and dissociated with trypsin. Cultures were maintained at 37 oC in a 5% CO2 humidified incubator. For microglia isolation, 10-17 DIV mixed glial culture flasks were agitated at 180 rpm  for 4h at 37 oC. The medium was collected and centrifuged at room temperature for 6 minutes at 1200 rpm. Cells were resuspended in serum-free medium containing Neurobasal, 1X B-27 supplement and 2 mM L-glutamine. Microglia were seeded on Poly-D-lysine (PDL)-coated coverslips (40.000-80.000 cells/cm2), on 1- and 3-μm pore transwells (60.000-80.000 cells/cm2) or in 35 mm μ-Dish polymer coverslip bottom dishes (90.000-100.000 cells/cm2). Treatments were performed at 12-14 DIV or 19-21DIV.

extract_protocol:
Microglia were seeded on top of a 1 μm-pore membrane of a transwell system. Cells  were transfected with a control siRNA or an Imp1-targeting siRNA, and the lower compartment was then treated with vehicle or LPS. After removing the cell material  from the upper compartment with a cotton swab (see publication for details), total RNA from PeMPs was isolated using the Direct-zol RNA Miniprep kit following manufacturer instructions (ZYMO Research, Irvine, California, USA). RNA quality was addressed in a Bioanalyzer electrophoresis system (Agilent Technologies, Santa Clara, California, 1075 USA)
After removing rRNAs, 2 ng of RNA was used to prepare total RNA libraries with the SMARTer Stranded Total RNA-Seq Kit (v3, Takara Bio, Kusatsu, Japan).  Sequencing was performed in a NovaSeq 6000 instrument (paired-end, 2x 100 bp. Illumina, San Diego, California, USA)

treatment_protocol: Lipopolysaccharides from Escherichia coli (LPS, BioXtra, Sigma Aldrich) were added to 901 cells at 150 ng/ml for 30 minutes or 24 hours. PBS was used as vehicle control.    Imp1 genetic silencing was performed using small interference RNAs (siRNA) in serum-free medium in the absence of antibiotics. Double stranded siRNAs were transfected with lipofectamine RNA iMAX (Invitrogen, Thermo Fisher) following manufacturer recommendations. Cells were transfected for 6 or 24 hours with Imp1-targeting siRNAs.

value: Primary cortical microglial culture

tag: genotype

value: 24h PBS

tag: batch

value: paired-end


title: C7H8_METTL3i-20uM

description:
Library name: iXist-chrX_METTL3i-20uM
RNA type: Chromatin-associated RNA (ChrRNA)

value: METTL3i (STM2457; 20uM) 6 h,  METTL3i + Dox 24 h


title: KD_3´IMP1_LPS_PeMPs_3

description: Library name: S24

value: 24h LPS


title: KD_CTRL_LPS_PeMPs_3

description: Library name: S22


title: KD_CTRL_PBS_PeMPs_3

description: Library name: S21


title: C7H8_METTL3i-10uM_Rep1

description:
Library name: iXist-chrX_METTL3i-10uM_Rep1
RNA type: Chromatin-associated RNA (ChrRNA)


title: C7H8_Ctrl_Rep2

description:
Library name: iXist-chrX_DMSO_Rep2
RNA type: Chromatin-associated RNA (ChrRNA)


title: Raw None rep2


title: C7H8_Ctrl_Rep1

description:
Library name: iXist-chrX_DMSO_Rep1
RNA type: Chromatin-associated RNA (ChrRNA)


title: KD_3´IMP1_LPS_PeMPs_1

description: Library name: S16


title: KD_3´IMP1_PBS_PeMPs_1

description: Library name: S15


title: 9043G_liver_Niacin

city: Auburn University

first: Xu

last: Wang

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

country: USA

institute: Auburn University

data_processing:
FastQC (version 11.5) software was used for quality check.
Sequencing adapter sequences and low-quality bases were trimmed using Trimmomatic v0.36
On average, 98.18% of the remaining high0quality reads were mapped to the cattle reference genome (GenBank: GCA_002263795.2) by Tophat-2.1.1
Gene reads counts were performed in three software packages, Cufflinks-2.2.1, Bedtools -2.30.0, and HT-seq
DESeq2 packages in R were used to perform normalization and detect significant differentially expressed genes (DEGs) [23; 24], at an FDR (False Discovery Rate) cutoff of 0.05. The log2 fold change (LogFC) was determined for each gene. In addition, a volcano plot was generated using VolcaNoseR tool
Assembly: Cattle reference genome (GenBank: GCA_002263795.2)
Supplementary files format and content: Gzipped, tab-delimiited text file inlcuding raw gene counts for every gene in all samples

organism: Bos taurus

source_name: Bos taurus liver biopsy

extract_protocol:
The total RNA of liver samples was extracted using the ZYMO Quick DNA/RNA Miniprep Plus Kit (Zymo Research, CA). For homogenization, tissue samples with DNA/RNA Shield were mechanically homogenized by Qiagen TissueRuptor II (Qiagen, MD). RNA concentrations were measured by Qubit fluorometer 3.0 (Thermo Fisher Scientific, MA) with Qubit RNA BR Assay Kit.
RNA sequencing libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, MA) and NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, MA), with a 1500 ng total RNA input. The concentrations and the size distribution of the libraries were checked by the LabChip GX Touch HT machine using the HT DNA NGS 3K Assay (Perkin Elmer, MA). The fragment size of final libraries ranged from 343 to 409 bp. The libraries were individually barcoded and pooled. The libraries were sequenced on an Illumina NovaSeq 6000 sequencing machine to generate 150-bp paired-end reads

treatment_protocol: The diet offered was ad libitum Bermudagrass hay combined with a nutritional supplement composed of 1.61 kg of endophyte-free tall fescue seeds, and 1.61 kg of pellets composed of 46.5% ground corn, 46.5% soybean meal, 5% wheat middlings, and 2% soybean oil; and 0.1 kg of molasses per animal per day. Rumen-protected niacin was only administered for the treatment group,

tag: breed

value: Angus x Simmental

value: liver

tag: agent

value: Niacin


title: ZFC3H1_FKBP12^F36V, 11A clone, Dox 24h

description: RNA type: Chromatin-associated RNA (ChrRNA)

data_processing:
The ChrRNA-seq data mapping pipeline used in this study was similar to our previous work (Pintacuda et al 2017; Nesterova et al 2019). Briefly, the raw fastq files of read pairs were first mapped to an rRNA build by bowtie2 and rRNA-mapped reads discarded. The remaining unmapped reads were aligned to the ‘N-masked’ genome (mm10) with STAR using parameters (--twopassMode Basic --outSAMstrandField intronMotif --outFilterMismatchNoverReadLmax 0.06 --outFilterMultimapNmax 1 --alignEndsType EndToEnd) for all the sequencing libraries. Unique alignments were retained for further analysis. We made use of 23,005,850 SNPs between Cast and 129S genomes and employed SNPsplit (v0.4.0dev, Babraham Institute, Cambridge, UK) to split the alignment into distinct alleles (Cast and 129S) using the parameter “--paired”. The (allelic) read numbers were counted by the program featureCounts (-t transcript -g gene_id -s 2) and the alignments were sorted by Samtools. Files of bigWig were generated by Bedtools and visualized by IGV or UCSC Genome Browser. Metagene profile and heatmap were generated by deepTools, as well as custom python scripts. For biallelic analysis, counts were normalized to 1 million mapped read pairs (as CPM) by the R package of edgeR. Genes with at least 10 SNP-covering reads across all the samples were further taken to calculate the allelic ratio of Xi/(Xi+Xa) where Xi and Xa indicate inactive and active allele, respectively. Principal components analysis (PCA) was done using the prcomp function in R and plotted using the ggplot2 package. Allelic ratio of samples derived from SPEN KO or deletion of Xist B/C-repeat were taken from the previous studies, gene categories including initial X-linked gene expression level and promoter chromatin landscape were taken from Nesterova et al, 2019 and Pintacuda et al 2017, gene silencing kinetics data were taken from Bowness et al, 2022.
Assembly: mm10
Supplementary files format and content: text file, with allelic ratio called for each X-linked genes
Library strategy: ChrRNA-seq

growth_protocol: ES cells were grown in DMEM media supplemented with 10% fetal calf serum (Seralab), 2 mM L-glutamine, 1X non-essential amino acids, 50 µM β-mercaptoethanol, 1X penicillin / streptomycin (all from Life Technologies) and 1000 U/mL LIF (made in-house). Mitomycin-inactivated mouse fibroblasts were used as feeders. All ES cells were grown in feeder-dependent conditions on gelatinised plates at 37°C with 5% CO2.

extract_protocol:
Chromatin RNA was extracted from one confluent T25 plates of mESCs. Briefly, cells were trypsinised and washed in PBS. Cells were lysed on ice in RLB (10 mM Tris pH 7.5, 10 mM KCl, 1.5 mM MgCl2, and 0.1% NP40), and nuclei were purified by centrifugation through a sucrose cushion (24% sucrose in RLB). The nuclei pellet was resuspended in NUN1 (20 mM Tris pH 7.5, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol), then lysed with NUN2 (20 mM Hepes pH 7.9, 300 mM, 7.5 mM MgCl2, 0.2 mM EDTA, 1 M Urea). Samples were incubated for 15 minutes on ice then centrifuged at 2800 g to isolate the insoluble chromatin fraction. The chromatin pellet was resuspended in TRIzol by passing multiple times through a 23 gauge needle. Finally chromatin-associated RNA was purified through standard TRIzol/chloroform extraction followed by isopropanol precipitation. Samples were then treated with Turbo DNAse.
Approximal 200 - 500 ng of RNA was used for library preparation using the Illumina TruSeq stranded total RNA kit. Libraries were quantified by qPCR with KAPA Library Quantification DNA standards (KAPA Biosystems). The libraries were pooled and 2X 81 paired end sequencing was performed using Illumina NextSeq 500/550.

treatment_protocol: Inducible Xist expression was driven by a TetOn promoter induced by addition of 1.0 µg/mL of doxycycline for 24 hours. Degron for protein of interest, i.e. METTL3, YTHDC1, ZCCHC8, ZFC3H1 in this study, are induced by dTAG-13 for two hours, which is sufficient to acute deplete the FKBP12^F36V fused protein.

value: Dox for 24 hours


title: KD_CTRL_LPS_PeMPs_1

description: Library name: S14


title: ZFC3H1_FKBP12^F36V, 11A clone, dTAG 2h + dTAGDox 24h

value: dTAG-13 for 2 hours, followed by dTAG-13 and Dox for 24 hours


title: ZFC3H1_FKBP12^F36V, 11A clone, dTAG 26h

value: dTAG-13 for 2 hours


title: KD_CTRL_PBS_PeMPs_1

description: Library name: S13


title: C3_Dox24h_m6AIP

description:
Library name: C3_Dox24h_m6AIP
RNA type: m6A-containing RNA

data_processing:
rm6A-seq and input raw fastq files were mapped to mm10 by STAR (v2.5.2b).
Sequencing reads were split into positive and negative strands, and bigwig files were generated accordingly. Ten million mapped reads / library was used to perform normalization in conventional MeRIP-seq analysis.
Assembly: mm10
Supplementary files format and content: Bigwig, normalised, strand-spefici

molecule: protein

growth_protocol: ES cells were grown in DMEM media supplemented with 10% Fetal Calf Serum (ThermoFisher), 0.1mM non-essential amino acids, 2mM L-glutamine, 50μM β-mercaptoethanol, 100 U/ml Penicillin/100 μg/ml Streptomycin (all from Life Technologies) and 1000U/mL Leukemia Inhibitory Factor (LIF) (made in-house). Mitomycin-inactivated mouse fibroblasts were used as feeders. All ES cells were grown in feeder-dependent conditions on gelatinised plates at 37°C with 5% CO2. Differentiating cells were grown in DMEM media supplemented with 10% Fetal Calf Serum (ThermoFisher), 0.1mM non-essential amino acids, 2mM L-glutamine, 50μM β-mercaptoethanol, 100 U/ml Penicillin/100 μg/ml Streptomycin (all from Life Technologies) and 1μg/ml doxycycline (Sigma). Differentiating cells were grown without feeders on gelatinised plates at 37°C with 5% CO2.

extract_protocol:
Total RNA was isolated, and m⁶A-containing RNA was immunoprecipitated using an anti-m⁶A antibody.
Approximal 100 - 500 ng of RNA was used for library preparation using the Illumina TruSeq stranded total RNA kit. Libraries were quantified by Qubit. The libraries were pooled and 2X 81 paired end sequencing was performed using Illumina NextSeq 500/550.

treatment_protocol: Inducible Xist expression was driven by a TetOn promoter induced by addition of 1.0 µg/mL of doxycycline for 24 hours. Cells were either treated with dTAG-13 for 24 hours or not (control).

value: Cast x 129S


title: ZFC3H1_FKBP12^F36V, 8H clone, dTAG 2h + dTAGDox 24h

value: mESC


title: CUT&Tag, peritoneal B1-a cell, male, FLAG

city: shanghai

first: Yong

last: Yu

address: 1239 Siping Road

department: School of Life Sciences and Technology

country: China

institute: Tongji University

library_source: genomic

data_processing:
We employed the nf-core/cutandrun (v3.2.2) bioinformatics analysis pipeline to analyze CUT&Tag data. To be specific, adapter and quality trimming were performed using TrimGalore (v0.6.6), and alignment of read to the target genome mm10 using Bowtie 2 (v2.4.4). The spike-in species used was E. coli. Peak calling was performed using SEACR (v1.3) tool, and peak annotation was conducted with ChIPseeker (v1.38.0) R package. The deepTools (v3.5.1) was utilized for fragment-based quality control and heatmap peak analysis. The bedGraph files were generated with BEDTools (v2.30.0), and bigWig coverage files were created using the bedGraphToBigWig program. All track files were visualized in IGV software (v2.16.2).
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: peritoneal B1-a cell

extract_protocol:
CUT&Tag (Vazyme, TD904)  assay was conducted following the manufacturer’s protocol. Briefly, B-1a cells were incubated with ConA Beads Pro at room temperature for 10 min. Rabbit anti-Bcl11a antibody (Abcam, #Ab191401, 1:200) was added and incubated with the cells overnight at 4°C, and further incubated with goat anti-Rabit IgG (H+L) secondary antibody (Vazyme, Ab208) at room temperature for 1 hour. After two cell washes, pA/G-Transposon Pro Enzyme was added and incubated with cells at 4°C for 1 h, followed by fragmentation with Mgcl2.
CUT&Tag libraries of sorted B-1a cells were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, TD904), and qualified by using a Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) and Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA). The libraries with different indices were multiplexed and loaded onto an Illumina HiSeq 4000 instrument following the manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was conducted using a 2 × 150 paired-end (PE) configuration. The antibodies used for CUT&Tag were rabbit anti-Bcl11a (Abcam, #Ab191401, 1:50), normal mouse IgG control (CST, 68860L, 1:50), and goat anti-Rabbit IgG (H+L) secondary antibody (Vazyme, Ab208)

value: peritoneal B1-a cell


title: ZFC3H1_FKBP12^F36V, 8H clone, Dox 24h

value: Endogenous Xist


title: ZFC3H1_FKBP12^F36V, 11A clone

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)


title: ZFC3H1_FKBP12^F36V, 8H clone, dTAG 26h


title: CUT&Tag, peritoneal B1-a cell, Female, FLAG


title: ZCCHC8_FKBP12^F36V, Z12H clone, dTAG 2h + dTAGDox 24h

source_name: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

value: Endogenous Xist + Bgl


title: Liver, PcAS GRiKO, 10 dpi, mouse 5

city: Leuven

first: Philippe

last: Van den Steen

address: Herestraat 49 Box 1044

country: Belgium

institute: KU Leuven

data_processing:
Quality control of raw reads was performed with FastQC v0.11.7.
Adapters were filtered with ea-utils fastq-mcf v1.05.
Splice-aware alignment was performed with HISAT2 against the reference genome mm10 using the default parameters.
Reads mapping to multiple loci in the reference genome were discarded.
Resulting BAM alignment files were handled with Samtools v1.5.
Quantification of reads per gene was performed with HT-seq Count v0.10.0, Python v2.7.14.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Liver

growth_protocol: Liver tissues were collected from uninfected and PcAS-infected WT and GRiKO C57BL/6 mice, at 10 dpi.

extract_protocol:
RNA was harvested using the RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit (LexoGen), following manufacturer's protocols.

value: Liver

tag: strain

value: GRiKO


title: Liver, PcAS GRiKO, 10 dpi, mouse 4


title: ZCCHC8_FKBP12^F36V, Z12H clone, Dox 24h

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)


title: Liver, PcAS GRiKO, 10 dpi, mouse 3


title: ZCCHC8_FKBP12^F36V, Z12H clone, dTAG 26h


title: ZCCHC8_FKBP12^F36V, Z12H clone


title: Liver, PcAS GRiKO, 10 dpi, mouse 2


title: Liver, PcAS GRiKO, 10 dpi, mouse 1


title: ZCCHC8_FKBP12^F36V, Z4F clone, dTAG 2h + dTAGDox 24h


title: Liver, PcAS WT, 10 dpi, mouse 4

value: WT


title: ZCCHC8_FKBP12^F36V, Z4F clone, Dox 24h


title: Liver, PcAS WT, 10 dpi, mouse 3


title: ZCCHC8_FKBP12^F36V, Z4F clone, dTAG 26h


title: Liver, PcAS WT, 10 dpi,mouse 2


title: ZCCHC8_FKBP12^F36V, Z4F clone


title: Liver, PcAS WT, 10 dpi, mouse 1


title: CKO, DDC, rep2

city: CINCINNATI

first: Soona

last: Shin

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: FT4
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using Cell Ranger software v5.0.1
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

molecule: polyA RNA

extract_protocol:
Nuclei were prepared from fresh-frozen mouse livers using the protocol published by Humpherys and Kirita (doi.org/10.1038/nmeth.4407; dx.doi.org/10.17504/protocols.io.nahdab6) with a modification: Addition of 50 µL of 4% paraformaldehyde to the homogenate after passing through a cell strainer (dx.doi.org/10.17504/protocols.io.bhpej5je).
The single-nucleus RNA sequencing (sNuc-seq) assay was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index), 10x Genomics). Briefly, nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate a gel bead-in-emulsion. The poly-A RNA from the cell lysate contained in every gel bead-in-emulsion was reverse transcribed to cDNA, adding an Illumina R1 primer sequence, unique molecular identifiers (UMIs), and the 10x Barcode. The barcoded cDNA was then cleaned up with Silane DynaBeads and amplified for 18 cycles. Full-length, barcoded cDNA was then enzymatically fragmented, sized-selected using SPRIselect reagent, adapter-ligated, and amplified for library construction. During library construction, Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and sample indexes were added. Libraries were pooled and sequenced on the NovaSeq 6000 using S4 flow cells with the following sequencing parameters: R1: 28 cycles, i7: 10 cycles, i5: 10 cycles, R2: 90 cycles.

tag: Sex

value: male

value: CKO

value: DDC 4 weeks

tag: age at_treatment_initation

value: 10-11 weeks


title: CKO, DDC, rep1

description:
Library name: FT1
10x Genomics


title: WT, DDC, rep2

description:
Library name: CT4
10x Genomics


title: YTHDC1_FKBP12^F36V, Y12H clone, dTAG 2h + dTAGDox 24h, Rep2


title: Liver, PcAS GRiKO, 10 dpi, mouse 6


title: Liver, CON GRiKO, 10 dpi, mouse 4


title: WT, DDC, rep1

description:
Library name: CT1
10x Genomics


title: ZFC3H1_FKBP12^F36V, 8H clone


title: YTHDC1_FKBP12^F36V, Y12H clone, Dox 24h, Rep2

value: Dox for 24 hours


title: RNA-seq, mESC-Pou5F1-lin-del, Clone7, LIF-2i

city: Edinburgh

first: Abdenour

last: Soufi

address: 5 Little France Drive

department: School of Biological Sciences

institute: University of Edinburgh

description: Library name: RNA-seq_mESC-Pou5F1-lin-del-CL7_LIF-2i

data_processing:
RNA-seq pair-end reads were aligned to the mouse genome MGSCv37 (mm9)  using STAR (v2.5.3a).
Reads were normalised to fcounts on mm9 gene annotaion (GTF) using featureCounts.
Assembly: MGSCv37 (mm9)
Supplementary files format and content: tab-delimited text file includes normalised counts (fcounts) for each Sample.

source_name: embryonic

growth_protocol: Mouse embryonic stem cells were grown on Glasgow's Minimum Essential Medium (GMEM) containing 1mM Sodium Pyruvate (Gibco #11360-039), 1mM glutamine (Gibco #25030-024), 10% FCS (Gibco #10270-106), penicillin-streptomycin solution (Gibco #10270-106), non-essential amino acids (Gibco #11140-035), 50mM 2-mercaptoethanol (Gibco #31350-010) supplemented with 100U/ml LIF. Under naive culture conditions (2i/LIF) the media was supplemented with 100U/ml LIF, 10mM of PD03 (PD0325901 StemCell Technologies #72182) and 10mM of CHIRON (CHIR99021 StemCell Technologies # #72052). The cells were maintained at 37C and 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared from 500 ng starting material and amplified for 8 cycles using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490), NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB E7770) and NEBNext Multiplex Oligos for Illumina (NEB E7600).

treatment_protocol: LIF or LIF-2i treatment

value: embryonic

value: mouse embryonic stem cells

value: Pou5F1lin-del mutant


title: RNA-seq, mESC-Pou5F1-lin-del, Clone3, LIF-2i

description: Library name: RNA-seq_mESC-Pou5F1-lin-del-CL3_LIF-2i


title: Liver, CON GRiKO, 10 dpi, mouse 3


title: RNA-seq, mESC-Pou5F1-lin-del, Clone7, LIF

description: Library name: RNA-seq_mESC-Pou5F1-lin-del-CL7_LIF

value: LIF


title: YTHDC1_FKBP12^F36V, Y12H clone, dTAG 26h, Rep2

value: Cast x 129S

value: mESC

value: dTAG-13 for 2 hours


title: RNA-seq, mESC-Pou5F1-lin-del, Clone3, LIF

description: Library name: RNA-seq_mESC-Pou5F1-lin-del-CL3_LIF


title: RNA-seq, mESC-Pou5F1-lin-del, Clone1, LIF-2i

description: Library name: RNA-seq_mESC-Pou5F1-lin-del-CL1_LIF-2i


title: RNA-seq, mESC-Pou5F1-lin-del, Clone1, LIF

description: Library name: RNA-seq_mESC-Pou5F1-lin-del-CL1_LIF


title: Liver, CON GRiKO, 10 dpi, mouse 2


title: YTHDC1_FKBP12^F36V, Y9F clone, dTAG 2h + dTAGDox 24h, Rep2

value: Endogenous Xist + Bgl

value: dTAG-13 for 2 hours, followed by dTAG-13 and Dox for 24 hours


title: Liver, CON GRiKO, 10 dpi, mouse 1

value: Liver

value: GRiKO


title: RNA-seq, mESC-WT, LIF

description: Library name: RNA-seq_mESC-WT_LIF

value: wildtype


title: Liver, CON WT, 10 dpi, mouse 4

value: WT


title: YTHDC1_FKBP12^F36V, Y9F clone, Dox 24h, Rep2

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)


title: ATAC-seq, mESC-WT, rep2

description: Library name: ATAC_mESC-WT_rep2

data_processing:
The contaminating ME sequences (CTGTCTCTTATACACATCT) were trimmed from the ATAC-seq reads with Cutadapt to prevent multimapping.
The ATAC-seq pair-end reads were mapped to the Mus musculus genome assembly MGSCv37 (mm9) using Bowtie (version 2.3.4.1) and very sensitive parameters.
Duplicated alignments were removed using Picard (https://broadinstitute.github.io/picard/).
ATAC-seq reads (bam files) from different replicates were merged and then normalised for sequencing coverage to 1x genome depth (reads per genome coverage, RPGC) using the bamCoverage tool from DeepTools and a bin size of 10 bp and extendReads parameters.
Assembly: MGSCv37 (mm9)
Supplementary files format and content: Bigwig files normalised for sequencing depth and merged replicates.

growth_protocol: Mouse embryonic stem cells were cultured in GMEM medium supplemented with 10% FCS, 1 mM sodium pyruvate (#11360-039; Gibco), 1 mM glutamine (#25030-024; Gibco), Non-Essential Amino Acids (#11140050; Gibco), and 50 µM 2-mercaptoethanol (#11528926; Gibco), supplemented with 100U/ml LIF and grown at 37°C and 5% CO2.

extract_protocol:
50,000 of freshly harvested cells were resuspended in ice-cold RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2). The suspension was centrifuged at 500xg for 3 min using a refrigerated centrifuge. The cell pellet was washed once with 50 μl ice-cold PBS and centrifuged at 500xg for 3 min at 4°C. The cell pellet was resuspended in ice-cold Lysis Buffer (48.5 μl RSB buffer supplemented with 0.5 μl of 10% NP-40, 0.5 μl of 10% Tween-20, 0.5 μl of 1% Digitonin) and kept on ice for 3 min. Then, 1 ml of wash buffer (RSB buffer supplemented with 0.1% Tween-20) was added on the lysed cells. Nuclei were pelleted at 500xg for 10 min at 4°C and the supernatant (cytoplasm fraction) was carefully discarded. The nuclei were resuspended in the transposition mix (25 μl of 2X Tagment DNA Buffer (Illumina, #20034197), 16.5 μl of 1X PBS, 0.5 μl 10% of Tween-20, 0.5 μl of 1% Digitonin, 5 μl nuclease-free H2O). Next, 2.5 μl of Tn5 Transposase (Illumina, #20034197) was added to the reaction mix by pipetting up and down 6 times. The reaction was then incubated at 37℃ for 30 minutes on a thermomixer at 1,000 rpm. Finally, the tagmented DNA was isolated using Qiagen MinElute Reaction Cleanup Kit (Qiagen, # 28204) following the manufacturer’s instructions.
ATAC-seq libraries were generated by PCR amplification using custom-made barcodes. Libraries were amplified with 7-10 cycles using NEBNext High-Fidelity 2X PCR Master Mix (NEB, #M0541S). To remove primer dimers and DNA fragments shorter than 150bp, libraries were purified with SpeedBeads beads. 1.8X volume of SpeedBeads beads (81 μl beads for 45 μl PCR reaction) was used to clean PCR amplified DNA library. The quality of the DNA libraries was assessed using Agilent HS DNA Screen Tape (Agilent. Santa Clara, CA). The concentration of the DNA libraries was measured by Qubit Fluorometric Quantitation. Equimolar DNA libraries were pooled to a final concentration of 2 nM. The ATAC-seq libraries were sequenced by Novagene (Novogene, UK) on Illumina HiSeq 6000 using pair-ends PE150 in biological duplicates (Illumina, San Diego, CA).


title: Liver, CON WT, 10 dpi, mouse 3


title: YTHDC1_FKBP12^F36V, Y9F clone, dTAG 26h, Rep2


title: ATAC-seq, mESC-WT, rep1

description: Library name: ATAC_mESC-WT_rep1


title: ATAC-seq, mESC-Pou5F1-lin-del, Clone7, rep2

description: Library name: ATAC_mESC-Pou5F1-lin-del_CL7_rep2


title: ATAC-seq, mESC-Pou5F1-lin-del, Clone7, rep1

description: Library name: ATAC_mESC-Pou5F1-lin-del_CL7_rep1


title: YTHDC1_FKBP12^F36V, Y12H clone, Rep2


title: Liver, CON WT, 10 di, mouse 2


title: YTHDC1_FKBP12^F36V, Y9F clone, Rep2


title: ATAC-seq, mESC-Pou5F1-lin-del, Clone1, rep1

description: Library name: ATAC_mESC-Pou5F1-lin-del_CL1_rep1


title: ATAC-seq, mESC-Pou5F1-lin-del, Clone1, rep2

description: Library name: ATAC_mESC-Pou5F1-lin-del_CL1_rep2


title: YTHDC1_FKBP12^F36V, Y12H clone, dTAG 2h + dTAGDox 24h


title: Liver, CON WT, 10 dpi, mouse 1


title: ATAC-seq, mESC-Pou5F1-lin-del, Clone3, rep2

description: Library name: ATAC_mESC-Pou5F1-lin-del_CL3_rep2


title: YTHDC1_FKBP12^F36V, Y12H clone, Dox 24h


title: ATAC-seq, mESC-Pou5F1-lin-del, Clone3, rep1

description: Library name: ATAC_mESC-Pou5F1-lin-del_CL3_rep1


title: RNA-seq, mESC-WT, LIF-2i

description: Library name: RNA-seq_mESC-WT_LIF-2i


title: K562_S24 46hr

city: Durham

first: Steven

middle: B

last: Haase

state: North Carolina

department: Biology

institute: Duke University

description: k562_timeseries - 46

data_processing:
Sequenced reads mapped to the respective yeast genome using STAR.
Transcripts were quantified in  Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using Cufflinks/Cuffnorm
These resulting TPM were combined into a single .tsv file containing all transcripts at all timepoints
This final .tsv file was z-score normalized and quantile normalized to produce the cleaned .tsv file
Assembly: Homo Sapiens Ensembl GRCh37 downloaded from Illumina iGenomes
Supplementary files format and content: Each dataset has a final raw .tsv file. Consisting of either FPKM/TPM transcript levels (see above) for each each for each timepoint
Supplementary files format and content: Each dataset has a final cleaned .tsv file. Consisting of the Z-score normalized and then quantile normalized  (z-score quantile normalized) data for each gene for each timepoint.

organism: Homo sapiens

growth_protocol: Cells were grown in RPMI + 10% BCS (bovine calf serum) + P/S.

extract_protocol:
Cells were removed at each time point and flash frozen on dry ice. RNA was harvested using standard yeast methods using  an acid phenol/chloroform protocol.
Illumina HiSeq 2500 protocols

treatment_protocol: synchronous populations were collected using centrifugal elutriation.

tag: time

value: 46 hours

tag: experimental conditions


title: YTHDC1_FKBP12^F36V, Y12H clone, dTAG 26h


title: GE3

city: Changchun

first: Jiapei

last: Cai

state: Jilin

address: Xi‘an Road 5333

institute: Jilin University

description: Library name: GE3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: ensembl107
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: endometrial epithelial cells

extract_protocol:
SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribeTM Reverse Transcriptase reaches the 5' end of the mRNA, the enzyme's terminal transferase activity adds a few additional nucleotides to the 3' end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5' end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.
cDNA was fragmented by dsDNA Fragmentase (NEB, M0348S) by incubate at 37°C for 30min. Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand, indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR. And then we performed the paired-end sequencing on an Illumina NovaseqTM 6000 at the (LC Sceiences, USA) following the vendor's recommended protocol.

value: endometrial epithelial cells

value: received galactose treatment


title: GE1

description: Library name: GE1


title: GE2

description: Library name: GE2


title: K562_S23 44hr

description: k562_timeseries - 44

value: 44 hours

value: RPMI + 10% BCS (bovine calf serum) + P/S


title: ECO3

description: Library name: ECO3

value: without galactose treatment


title: K562_S22 42hr

description: k562_timeseries - 42

value: 42 hours


title: YTHDC1_FKBP12^F36V, Y12H clone

value: Cast x 129S


title: ECO2

description: Library name: ECO2


title: AA cells, shERK5, Day 3

city: Albacete

first: Francisco

middle: J.

last: Cimas

state: Albacete

address: Almansa 14

institute: UCLM

description: Library name: AA_455_6

data_processing:
Sequencing data filtering was done using the filtering software SOAPnuke (Version v1.5.2, Parameters -l 15 -q 0.2 -n 0.05) developed by BGI. The specific steps are as follows: 1) Remove the reads containing the adaptor(adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" are saved in FASTQ format.
Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT) was used for mapping RNA-seq reads. HISAT2 Version：v2.0.4.  Parameters：--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF
We used Bowtie2  Version：v2.2.5 to map the clean reads to the reference gene sequence (transcriptome), and then used RSEM to calculate the gene expression level of each sample. Parameters：-q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
RSEM Version：v1.2.8 . Parameters：-p 8 --forward-prob 0 --paired-end
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: xls file including fkpm, tm, read count and normalised read count values for each sample

source_name: AA

growth_protocol: SK-UT-1 cell lines were  maintained at 37°C in a humidified atmosphere with 5% CO2 and cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% Fetal Bovine Serum (FBS), 1% L-glutamine 1% penicillin-streptomycin antibiotics, and 1% fungizone. AA cell line was cultured in Ham's Nutrient Mixture F10 with L-glutamine supplemented with 10% FBS, 1% penicillin-streptomycin antibiotics, and 1% fungizone

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen) and manufacturers instructions
1) mRNA enrichment and purification: Oligo dT Selection (mRNA enrichment): Use oligo dT beads to enrich mRNA with poly A tail. 2) RNA fragment and reverse transcription: Fragment the RNA and first-strand cDNA was generated using random N6-primed reverse transcription, followed by a second-strand cDNA synthesis with dUTP instead of dTTP. 3) End repair, add A and adaptor ligation: The synthesized cDNA was subjected to end-repair and then was 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 4) PCR amplification: Prior to PCR amplification, the dUTP-marked strand is selectively degraded by Uracil-DNA-Glycosylase(UDG). The remaining strand is amplified to generate a cDNA library suitable for sequencing. Many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer; 5) Single strand separation and cyclization: Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase; 6) DNA nanoball synthesis

value: AA

value: Leiomyosarcoma

value: ERK5 knockdown


title: K562_S21 40hr

description: k562_timeseries - 40

value: 40 hours


title: AA cells, shSCB, Day 3

description: Library name: AA_EV_5


title: YTHDC1_FKBP12^F36V, Y9F clone, dTAG 2h + dTAGDox 24h

value: Endogenous Xist + Bgl

value: mESC

value: dTAG-13 for 2 hours, followed by dTAG-13 and Dox for 24 hours


title: K562_S20 38hr

description: k562_timeseries - 38

value: 38 hours


title: ECO1

description: Library name: ECO1


title: YTHDC1_FKBP12^F36V, Y9F clone, Dox 24h

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

value: Dox for 24 hours


title: AA cells, shERK5, Day 2

description: Library name: AA_455_4


title: AA cells, shSCB, Day 2

description: Library name: AA_EV_3

value: WT


title: KO, B1-a cell, 3month, Female, rep2

description:
raw_gene_counts.tsv.gz
raw_gene_tpm.tsv.gz

data_processing:
We employed the nf-core/rnaseq (v 3.12.0) pipeline to analyze RNA sequencing data. Specifically, FASTQ files were initially trimmed to remove adapters using TrimGalore (v0.6.7). Reads were aligned to the mouse reference genome (mm10 assembly) with STAR (v2.7.10a) and subsequently quantified with RSEM (v1.3.1). Differential gene expression was calculated using the default parameters of the RNAseqStat (v0.1.0) R package, with output derived from the DESeq2 algorithm.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample

extract_protocol:
5000 B-1a cell were isolated into lysis buffer,then  the process involves the following steps: Reverse transcription of RNA into cDNA; Amplify and purify the cDNA ; two replicates of each sample were done. 5000 cells analysed per experiment.
Low-input libraries were constructed using the Smart-seq2 method(Picelli S, Faridani OR, Bjorklund AK, Winberg G, Sagasser S, Sandberg R. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9, 171-695 181 (2014))

tag: age

value: female

value: peritoneal B1-a cell

value: KO

value: PBS


title: YTHDC1_FKBP12^F36V, Y9F clone, dTAG 26h

value: dTAG-13 for 2 hours


title: K562_S19 36hr

description: k562_timeseries - 36

value: 36 hours

value: RPMI + 10% BCS (bovine calf serum) + P/S


title: KO, B1-a cell, 3month, Female, rep1


title: K562_S18 34hr

description: k562_timeseries - 34

value: 34 hours


title: KO, B1-a cell, 24month, Female, rep2


title: YTHDC1_FKBP12^F36V, Y9F clone

value: Cast x 129S


title: KO, B1-a cell, 24month, Female, rep1


title: K562_S16 30hr

description: k562_timeseries - 30

value: 30 hours


title: SK-UT-1 cells, shERK5, Day 3

description: Library name: SKUT1_455_6

value: Leiomyosarcoma

value: ERK5 knockdown


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, D395A_9F clone, XiO, dTAG 2h + dTAGDox 24h, Rep2

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: Endogenous Xist

value: mESC

value: dTAG-13 for 2 hours, followed by dTAG-13 and Dox for 24 hours


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, D395A_9F clone, XiO, Dox 24h, Rep2

value: Dox for 24 hours


title: AA cells, shSCB, Day 1

description: Library name: AA_EV_1

value: AA

value: WT


title: AA cells, shERK5, Day 1

description: Library name: AA_455_2


title: K562_S15 28hr

description: k562_timeseries - 28

value: 28 hours


title: SK-UT-1 cells, shSCB, Day 3

description: Library name: SKUT1_EV_5


title: ATAC_seq_KO, old, Female, rep1

data_processing:
The nfcore/atacseq (v2.1.2) pipeline was utilized to analyze ATAC-seq data. in brief, raw reads underwent initial trimming to remove adapters using TrimGalore (v0.6.7) and then mapped to the mm10 mouse reference genome using BWA (v0.7.17). Mitochondrial DNA, blacklisted regions and duplicate reads marked by Picard (3.0.0) (https://github.com/broadinstitute/picard) were removed from Bam files using Samtools (v1.15.1). Normalized BigWig files for genomic track visualization were generated using deepTools (v3.5.1). Peak calling was performed using MACS2 (v2.2.7.1), and peak annotation was conducted with the `annotatePeak` function in ChIPseeker (v1.38.0). Motif analysis was performed using findMotifsGenome.pl program in HOMER (v4.11) with default settings. Differential peak calling was conducted using the DiffBind (v3.12.0).R package, with differential peaks exhibiting a P value < 0.05 considered significant.
Assembly: mm10
Supplementary files format and content: bigWig,narrowPeak

extract_protocol:
Briefly, the process involves the following steps: Collect and lyse cells to obtain purified nuclei; Carry out the Tn5 enzyme transposition reaction to fragment the open regions of chromatin; Purify the fragmented DNA; Select target fragments to do the amplification.
ATAC-seq was conducted following the protocol provided by 10K Genomics, Shanghai, China. Purified the above products using DNA Purification Kit (MN，740609). To determine PCR cycle number, take a small amount of the purified product and do a pre-amplification.After the pre-amplified bands were correct, then done formal amplification. After determining the yield and the band type, purified and constructed the library.Illumina NovaSeq 6000 sequencing platform was usually used, and PE150 sequencing mode was adopted.

value: KO

value: female

value: peritoneal B1-a cell

value: old

value: PBS


title: SK-UT-1 cells, shERK5, Day 2

description: Library name: SKUT1_455_4


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, D395A_9F clone, XiO, dTAG 26h, Rep2

value: Cast x 129S

value: dTAG-13 for 2 hours


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, D395A_9F clone, XiO, Rep2


title: K562_S13 24hr

description: k562_timeseries - 24

value: 24 hours

value: RPMI + 10% BCS (bovine calf serum) + P/S


title: ATAC_seq_KO, young, Female, rep2

value: young


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, D395A_9F clone, XiO, dTAG 2h + dTAGDox 24h

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: Endogenous Xist


title: K562_S12 22hr

description: k562_timeseries - 22

value: 22 hours


title: ATAC_seq_KO, young, Female, rep1


title: SK-UT-1 cells, shERK5, Day 1

description: Library name: SKUT1_455_2

value: Leiomyosarcoma

value: ERK5 knockdown


title: K562_S17 32hr

description: k562_timeseries - 32

value: 32 hours


title: ATAC_seq_KO, old, Male, rep2

value: male


title: SK-UT-1 cells, shSCB, Day 1

description: Library name: SKUT1_EV_1

value: WT


title: K562_S11 20hr

description: k562_timeseries - 20

value: 20 hours


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, D395A_9F clone, XiO, dTAG 26h

value: mESC


title: ATAC_seq_KO, old, Female, rep2

value: KO

value: female

value: peritoneal B1-a cell

value: old


title: ATAC_seq_KO, old, Male, rep1

value: PBS


title: K562_S10 18hr

description: k562_timeseries - 18

value: 18 hours

value: RPMI + 10% BCS (bovine calf serum) + P/S


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, D395A_9F clone, XiO

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)


title: K562_S14 26hr

description: k562_timeseries - 26

value: 26 hours


title: KO, B1-a cell, 26month, female

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, aggregation and BCR results were using the Cell Ranger software V6.0.1.
Assembly: mm10
Supplementary files format and content: Tab-delimited values files and matrix files

extract_protocol:
5000 B-1a cell were isolated into lysis buffer,then  the process involves the following steps: Reverse transcription of RNA into cDNA; Amplify and purify the cDNA; two replicates of each sample were done. 5000 cells analysed per experiment. Quality control and counting of single cell suspensions, generally requiring a cell viability of 85% or more, washed and resuspended to a suitable cell concentration of 700~1200 cells/µl, ready for uploading onto the 10x Genomics Chromium™ system.
Library was performed according to the manufacter’s instructions(single cell 3’ v2 protocol, 10x Genomics). The cDNA qualified by QC is subjected to second-generation sequencing library construction, and the library is finally subjected to quantitative QC after fragmentation, ligation of sequencing junctions, and sample Index PCR, and other experimental processes.


title: KO, B1-a cell, 15month, female

description: 10x Genomics


title: K562_S08 14hr

description: k562_timeseries - 14

value: 14 hours


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, WT_1A clone, XiO, dTAG 2h + dTAGDox 24h, Rep2

value: Endogenous Xist

value: dTAG-13 for 2 hours, followed by dTAG-13 and Dox for 24 hours


title: donor1, refrozen PBMC in trizol

city: Gent

first: Eufra

last: Van Damme

address: Technologiepark 75

department: CMB

institute: VIB-UGent

description:
Library name: trizol1
columnname in estcounts_gene_names.csv : trizol1_estcounts

data_processing:
Pseudo-alignment and transcript quantification was obtained by Kallisto13 (version 0.48.0) using a GRCh38 Ensembl v 100 index.
To achieve a uniform sequencing depth for all samples, allowing a fair comparison, random subsampling was performed using setqk (version 1.4) and adjusted to the minimum read count (18 million).
Assembly: GRCh38
Supplementary files format and content: tsv files included counts per sample
Supplementary files format and content: csv file is a summary is all samples together

source_name: PBMC

extract_protocol:
miRNeasy Mini kit (Qiagen)
TruSeq mRNA protocol (Illumina)

value: PBMC

value: refreezing in trizol


title: KO, B1-a cell,  2month, female

description: 10x Genomics


title: donor3, refrozen PBMC in FM

description:
Library name: FM3
columnname in estcounts_gene_names.csv : FM3_estcounts

value: refreezing FM


title: donor2, refrozen PBMC in trizol

description:
Library name: trizol2
columnname in estcounts_gene_names.csv : trizol2_estcounts


title: K562_S07 12hr

description: k562_timeseries - 12

value: 12 hours


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, WT_1A clone, XiO, dTAG 26h, Rep2

description: RNA type: Chromatin-associated RNA (ChrRNA)

value: mESC

value: dTAG-13 for 2 hours


title: SK-UT-1 cells, shSCB, Day 2

description: Library name: SKUT1_EV_3

value: Leiomyosarcoma

value: WT


title: WT, B1-a cell, 26month, female

description: 10x Genomics

value: female

value: peritoneal B1-a cell

value: PBS


title: K562_S06 10hr

description: k562_timeseries - 10

value: 10 hours

value: RPMI + 10% BCS (bovine calf serum) + P/S


title: donor2, refrozen PBMC in FM

description:
Library name: FM2
columnname in estcounts_gene_names.csv : FM2_estcounts


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, D395A_9F clone, XiO, Dox 24h,

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: Dox for 24 hours


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, WT_1A clone, XiO, Rep2

value: Endogenous Xist


title: donor1, refrozen PBMC in FM

description:
Library name: FM1
columnname in estcounts_gene_names.csv : FM1_estcounts

value: PBMC


title: WT, B1-a cell, 15month, female

description: 10x Genomics


title: K562_S05 8hr

description: k562_timeseries - 8

value: 8 hours


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, WT_1A clone, XiO, dTAG 2h + dTAGDox 24h

value: dTAG-13 for 2 hours, followed by dTAG-13 and Dox for 24 hours


title: donor3, refrozen PBMC in trizol

description:
Library name: trizol3
columnname in estcounts_gene_names.csv : trizol3_estcounts

value: refreezing in trizol


title: WT, B1-a cell,  2month, female

description: 10x Genomics


title: donor3, 1x defrosted PBMC

description:
Library name: defrost3
columnname in estcounts_gene_names.csv : defrost3_estcounts

value: 1x defrosting


title: K562_S09 16hr

description: k562_timeseries - 16

value: 16 hours


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, WT_1A clone, XiO, Dox 24h,

value: mESC


title: donor2, 1x defrosted PBMC

description:
Library name: defrost2
columnname in estcounts_gene_names.csv : defrost2_estcounts


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, WT_1A clone, XiO, Dox 24h, Rep2


title: donor1, 1x defrosted PBMC

description:
Library name: defrost1
columnname in estcounts_gene_names.csv : defrost1_estcounts


title: K562_S03 4hr

description: k562_timeseries - 4

value: 4 hours


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, WT_1A clone, XiO


title: Evf1_2 WT rep1 HiC

city: Chicago

first: Jhumku

last: Kohtz

state: Illinois

address: 303 E Chicago

department: Neurology

institute: Northwestern University

description: HiC

data_processing:
HiC Data analysis: Adaptor sequences were removed from fastq files by trimming the first 5 base pairs from each read. The HiC-Pro pipeline (v3.1.0) was used to obtain the normalized contact maps with default parameters. Briefly, trimmed reads were mapped to the mouse mm9 reference genome using bowtie2 (v2.4.4) with min. mapping quality >= 10 and ‘--very sensitive’ local parameters. Valid pairs are then extracted from the BAM file, and the contact map is built considering the ligation sites ‘GATCGATC, GANTGATC, GANTANTC, GATCANTC’.  HiCLift was used to generate .hic files from the matrices. Loop analysis: Loops are defined as interactions between two anchors in the HiC map. Fithic 2.0 was used to identify significant loops at 20kb resolution. For stringency, we first filtered loops with FDR<=0.01 and Contact Count>=5 and then kept only significant loops that were found in both replicates. Bedtools v2.30.0 ‘pairtopair’ command was used for all overlaps.HiCPro:Servant N., Varoquaux N., Lajoie BR., Viara E., Chen CJ., Vert JP., Dekker J., Heard E., Barillot E. HiC-Pro: An optimized and flexible pipeline for Hi-C processing. Genome Biology 2015, 16:259 doi:10.1186/s13059-015-0831-x, Bowtie2: Langmead, B., Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357–359 (2012). https://doi.org/10.1038/nmeth.1923, Hiclift: Wang, X., Yue, F. HiCLift: A fast and efficient tool for converting chromatin interaction data between genome assemblies. Bioinformatics. 2023. Fithic 2: Arya Kaul, Sourya Bhattacharyya & Ferhat Ay 2020. "Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2." Nature Protocols. 15:991-1012, 2020. doi: 10.1038/s41596-019-0273-0., Ferhat Ay, Timothy L. Bailey, William S. Noble. 2014. "Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts." Genome Research. 24(6):999-1011, 2014. doi: 10.1101/gr.160374.113., Bedtools: Aaron R. Quinlan, Ira M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, Volume 26, Issue 6, March 2010, Pages 841–842, https://doi.org/10.1093/bioinformatics/btq033
Supplementary files format and content: 2_evf1_2plspls.hic: Visualization of HiC loops in wildtype E13.5GE chromatin (rep1)
Supplementary files format and content: 4_evf1_2plspls.hic: Visualization of HiC loops in wildtype E13.5GE chromatin (rep2)
Supplementary files format and content: HiC_inter_intra_Evf1_2WT.xlsx: Lists intra-chromosomal and inter-chromosomal interactions sites in wildtype dual crosslinked chromatin (qval<0.01) across two biological replicates

source_name: Ventral forebrain

extract_protocol:
HiCseq: HiC was performed using the Arima-HiC kit (A510008), according to the manufacturers protocols with modifications as described previously (Lafontaine et al., 2021, Curr Protoc. 2021;1(7):e198. doi:10.1002/cpz1.198). 12-16 E13.5 ganglionic eminences were isolated from 6-8 mouse embryonic brains and dissociated in L15 media gently first with a 1000 µL tip and then with a 200 µL tip 10-15 times to create a single cell suspension. Cells were spun for 2.5 minutes at 1000 rpm and 4°C. The L15 was aspirated and cells were resuspended in 500 µL of ice-cold Nuclear Extraction Buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 20 mM Tris-HCl pH 8.0, 0.1% TritonX-100) and incubated on ice for 10 minutes. Nuclei were pelleted at 100 for 2.5 minutes at 4°C. Nuclei Extraction Buffer was removed and nuclei were resuspended in 1X PBS. Nuclei were fixed in 10 mL of PBS with 1% formaldehyde with rotation for 10 minutes at room temperature. Crosslinking was then quenched with glycine to a final concentration of 125 mM for 5 minutes at room temperature. Nuclei were washed with 1x PBS and pelleted for 15 minutes at 500g and 4°C. Nuclei were then crosslinked with fresh 3 mM DSG (disuccinimidyl glutarate) in PBS for 40 minutes with rotation at room temperature. Crosslinking was quenched with 0.4 M glycine for 5 minutes, and then washed with 1X PBS. The nuclei were flash frozen in liquid nitrogen. The input amount was estimated following the Arima-HiC instruction protocol.  Nuclei were processed according to the Arima-HiC protocol, briefly: DNA was extracted using AMPure XP Beads and then quantified with Qubit. 75 ng of the sample was transferred to a new tube and used for quality control to determine the percentage of biotin labeling following the Arima-HiC protocol.
Library preparation was performed using the Arima Library Prep for Arima HiC+ Kit (A510008, A303011) according to the manufacturer protocols. DNA was fragmented with Covaris for an average fragment size of 400bp. Volumes for the protocol were adjusted for an initial volume of 130 µL for DNA fragmentation. DNA was size selected with AMPure XP Beads and then enriched with biotin using the kit provided T1 beads. Library preparation was performed according to the protocol and a unique index pair was added to each sample before the samples were amplified with PCR and purified with AMPure XP Beads.

value: Ventral forebrain

tag: region

value: Ganglionic Eminence

value: Wildtype


title: KO, B1-a cell，24month, male, rep2

extract_protocol:
5000 B-1a cell were isolated into lysis buffer,then  the process involves the following steps: Reverse transcription of RNA into cDNA; Amplify and purify the cDNA; Fragment cDNA with Tn5 enzyme and construct the library ; two replicates of each sample were done. 5000 cells analysed per experiment.
The purified cDNA samples were added to TN5 buffer and TN5 enzyme-1, and the reaction was interrupted according to the program. After the reaction, mix Smart Amp buffer-2, Smart Amp enzyme-2 for library construction, purify and send for testing.Illumina NovaSeq 6000 sequencing platform was usually used, and PE150 sequencing mode was adopted.

value: peritoneal B1-a cell

value: KO 24month male

value: PBS


title: K562_S01 0hr

description: k562_timeseries - 0

value: 0 hours

value: RPMI + 10% BCS (bovine calf serum) + P/S


title: donor3, fresh PBMC

description:
Library name: fresh3
columnname in estcounts_gene_names.csv : fresh3_estcounts

value: fresh


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, D395A_1F clone, dTAG 2h + dTAGDox 24h, Rep2

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: Endogenous Xist


title: donor2, fresh PBMC

description:
Library name: fresh2
columnname in estcounts_gene_names.csv : fresh2_estcounts

value: PBMC


title: KO, B1-a cell，24month, male, rep1


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, D395A_1F clone, Dox 24h, Rep2

value: Dox for 24 hours


title: KO, B1-a cell，3month, male, rep2

value: KO 3month male


title: 38_5C-290min_S30

description: scer_38_5C_timeseries - 290

data_processing:
Sequenced reads mapped to the respective yeast genome using STAR.
Transcripts were quantified in Transcripts Per Million (TPM) using RSEM.
These resulting TPM were combined into a single .tsv file containing all transcripts at all timepoints
This final .tsv file was z-score normalized and quantile normalized to produce the cleaned .tsv file
Assembly: Saccharomyces cerevisiae S288C Ensembl R64-1-1 downloaded from Illumina iGenomes.
Supplementary files format and content: Each dataset has a final raw .tsv file. Consisting of either FPKM/TPM transcript levels (see above) for each each for each timepoint
Supplementary files format and content: Each dataset has a final cleaned .tsv file. Consisting of the Z-score normalized and then quantile normalized  (z-score quantile normalized) data for each gene for each timepoint.

organism: Saccharomyces cerevisiae

source_name: BF264-15D MATa bar1

growth_protocol: Cells were grown in YEPDextrose at 38.5c.

extract_protocol:
Cells were removed at each time point and flash frozen on dry ice. RNA was harvested using standard yeast methods using  an acid phenol/chloroform protocol.
Illumina Stranded mRNA Prep, NovaSeq 6000 S-Prime.

treatment_protocol: Synchronous G1 populations collected by alpha-factor mating pheromone (40 ng/ml, 150 minutes) arrest-release.

value: 290 minutes

value: YEPDextrose 38.5C


title: 38_5C-280min_S29

description: scer_38_5C_timeseries - 280

value: 280 minutes


title: donor1, fresh PBMC

description:
Library name: fresh1
columnname in estcounts_gene_names.csv : fresh1_estcounts


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, D395A_1F clone, dTAG 26h, Rep2

extract_protocol:
Chromatin RNA was extracted from one confluent T25 plates of mESCs. Briefly, cells were trypsinised and washed in PBS. Cells were lysed on ice in RLB (10 mM Tris pH 7.5, 10 mM KCl, 1.5 mM MgCl2, and 0.1% NP40), and nuclei were purified by centrifugation through a sucrose cushion (24% sucrose in RLB). The nuclei pellet was resuspended in NUN1 (20 mM Tris pH 7.5, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol), then lysed with NUN2 (20 mM Hepes pH 7.9, 300 mM, 7.5 mM MgCl2, 0.2 mM EDTA, 1 M Urea). Samples were incubated for 15 minutes on ice then centrifuged at 2800 g to isolate the insoluble chromatin fraction. The chromatin pellet was resuspended in TRIzol by passing multiple times through a 23 gauge needle. Finally chromatin-associated RNA was purified through standard TRIzol/chloroform extraction followed by isopropanol precipitation. Samples were then treated with Turbo DNAse.
Approximal 200 - 500 ng of RNA was used for library preparation using the Illumina TruSeq stranded total RNA kit. Libraries were quantified by qPCR with KAPA Library Quantification DNA standards (KAPA Biosystems). The libraries were pooled and 2X 81 paired end sequencing was performed using Illumina NextSeq 500/550.

value: mESC

value: dTAG-13 for 2 hours


title: KO, B1-a cell，3month, male, rep1

value: peritoneal B1-a cell


title: K562_S04 6hr

description: k562_timeseries - 6

value: 6 hours


title: 38_5C-270min_S28

description: scer_38_5C_timeseries - 270

value: 270 minutes


title: Evf1_2 WT rep2 HiC

description: HiC

tag: tissue

value: Ventral forebrain

value: Ganglionic Eminence

value: Wildtype


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, D395A_1F clone, Rep2

value: Cast x 129S

tag: cell line


title: WT, B1-a cell，3month, female, rep2

tag: cell type

value: WT 3month female

value: PBS


title: 38_5C-260min_S27

description: scer_38_5C_timeseries - 260

value: 260 minutes


title: K562_S02 2hr

description: k562_timeseries - 2

value: 2 hours

value: RPMI + 10% BCS (bovine calf serum) + P/S


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, D395A_1F clone, dTAG 2h + dTAGDox 24h

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: Endogenous Xist

tag: treatment

value: dTAG-13 for 2 hours, followed by dTAG-13 and Dox for 24 hours


title: 38_5C-250min_S26

description: scer_38_5C_timeseries - 250

value: 250 minutes

value: YEPDextrose 38.5C


title: WT, B1-a cell，3month, female, rep1

value: peritoneal B1-a cell


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, WT_1A clone, XiO, dTAG 26h

tag: strain background

value: mESC

value: dTAG-13 for 2 hours


title: P108_ST

city: Stockholm

first: Kristina

last: Broliden

state: Solna

address: Visionsgatan 4, J7:20

department: Dept. of Medicine Solna

country: Sweden

institute: Karolinska Institutet

description:
Library name: P108
Visium (10X)

data_processing:
The Bcl to FastQ conversion was carried out using bcl2fastq_v2.20.0.422 from the CASAVA software suite
Raw reads were processed utilizing the spaceranger command line tool (version 1.2.0, 10x Genomics) and mapped to the human reference genome (Homo sapiens, GRCh38-2020-A).
Assembly: Homo sapiens, GRCh38
Supplementary files format and content: Gzip files containing output from SpaceRanger: .h5-files with raw and filtered feature matrix, tissue images and tissue positions
Supplementary files format and content: RDS file with Seurat object containing all samples and metadata
Library strategy: Spatial Transcriptomics

source_name: Ectocervix

extract_protocol:
Fresh frozen tisue were sliced to a thickness of 10 μm using a pre-cooled cryostat.
Library preparation for sequencing adhered to the manufacturer’s instructions (10x Genomics, Visium Spatial Transcriptomic). Sequencing was conducted on a NovaSeq6000 flowcell in ‘SP’ mode, with specification of 28 bases for Read 1, 10 bases for Index 1 and 2, and 90 bases for Read 2.

value: Ectocervix

tag: contraception

value: DMPA

value: female


title: P114_ST

description:
Library name: P114
Visium (10X)


title: 38_5C-240min_S25

description: scer_38_5C_timeseries - 240

value: 240 minutes


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, D395A_1F clone, dTAG 26h

data_processing:
The ChrRNA-seq data mapping pipeline used in this study was similar to our previous work (Pintacuda et al 2017; Nesterova et al 2019). Briefly, the raw fastq files of read pairs were first mapped to an rRNA build by bowtie2 and rRNA-mapped reads discarded. The remaining unmapped reads were aligned to the ‘N-masked’ genome (mm10) with STAR using parameters (--twopassMode Basic --outSAMstrandField intronMotif --outFilterMismatchNoverReadLmax 0.06 --outFilterMultimapNmax 1 --alignEndsType EndToEnd) for all the sequencing libraries. Unique alignments were retained for further analysis. We made use of 23,005,850 SNPs between Cast and 129S genomes and employed SNPsplit (v0.4.0dev, Babraham Institute, Cambridge, UK) to split the alignment into distinct alleles (Cast and 129S) using the parameter “--paired”. The (allelic) read numbers were counted by the program featureCounts (-t transcript -g gene_id -s 2) and the alignments were sorted by Samtools. Files of bigWig were generated by Bedtools and visualized by IGV or UCSC Genome Browser. Metagene profile and heatmap were generated by deepTools, as well as custom python scripts. For biallelic analysis, counts were normalized to 1 million mapped read pairs (as CPM) by the R package of edgeR. Genes with at least 10 SNP-covering reads across all the samples were further taken to calculate the allelic ratio of Xi/(Xi+Xa) where Xi and Xa indicate inactive and active allele, respectively. Principal components analysis (PCA) was done using the prcomp function in R and plotted using the ggplot2 package. Allelic ratio of samples derived from SPEN KO or deletion of Xist B/C-repeat were taken from the previous studies, gene categories including initial X-linked gene expression level and promoter chromatin landscape were taken from Nesterova et al, 2019 and Pintacuda et al 2017, gene silencing kinetics data were taken from Bowness et al, 2022.
Assembly: mm10
Supplementary files format and content: text file, with allelic ratio called for each X-linked genes
Library strategy: ChrRNA-seq

value: Cast x 129S

tag: xist type


title: WT, B1-a cell，24month, male, rep1

tag: genotype

value: WT 24month male

value: PBS


title: 38_5C-230min_S24

description: scer_38_5C_timeseries - 230

value: 230 minutes


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, D395A_1F clone, Dox 24h

value: Dox for 24 hours


title: P107_ST

description:
Library name: P107
Visium (10X)


title: WT, B1-a cell，3month, male, rep2

value: WT 3month male


title: P097_ST

description:
Library name: P097
Visium (10X)


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, D395A_1F clone

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: Endogenous Xist


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, WT_P2B3 clone, dTAG 2h + dTAGDox 24h, Rep2

value: dTAG-13 for 2 hours, followed by dTAG-13 and Dox for 24 hours


title: P105_ST

description:
Library name: P105
Visium (10X)

value: Control


title: P118_ST

description:
Library name: P118
Visium (10X)


title: 38_5C-210min_S22

description: scer_38_5C_timeseries - 210

value: 210 minutes

value: YEPDextrose 38.5C


title: WT, B1-a cell，3month, male, rep1

value: peritoneal B1-a cell


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, WT_P2B3 clone, Dox 24h, Rep2

value: mESC


title: P031_ST

description:
Library name: P031
Visium (10X)

value: Ectocervix


title: WT, B1-a cell，24month, female, rep2

value: WT 24month female


title: WT, B1-a cell,  24month, female, rep1


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, WT_P2B3 clone, dTAG 26h, Rep2

value: dTAG-13 for 2 hours


title: 38_5C-190min_S20

description: scer_38_5C_timeseries - 190

value: 190 minutes


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, WT_P2B3 clone, Rep2

value: Cast x 129S


title: WT, B1-a cell，24month, male, rep2

value: WT 24month male

value: PBS


title: 38_5C-180min_S19

description: scer_38_5C_timeseries - 180

value: 180 minutes


title: ATAC_seq_KO, young, Male, rep2


title: 38_5C-200min_S21

description: scer_38_5C_timeseries - 200

value: 200 minutes


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, WT_P2B3 clone, dTAG 2h + dTAGDox 24h

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)


title: 38_5C-170min_S18

description: scer_38_5C_timeseries - 170

value: 170 minutes


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, WT_P2B3 clone, Dox 24h

value: Endogenous Xist

value: Dox for 24 hours


title: ATAC_seq_KO, young, Male, rep1


title: ATAC_seq_WT, old, male, rep2


title: 38_5C-160min_S17

description: scer_38_5C_timeseries - 160

value: 160 minutes


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, WT_P2B3 clone, dTAG 26h


title: 38_5C-220min_S23

description: scer_38_5C_timeseries - 220

value: 220 minutes

value: YEPDextrose 38.5C


title: ATAC_seq_WT, old, male, rep1

value: peritoneal B1-a cell


title: ATAC_seq_WT, young, male, rep2


title: METTL3_FKBP12^F36V (H5 clone) + Rosa_GFP-METTL3, WT_P2B3 clone

value: mESC


title: METTL3_FKBP12^F36V, H5 clone, dTAG 2h + dTAGDox 24h

value: dTAG-13 for 2 hours, followed by dTAG-13 and Dox for 24 hours


title: P080_ST

description:
Library name: P080
Visium (10X)

value: Ectocervix

value: Control

value: female


title: OSKM48h, TNIP2_siRNA, ATAC-seq, rep2

description: Library name: OSKM48h_TNIP2_siRNA_ATAC_rep2

data_processing:
The contaminating ME sequences (CTGTCTCTTATACACATCT) were trimmed from the ATAC-seq reads with Cutadapt to prevent multimapping.
The ATAC-seq pair-end reads were mapped to the Mus musculus genome assembly GRCh37 (hg19) using Bowtie (version 2.3.4.1) and very sensitive parameters.
Duplicated alignments were removed using Picard (https://broadinstitute.github.io/picard/).
ATAC-seq reads (bam files) from different replicates were merged and then normalised for sequencing coverage to 1x genome depth (reads per genome coverage, RPGC) using the bamCoverage tool from DeepTools and a bin size of 10 bp and extendReads parameters.
Assembly: GRCh37 (hg19)
Supplementary files format and content: Bigwig files normalised for sequencing depth and merged replicates.

source_name: hFib (HF176)

growth_protocol: human fibroblasts (HF176) were cultured in GMEM supplemented with 10% FCS, 1X 13 non-essential amino acids, 1 mM Sodium Pyruvate, 1 mM glutamine and 0.1 mM 2-mercaptoethanol at 37C and 5% CO2.

treatment_protocol: hFibs were transfected with siRNA targeting STAT3, TNIP2 or a control non-targeting siRNA, which were then infected with lentiviruses to over express OSKM for 48h (OSKM48h).

value: hFib (HF176)

value: human fibroblasts

value: OSKM72h and TNIP2_siRNA


title: ATAC_seq_WT, young, male, rep1

value: PBS


title: 38_5C-130min_S14

description: scer_38_5C_timeseries - 130

value: 130 minutes


title: METTL3_FKBP12^F36V, H5 clone, Dox 24h

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)


title: ATAC_seq_WT, old, Female, rep2


title: 38_5C-120min_S13

description: scer_38_5C_timeseries - 120

value: 120 minutes


title: OSKM48h, STAT3_siRNA, ATAC-seq, rep2

description: Library name: OSKM48h_STAT3_siRNA_ATAC_rep2

value: OSKM72h and STAT3_siRNA


title: METTL3_FKBP12^F36V, H5 clone, dTAG 26h

value: Endogenous Xist

value: dTAG-13 for 2 hours


title: METTL3_FKBP12^F36V, H5 clone


title: ATAC_seq_WT, old, Female, rep1

value: peritoneal B1-a cell


title: OSKM48h, STAT3_siRNA, ATAC-seq, rep1

description: Library name: OSKM48h_STAT3_siRNA_ATAC_rep1


title: 38_5C-110min_S12

description: scer_38_5C_timeseries - 110

value: 110 minutes

value: YEPDextrose 38.5C


title: OSKM48h, CTRL_siRNA, ATAC-seq, rep2

description: Library name: OSKM48h_CTRL_siRNA_ATAC_rep2

value: OSKM72h and ctrl_siRNA


title: 38_5C-100min_S11

description: scer_38_5C_timeseries - 100

value: 100 minutes


title: ATAC_seq_WT, young, female, rep2


title: METTL3_FKBP12^F36V, C3 clone, dTAG 2h + dTAGDox 24h

value: mESC

value: dTAG-13 for 2 hours, followed by dTAG-13 and Dox for 24 hours


title: 38_5C-150min_S16

description: scer_38_5C_timeseries - 150

value: 150 minutes


title: METTL3_FKBP12^F36V, C3 clone, Dox 24h

value: Dox for 24 hours


title: ATAC_seq_WT, young, female, rep1

value: PBS


title: 38_5C-140min_S15

description: scer_38_5C_timeseries - 140

value: 140 minutes


title: 38_5C-80min_S9

description: scer_38_5C_timeseries - 80

value: 80 minutes


title: hFib, ATAC-seq, rep2

description: Library name: hFib_ATAC_rep2

value: hFib (HF176)

value: human fibroblasts

value: wildtype


title: 38_5C-90min_S10

description: scer_38_5C_timeseries - 90

value: 90 minutes


title: Input sanmple of MGAdeltaFAM ESCs for ChIP-seq

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Division of Biomedical Sciences, Research Center for Genomic Medicine

institute: Saitama Medical University

description: reference to dFAM_K9me3 (ChIP-seq)

data_processing:
(RNA-seq) Sequence reads were trimmed for adaptor sequence/low-quality sequence using sickle (parameter- -q 30 -l 20 ), Trimmed sequence reads were mapped to mm10 using hisat2 and samtools, Read count extraction and normalization were performed using Stringtie
(ChIP-seq) Sequence reads were trimmed for adaptor sequence/low-quality sequence using sickle (parameter- -q 20 -l 20 ), Trimmed sequence reads were mapped to mm10 using bowtie2 and samtools, BigWig files were created using bamCompare
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each Sample
Supplementary files format and content: BigWig files show H3K9me3 intensity for each sample

source_name: embryonic stem cells

growth_protocol: Wildtype and MGAdeltaFAM ESCs cultured under conventional ES culture condition with LIF.

extract_protocol:
Total RNAs for RNA-sequence were prepared by using RNeasy mini kit from QIAGEN (74904), chromatins for ChIP-sequence were prepared from ESCs by following standardized method of fixation, cell lysis and fragmentation.
RNA libraries for RNA-seq were prepared with total RNAs (N=2 for each condition) using TruSeq Stranded Total RNA Library Prep Gold Kit from Illumina (San Diego, California) with Ribozero Gold (Illumina #MRZG126) according to the manufacturer, while DNA libraries for ChIP-seq were prepared according to Illumina’s instructions using New England Biolab’s Next ChIP-seq Library Set (#E6200) and their quantity and average size were estimated using a KAPA Quantification Kit (Millipore) and Bioanalyzer (Agilent Technology).

value: embryonic stem cells

value: deltaFAM

tag: antibody

value: none (input)


title: OSKM48h, TNIP2_siRNA, ATAC-seq, rep1

description: Library name: OSKM48h_TNIP2_siRNA_ATAC_rep1

value: OSKM72h and TNIP2_siRNA


title: METTL3_FKBP12^F36V, C3 clone

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: Endogenous Xist


title: H3K9me3 sample of MGAdeltaFAM ESCs for ChIP-seq

value: anti-H3K9me3 as ChIP antibody


title: hFib, ATAC-seq, rep1

description: Library name: hFib_ATAC_rep1


title: H3K9me3 sample of control ESCs for ChIP-seq


title: METTL3_FKBP12^F36V, C3 clone, dTAG 26h

value: mESC

value: dTAG-13 for 2 hours


title: RNA-seq hiPSCs-O-lin-mini

description: Library name: hiPSCs-O-lin-mini

data_processing:
RNA-seq pair-end reads were aligned to the human genome (hg19) using STAR (v2.5.3a).
Reads were normalised to fcounts on hg19 gene annotaion (GTF) using featureCounts.
Assembly: GRCh37 (hg19)
Supplementary files format and content: tab-delimited text file includes normalised counts (fcounts) for each Sample.

source_name: human iPSCs

growth_protocol: human fibroblasts (HF176) were cultured in GMEM supplemented with 10% FCS, 1X 13 non-essential amino acids, 1 mM Sodium Pyruvate, 1 mM glutamine and 0.1 mM 2-mercaptoethanol at 37C and 5% CO2. Human Embryonic Stem Cells (hESCs) Master Sheffield 7 (MS7) and human induced pluripotent stem cells (hiPSCs) were cultured in Essential 8 Medium (#A2858501, Gibco) in plates coated with 4g/mL of Human Recombinant Laminin 521/DPBS Ca++, Mg++ (#800110, BioLamina; #14040133, Gibco) at 37C and 5% CO2.

value: human iPSCs

value: Oct4-lin-mini mutant

value: human induced pluripotent stem cells


title: RNA-seq hiPSCs-O-lin95-117

description: Library name: hiPSCs-O-lin95-117

value: Oct4-lin95-117 mutant


title: 38_5C-60min_S7

description: scer_38_5C_timeseries - 60

value: 60 minutes

value: YEPDextrose 38.5C


title: FKBP12^F36V_METTL3, H1 clone, dTAG 2h + dTAGDox 24h

value: dTAG-13 for 2 hours, followed by dTAG-13 and Dox for 24 hours


title: 38_5C-50min_S6

description: scer_38_5C_timeseries - 50

value: 50 minutes


title: Input sample of control ESCs for ChIP-seq

description: reference to control_K9me3 (ChIP-seq)

value: embryonic stem cells

value: wildtype


title: MGAdeltaFAM2 ESCs for RNA-seq

value: deltaFAM


title: FKBP12^F36V_METTL3, H1 clone, Dox 24h

value: Cast x 129S

value: Dox for 24 hours


title: RNA-seq hiPSCs-O-WT

description: Library name: hiPSCs-O-WT


title: FKBP12^F36V_METTL3, H1 clone, dTAG 26h

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: Endogenous Xist


title: RNA-seq hESCs

description: Library name: hESCs

source_name: human ESCs

value: human ESCs

value: human embryonic stem cells


title: 38_5C-30min_S4

description: scer_38_5C_timeseries - 30

value: 30 minutes


title: RNA-seq hFibs

description: Library name: hFibs

source_name: human fibroblasts

value: human fibroblasts


title: 38_5C-40min_S5

description: scer_38_5C_timeseries - 40

value: 40 minutes


title: MGAdeltaFAM1 ESCs for RNA-seq


title: control2 ESCs for RNA-seq

description: reference to Sample 4 (RNA-seq)


title: Input DNA hESCs

description: Library name: Input DNA hESCs

data_processing:
The ChIP-seq pair-end reads were mapped to the human genome assembly GRCh37 (hg9) using Bowtie (version 2.3.4.1) and very sensitive parameters.
Duplicated reads were then removed using MarkDuplicates from the Picard toolkit.
Reads mapping to the backlisted regions as determined by Encyclopaedia of DNA Elements (ENCODE) were discarded.
The sequencing coverage and the insert size distribution were measured from the resulting bam files using Qualimap (version 2.2.1).
The peaks of OCT4 wild-type and mutants showing significant enrichment over input DNA were called using MACS2 (version 2.1.1.20160309), and a fragment size of 200 bp and were controlled to a q-value (minimum FDR) cut-off of 0.01. The peaks that overlapped with the ENCODE blacklist were removed.
Assembly: GRCh37 (hg19)
Supplementary files format and content: The aligned ChIP-seq reads were normalised for sequencing coverage to 1x genome depth (reads per genome coverage, RPGC) using the bamCoverage tool from DeepTools and a bin size of 10 bp and extendReads parameters. Replicates were merged before normalized for coverage to produce the final BigWig (.bw) file.

extract_protocol:
Cells were washed 3X with PBS at RT on 15 cm dishes. After final wash, 15mL of PBS/MgCl2 was added to each plate and 120ul of fresh DSG (0.25M stock prepared by adding 613L DMSO to 50mg of DSG) were added to each plate to get a final concentration of 2mM. Plates were incubated at RT for 45min in a horizontal shaker with constant moving followed by 3X washes of PBS. After the last wash, 20 mL of PBS were added to each plate followed by adding 3mL of Formaldehyde crosslinking buffer (50mM HEPES-KOH, pH7.5, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 11% formaldehyde). Crosslinking was blocked by adding 1.65 mL of 2.5M Glycine and incubating for 5 minutes at room temperature. Cells were harvested using a silicon scraper and centrifuged for 5 minutes at 1,350 rcf at 4C. Cell pellets were then re-suspended in 10ml Lysis Buffer 1 (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40 Substitute, 0.25% Triton X100 and cOmplete Ultra Protease Inhibitor rotated for 10 minutes at 4C. Cells were disrupted using a tight 7mL dounce homogeniser with 80 strokes on ice. Nuclei were collected by centrifugation at 1350rcf for 5 minutes at 4C. The nuclei were washed in 10ml Lysis Buffer 2 (10mM Tris-HCl pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA and cOmplete Ultra Protease Inhibitor) for 10 minutes a rotator at room temperature. The nuclei were collected by centrifugation and resuspended in Lysis Buffer 3 (10mM Tris-HCl pH8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine and cOmplete Ultra Protease Inhibitor). Samples were sonicated for 140 min in 10 minutes intervals using a Covaris M220 sonicator. To solubilise chromatin following sonication, 100ul of 10% Triton X-100 was added per 1ml of sonicated chromatin. Before ChIP, 50ul of sonicated chromatin were collected to confirm optimum DNA fragmentation (~ 200 bp) was achieved by agarose gel electrophoresis. Three ChIPs were performed for each ChIP-seq sample (OCT4 WT and mutants). Dyna G Magnetic Beads were transferred to a Prechilled LoBind tube and washed 3X with 1ml of Blocking buffer (0.5 BSA in PBS). Beads were resuspended in 800 ul of Blocking buffer and incubated with 10ug of OCT4 antibody per ChIP and incubated for 6 hr (minimum) on a rotating platform at 4C. Beads were washed 3X in 1ml of blocking solution and resuspended in 100ul Lysis buffer 3. Sonicated chromatin (40 ug) were added to each ChIP and volume was top up to 900 ul with Lysis buffer 3 buffer containing protease inhibitors. ChIPs were incubated overnight in a rotating platform at 4C. To reduce background the ChIP reactions were transferred to fresh pre-chill LoBind tube. Beads were washed 4X with cold RIPA-wash buffer (50 mM Hepes-KOH pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) using magnetic rack. Beads were washed once with TE+NaCl (10mM Tris-HCl pH 8, 1mM EDTA pH 8 and 50mM NaCl), followed by a spin at 300 x g for 3 minutes at 4C and to remove any residual TE buffer. Bound chromatin fragments were eluted by addin 210 ul elution buffer to the beads and incubated at 65C for 30 minutes shaking at 1200rpm. Tubes were centrifuged at 16,000 x g for 1 minute at room temperature and 200ul of supernatant was transferred to a new tube. In parallel, 50ul of sonicated chromatin from the INPUT after sonication was thawed before adding 150ul of ChIP elution buffer. ChIPs and input were reverse cross-linked by incubating at 65C overnight (shake 700rpm). An equal volume (200ul) of TE (10mM Tris-HCl pH8, 1mM EDTA) was added and incubated with 0.2mg/mL RNAse A for 2 hours at 37C. Proteins were then digested by incubating with 0.2mg/mL Proteinase K for 2 hours at 55C. To extract DNA, 400ul Phenol:chloroform:isoamyl alcohol were added to the samples to separate phases by spinning the sample at top speed for 5 min. The aqueous layer was transferred to a new tube containing 16ul of 5M NaCl (200 mM final concentration) and 1.5ul of 20 g/L glycogen (30 g total). DNA precipitation was performed by adding 0.8ml of cold 100% EtOH and incubated for 180 min at least at -20C. Tubes were centrifuged 20,000 x g for 10 minutes at 4C to pellet DNA. Supernatants were carefully decanted without disturbing the DNA pellet, which was further washed with 500ul of 80% EtOH and spining at 20,000 x g for 10 minutes at 4C. Supernatants were removed by pipetting and pellets were allowed to dry for 5 min. Each pellet was resuspended in 20ul MiniPrep Elution buffer (10mM Tris-HCl pH8.5, Qiagen) using a P20 pipette. DNA was quantified by Qubit 2.0 using the HS dsDNA quantification kit.
ChIP-seq DNA libraries were prepared using 20-50ng ChIP-DNA prepared by pooling equal volumes of 3X ChIP replicates for each OCT4 (WT and mutant) using the NEBNext Ultra II Library Preparation Kit with Dual Index Primers. Size selection for DNA fragments of approximately 200bp was carried out using SpeedBeads, which comprise magnetic carboxylate modified particles. PCR amplification during library preparation was limited such that samples underwent 10 cycles of PCR amplification. Libraries were quantified using a Qubit 2.0 device with a high sensitivity dsDNA kit and fragment size was determined using an Agilent 2200 Tapestation with D1000 HS reagents. The DNA libraries were then pooled by mixing an equal concentration of each ChIP DNA library. The concentration of the ChIP DNA library pool was determined by an Agilent 2200 Tapestation with D1000 HS reagents.

treatment_protocol: human fibroblasts were transduced with concentrated lentiviruses encoding for OCT4 (WT or mutants), SOX2, c-MYC, KLF4 at M.O.I of 5, and rtTA2M2 lentivirus at M.O.I of 3. After 16 hours of infection, the culture medium was replaced, and cells were cultured for 48 hours. OSKM protein expression was then induced by adding fresh medium containing 1g/mL of doxycycline. Cells were cultured for 48 hours at 37C and 5% CO2 before collection.


title: 38_5C-70min_S8

description: scer_38_5C_timeseries - 70

value: 70 minutes


title: 38_5C-10min_S2

description: scer_38_5C_timeseries -10

value: 10 minutes


title: control1 ESCs for RNA-seq

description: reference to Sample 3 (RNA-seq)


title: 38_5C-20min_S3

description: scer_38_5C_timeseries - 20

value: 20 minutes

value: YEPDextrose 38.5C


title: FKBP12^F36V_METTL3, H1 clone

source_name: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: mESC


title: FKBP12^F36V_METTL3, G4 clone, dTAG 2h + dTAGDox 24h

value: dTAG-13 for 2 hours, followed by dTAG-13 and Dox for 24 hours


title: OCT4 ChIP hESCs

description: Library name: OCT4 ChIP hESCs

value: wildtype


title: Evf1 GAPDH ++ CHIRPseq

description:
Evf2_expression_data.mtx
Evf2_cell_data.csv
Evf2_gene_data.csv

data_processing:
After mapping the reads, the peak callingwas performed using theMACS2 program (Zhang et al., 2008). An FDR cutoff of 0.05 was used to call the final set of peaks. The UCSC browser was used to visualize peaks, and perform alignments. Evf1/2 regulated peaks were defined are overlapping odd and even bound peaks in Evf1/2++ samples, absent from Evf1/2TSTS and GAPDH peaks.
Assembly: mm9
Supplementary files format and content: Tab separated values files and matrices
Library strategy: CHIRP

extract_protocol:
The method described in (Chu et al., 2011) was followed, and modified for embryonic day 13.5 ganglionic eminences (13.5GEs). For each sample ~16 E13.5GEs were dissected for each genotype (Evf1/2+/+, Evf1/2TS/TS) in ice cold L15, pipetted to produce a single cell suspension, pelleted for 4min, X 800 RCF, resuspended in PBS, pelleted for 4min, X 800 RCF, and resuspended in 5mL of 1% glutaraldehyde. Cells were cross-linked for 10 minutes, quenched with 500 µL of 1.25 M glycine for 5 minutes, pelleted for 5 min X 2000 RCF, 4°C, washed with PBS, pelleted for 5 min X 2000 RCF for 5min, 4°C, resuspended 1mL 4°C PBS per 8 embryos, pelleted X 2000 RCF for 3 minutes at 4°C, supernatant aspirated, and cell pellets flash frozen in liquid nitrogen and stored at -80°C.
Libraries were created with NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1), and 10M reads from PE100 sequenced on NOVAseq. Raw sequencing reads for ChIRPdatasets were aligned using bowtie2 (Langmead and Salzberg, 2012) mapper with the following settings '--local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700’.The datasets weremappedagainst the mm9 version of the mouse genome.

value: Ventral forebrain

value: Ganglionic Eminence

value: Wildtype


title: Evf1 GAPDH TSTS CHIRPseq


title: FKBP12^F36V_METTL3, G4 clone, Dox 24h

value: Cast x 129S

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele)

value: Dox for 24 hours


title: FKBP12^F36V_METTL3, G4 clone, dTAG 26h

value: Endogenous Xist

value: dTAG-13 for 2 hours


title: OCT4-lin95-117 ChIP OSKM48h

description: Library name: OCT4-lin95-117 ChIP OSKM48h

value: human fibroblasts

value: human fibroblasts overexpressing OSKM for 48 hours


title: Brn3b cKO, rep4, HA-IP

city: Evanston

first: Yue

last: Yang

state: IL

address: 2200 Campus Dr

department: Neurobiology

description:
Brn3bcKO4_IP
raw_counts2.xlsx

data_processing:
Reads were aligned to the mm10 reference genome using the Smart-seq3 github pipeline (https://github.com/sandberg-lab/Smart-seq3)
Assembly: mm10
Supplementary files format and content: .xlsx files contain raw counts for each RNA-seq library

source_name: retina

extract_protocol:
Retinas from the same animal were combined and homogenized in lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM KCl, 12 mM MgCl2, 1% NP-40, 0.4 unit/ml RNase inhibitor, 1 mM DTT, 100 μg/ml cycloheximide) with a dounce homogenizer. Lysates were incubated with 1 µg/µl heparin for 2 minutes on ice prior to centrifugation. The lysates were spun down at 10,000g for 10 minutes at 4C and the supernatant was used for immunoprecipitation using an antibody against HA-tag with Dynabeads protein G for overnight at 4C. 1.5% of lysate was saved as an input. After extensive washes with cold washing buffer (50 mM Tris-HCl pH 7.4, 300 mM KCl, 12 mM MgCl2, 1% NP-40, 0.5 mM DTT, 100 μg/ml cycloheximide), immunoprecipitated RNA and input RNA were purified with a RNeasy Micro Kit (Qiagen) following the manufacturer’s instructions and eluted in 10 µl of water.
2 µl of purified RNA were used for sequencing library preparation using the Smart-seq3 protocol with modifications. After reverse transcription followed by PCR amplification, 25 ng of cDNA was used for the Tn5 tagmentation reaction. Tagmentated cDNA was amplified with 8 cycles of PCR using primers containing indexes and Illumina adaptors.

value: retina

value: ipRGCs

value: Opn4-Cre; Rpl22-HA; Brn3bcKO-AP

value: female


title: FKBP12^F36V_METTL3, G4 clone

description: RNA type: Chromatin-associated RNA (ChrRNA)

value: mESC


title: Evf12 odd ++ rep2 CHIRPseq


title: Brn3b cKO, rep3, HA-IP

description:
Brn3bcKO3_IP
raw_counts2.xlsx

value: male


title: OCT4-lin29-42 ChIP OSKM48h

description: Library name: OCT4-lin29-42 ChIP OSKM48h

value: wildtype


title: ZCCHC8_FKBP12^F36V, Z12H clone, dTAG, 180min, rep2

data_processing:
Estimation of RNA half-life was performed using GRAND-SLAM. Briefly, the paired-end sequencing reads were first aligned to rRNA, and then the unmapped reads were mapped to mouse genome mm10 by STAR (v2.5.2b) with the key parameters (--twopassMode Basic --outSAMstrandField intronMotif --outSAMattributes All --outFilterMultimapNmax 1 --outFilterMismatchNoverReadLmax 0.06 --alignEndsType EndToEnd). Given that T to C conversion is the signature of SLAMseq, the T to C conversion rate was calculated as 4sU incorporation and the average of all the rest of the conversions was calculated as background due to errors from sequencing or library preparation. The T to C conversion rate and background rate were calculated accordingly for each sample. The RNA decay was assumed to follow an exponential model, so the corresponding background corrected T2C rates were fitted to the exponential model to estimate the Xist RNA’s half-life. Regarding X-linked gene silencing and Xist expression level, same procedure of allelic analysis was performed as ChrRNA-seq data.
Assembly: mm10
Supplementary files format and content: tsv file

extract_protocol:
When reaching 60 to 70% confluency, cells were either untreated or dTAG-13 treated for 2 hours, followed by additional 1 μg/ml doxycycline induction for 20 hours. Then, transcribed RNA was labelled with 4sU by incubation with medium containing 500 μM 4sU (Lexogen) and 1 μg/ml doxycycline for another 4 hours. Next, 4sU was withdrawn for all samples by medium washout. Different samples were washed with medium containing 1 μg/ml doxycycline and 50 mM uridine (in excess, Lexogen) for 1.5 and 3 hours. Cells are quickly washed with PBS once and directly lysed with Trizol/chloroform for total RNA isolation.
Equal amount of RNA samples (5 μg) was treated with Iodoacetamide to modify the 4-thiol group of S4U-containing nucleotides via the addition of a carboxyamidomethyl group by the SLAMseq Kinetics Kit. The RNA was recovered using RNAClean XP beads (Beckman Coulter), followed by resuspension in nuclease free water. Approximately 500 ng RNA of each sample was taken forward for library preparation using the Illumina TruSeq stranded total RNA kit. Quantification of the libraries was conducted by qPCR using KAPA Library Quantification DNA standards. Finally, the libraries were pooled and paired-end sequencing was performed using Illumina NextSeq500.

treatment_protocol: Inducible Xist expression was driven by a TetOn promoter induced by addition of 1.0 µg/mL of doxycycline for 24 hours. Degron for protein of interest, i.e. METTL3, YTHDC1, ZCCHC8 in this study, are induced by dTAG-13 for two hours, which is sufficient to acute deplete the FKBP12^F36V fused protein.

value: mouse embryonic stem cell

value: Endogenous Xist + Bgl

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

value: dTAG-13, Dox


title: Evf12 odd ++ rep1 CHIRPseq

value: Ventral forebrain

value: Ganglionic Eminence

value: Wildtype


title: Input DNA OSKM48h

description: Library name: Input DNA OSKM48h


title: Evf12 odd TSTS CHIRPseq


title: OCT4-WT ChIP OSKM48h

description: Library name: OCT4-WT ChIP OSKM48h


title: Brn3b cKO rep1, HA-IP

description:
Brn3bcKO1_IP
raw_counts2.xlsx


title: ZCCHC8_FKBP12^F36V, Z12H clone, dTAG, 0min, rep2

value: Cast x 129S


title: Brn3b WT, rep4, HA-IP

description:
Brn3bWT4_IP
raw_counts2.xlsx

value: Opn4-Cre; Rpl22-HA