title: 9sCa: NPCs_MSL2KO1_labeledTTseq_rep3

extract_protocol:
RNAseq: Total RNA was extracted using the Direct-zol RNA Miniprep Plus Kit (Zymo Research) according to the manufacturers’ instructions. Maxima First Strand cDNA Synthesis Kit (Thermo Scientific) was used to synthesize cDNA from total RNA according to the manufacturers’ instructions. Quantitative reverse transcription PCR was carried out on Roche LightCycler II using the Faststart SYBR Green Master (Rox) mix (Roche) at a final volume of 10μL.
TT-seq: In brief, 10 million NPCs were incubated with N2B27 medium supplemented with 500 uM 4- thiouridine (4sU, Sigma) for 5 minutes at 37°C. Total RNA was isolated, fragmented using Bioruptor Plus for 1 minute (30s ON, 30s OFF, high setting), and incubated with Biotin-HPDP (Thermo Scientific) for 2 hours. MyOne C1 Streptavidin magnetic beads (Thermo Scientific) were used to immunoprecipitate labelled RNA before elution in 5% beta-mercaptoethanol (Roth). FInal RNA was cleaned up using the Oligo Clean and Concentrator Kit (Zymo Research) according to the manufacturer’s instructions. Libraries were prepared from 100 ng of high quality RNA using the Ovation Universal RNA-Seq System (Nugen) according to the manufacturer’s instructions.
ChIPseq: MSL2 WT and KO NPCs were covered with 1% formaldehyde in culture media on the plate and incubated at room temperature (RT) on a rocking plate for 10 min. Media was removed and cells were washed twice with 1xPBS supplemented with 1x protease inhibitor cocktail (Roche). Cells were scraped off the plate, collected in ice-cold 1xPBS and centrifuged at 500g for 5 minutes. After an additional 1xPBS wash, cell pellets were stored at -80°C until usage. Nuclei were isolated using the NEXSON based nuclei isolation protocol. Cell pellets were thawed on ice and resuspended in ice cold 1ml of lysis buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% Igepal, 1x protease inhibitor cocktail). The cell suspension was then transferred into 1ml milliTUBE (Covaris) and sonicated in Covaris instrument (E220) for 30 sec at peak power 75W, duty factor 2% and 200 cycles/burst. Nuclei were pelleted at 1000g at 20°C for 5min. The cytoplasmic fraction in the supernatant was discarded and nuclear pellets were carefully resuspended in 0.5% SDS and incubated at room temperature for 10min. Sample was diluted 1:5 in the digestion buffer (Final concentration: 1.1% Triton, 1x CutSmart buffer, nuclease free H2O, 1x protease inhibitor cocktail). Chromatin of up to 1 million nuclei were digested in 250ul digestion buffer with Cvik1 (5U/100.000 cells, New England Biolabs) at 20°C for 16hrs, shaking at 800rpm. After the chromatin digestion, the nuclei were pelleted for 5min at 1000g and washed in cold nuclei wash solution (10mM Tris-HCl pH 8, 0.25% Triton, 0.2mg/ml BSA) and stored on ice. To confirm the enzymatic chromatin shearing efficiency, 5% of the nuclei solution was incubated together with a decrosslinking solution consisting of 2ul proteinase K, 1ul RNaseA and 4ul 5M NaCl at 37°C for 30min followed by a 2hr incubation at 65°C. DNA was purified using MinElute PCR purification kit (Qiagen) and analyzed on a Agilent Tapestation system (G2964AA) using the Agilent D1000 Screentape reagents.
ATACseq: In brief, nuclei of 50,000 cells per replicate were isolated in 50 μl of cold ATAC resuspension buffer (0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin (Promega)) by incubating on ice for 3 minutes. After lysis, 1 ml of cold ATAC resuspension buffer containing 0.1% Tween-20 (without NP-40 or digitonin) was added, and nuclei were then centrifuged at 500g for 10 minutes. Transposition was carried out using 50 μl of transposition mix (25 μl 2X TD buffer (Illumina), 2.5 μl transposase (Illumina), 16.5 μl 1X PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) at 37°C for 30 minutes in a thermomixer with shaking at 1000 rpm. Transposed DNA was collected using Zymo DNA Clean and Concentrator (Zymo Research) according to the manufacturer's instructions, and added to the PCR mix containing 25 μl of NEBNext Master Mix (New England Biolabs) and 5 μl of Index adapters (Illumina). Libraries were amplified using the following PCR program: 72°C for 5 minutes, 98°C for 30 seconds, then 10 cycles of: 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. Library quality was analyzed using the Fragment analyzer (Agilent Technologies) prior to sequencing.
BSseq: Bisulfite-Seq was performed using the NEBNext Enzymatic Methyl-seq Kit (E7120S) according to the manufacturer’s instructions. In brief, genomic DNA (gDNA) was extracted from wild-type and MSL2 knockout NPCs using the QIAamp DNA Mini kit (Qiagen) according to the manufacturer’s instructions.Subsequently, 50ng of high quality gDNA was sheared for 120 seconds using an E220 Covaris to obtain fragments between around 300 base pairs in length. Following end prep and EM-seq adapter ligation, DNA was oxidised and denatured using sodium hydroxide. Libraries were amplified for 6 PCR cycles, and sequenced with 2x100bp paired-end reads on an Illumina NovaSeq6000 sequencer.

value: labeledTTseq


title: DIRECT-K562-4

status: Public on Aug 10 2023

type: SRA

city: Xiamen

first: Xi

last: Zeng

state: Fujian

address: No.422, Siming South Road

country: China

institute: Xiamen University

description: DIRECT: single-cell DNA methylation and gene expression co-analysis in a single library

library_source: other

data_processing:
The original sequence data obtained contain 150bp paired-end sequences. Before alignment, Trim Galore version 0.6.7 was used for adapter removal. Trimmed clean sequences were aligned and de-duplicated with hg19/mm10 by the bisulfite alignment tool Bismark version v0.15.0. The obtained bam files were converted into sam files using samtools version 1.3.1.
For the sam files, after the initial comparison using Bismark, we obtained the methylation information of each read based on the XM-tag (methylation call string) in the sam files. We calculated the methylation levels of CHH and CHG for each read and distinguished the reads into methylomic reads and transcriptomic reads by the methylation levels. When the methylation level of the reads was greater than 90%, they were classified as transcriptomic reads, and when the methylation level of the reads was less than 50%, they were classified as methylomic reads. For the analysis of methylomic reads, we extracted CpG methylation site information using the common methylation analysis pipeline and the R package methylKit version 1.22.0. For the isolated transcriptomic reads, the transcriptome analysis pipeline was used, which mainly included realignment using STAR version 2.7.3a and obtaining the expression profiles of the cells using htseq version 0.12.4.
For clustering using transcriptome data, the expression matrix of cells was obtained from expression profiles and then clustered using R package SC3 version 1.24.0. For the clustering of the methylome data, the Pearson correlation coefficients for the methylation levels of the commonly covered methylation sites were calculated and clearer clusters could be seen on the correlation matrix.
We used the methylome data as DNA data to perform copy number variation analysis. We used the bwa tool version 0.7.17 to perform genomic alignment and analysis. The bam files after alignment were converted to bed files for input into ginkgo for copy number variation analysis. The length of a bin was set to the default of 1M. The cell copy number variance profiles were obtained by feeding the bed files to ginkgo.
We input the gene expression matrix obtained from the transcriptome analysis pipeline into the R package DESeq2 version 1.36.0, and obtained the differentially expressed genes. For the enriched pathway analysis, we input the gene list into the enrichGO function in the R package clusterProfiler version 4.4.4 to obtain the enriched pathways. The Gene Set Enrichment Analysis (GSEA) was performed using the python package gseapy version 1.0.5.
Assembly: hg19, mm10
Supplementary files format and content: CpG.txt file containing methylation information for CpG sites.
Supplementary files format and content: counts.txt file containing gene expression information.
Library strategy: DIRECT

molecule: other

organism: Homo sapiens

growth_protocol: All cultures were maintained at 37ºC in a humidified incubator with 5% CO2. The human chronic myeloid leukemia cell line K562 and acute myeloid leukemia cell line HL60 were cultured in IMDM, supplemented with 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin-Glutamine.

extract_protocol:
Single cells were isolated with the Digital microfluidics chip. By incorporating 2'-deoxy-5-methylcytidine 5'-triphosphate (5-methyl dCTP) during reverse transcription and cDNA amplification, the resulting library of RNA and gDNA sequencing reads exhibit drastically different methylation patterns. Single-cell DNA methylation and gene expression information were obtained simultaneously, without the need to physically separate DNA and RNA.
After single-cell isolation, droplets of lysis buffer are introduced to lyse the cells. The lysates are then subjected to RT and cDNA amplification using 5’-methyl-dCTP instead of dCTP, so that all cytosines in the synthesized cDNA are methylcytosines, while the genomic DNA remains unchanged during the process. Subsequently, both the cDNA and gDNA undergo bisulfite conversion concurrently, during which normal cytosines are converted to uracil, while methylated cytosines remain unchanged. Consequently, fully cytosine-methylated cDNA produced from RNA remains unaffected by the C-U transition. In contrast, less than 10% of mammalian genomic cytosines are endogenously methylated, resulting in a substantial conversion of gDNA cytosines to uracil, which will be identified as thymine in sequencing. After scBS-seq-based library construction, the DNA reads are distinguished from RNA reads based on the methylated cytosine density in reads, and thus both DNA methylation and gene expression information are obtained from a single-cell library.
smart-seq2 and scBS

treatment_protocol: Mouse embryonic stem cells (mESCs; E14, 129/Ola) were grown on 6-cm culture dishes with MEF feeder cells and cultured in a complete medium supplemented with leukemia inhibitory factor (LIF) to prevent differentiation. To induce undirectional differentiation, mESCs were dissociated and replated onto 0.1% gelatin-coated dishes, and cultured without LIF in a feeder-free manner for two passages.

tag: cell line

tag: cell type

value: chronic myeloid leukemia cells

tag: treatment


title: 9sCa: NPCs_MSL2KO1_labeledTTseq_rep2

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

library_source: transcriptomic

data_processing:
Library strategy: TT-Seq
RNAseq and TTseq: The data are processed via snakePipes mRNA-seq pipeline (developing branch) (Bhardwaj et al., 2019). SnakePipes removed adapters and low quality bases (< Q20) using TrimGalore (v0.6.5) with parameters '-q 20 --trim-n'. The trimmed reads are aligned with STAR (v2.7.4) (Dobin et al., 2013) to an ‘N-masked’ genome, which is a version of the mouse reference genome mm10 where all the polymorphicsites (SNPs) for Mus musculus CAST/EiJ and Mus musculus C57BL/6 (or 129S1/SvImJ) are masked by ambiguity nucleobase ‘N’ (Keane et al., 2011). The mapped reads are then passed to SNPSplit (0.3.4) (Krueger and Andrews, 2016) to generate allele-specific BAM files by separating the alignment into two distinct alleles (CAST/EiJ and C57BL/6 or 129S1/SvImJ) based on SNPs information downloaded from Mouse Genome Database (Keane et al., 2011). The aligned reads of standard and allele specific level are counted separately on Gencode GTF (m9) via featureCounts (v2.0.0) (Yang et al., 2014).
ChIPseq: The data are processed via snakePipes DNA-mapping and ChIP-seq pipeline (developing branch) (Bhardwaj et al., 2019). Adapters and low quality bases (< Q20) are removed using TrimGalore (v0.6.5) with parameters '-q 20 --trim-n'. For all samples, reads are then mapped to the ‘N-masked’’ genome with Bowtie2 (2.3.5) (Langmead and Salzberg, 2012). Reads mapped on blacklisted regions from Encode Consortium are discarded. Duplicated reads are also filtered with Picard MarkDuplicates (1.65) (https://broadinstitute.github.io/picard/). In the end, only properly paired mapped reads and reads with mapping quality over 3 are kept for further analysis. SNPSplit (0.3.4) (Krueger and Andrews, 2016) is then used to generate allele-specific BAM files and deepTools (v3.3.2) (Ramirez et al., 2014) is used to check data quality. In the ChIP-seq part, peak calling is performed with MACS2 (v2.2.6) (Zhang et al., 2008) with options [--qvalue 0.001]. It is done with input as control on total and allele specific ChIP-seq signals respectively. CSAW (v1.20.0) (Lun and Smyth, 2015) is additionally used to calculate log2FC on peak regions between MSL2 KO and WT or between allele2 and allele1. Bigwig files are created with deepTools bamCompare (v3.3.2) (Ramirez et al., 2014), using input normalization method and log2ratio and subtract option.
ATACseq: The data are processed via snakePipes DNA-mapping and ATAC-seq pipeline (developing branch) (Bhardwaj et al., 2019). In the DNA-mapping part, adapters and low quality bases (< Q20) are removed using TrimGalore (v0.6.5) with parameters '-q 20 --trim-n'. For all samples, reads are then mapped to the ‘N-masked’’ genome with Bowtie2 (v2.3.5) (Langmead and Salzberg, 2012). Reads mapped on blacklisted regions from Encode Consortium are discarded. Duplicated reads are also filtered with Picard MarkDuplicates (v1.65) (https://broadinstitute.github.io/picard/). In the end, only properly paired mapped reads and reads with mapping quality over 3 are kept for further analysis. SNPSplit (0.3.4) (Krueger and Andrews, 2016) is then used to generate allele-specific BAM files and deepTools (v3.3.2) (Ramirez et al., 2014) is used to check data quality. In the ATAC-seq part, the BAM files are filtered to include only properly paired reads with appropriate fragment sizes (<150 bases). To identify open/accessible regions, peak calling is done with MACS2 (v2.2.6) (Zhang et al., 2008) with options [--qvalue 0.001], on total and allele-specific ATAC-seq signal respectively. CSAW (v1.20.0) (Lun and Smyth, 2015) is additionally used to calculate log2FC on peak regions between MSL2 KO and WT or between allele2 and allele1. Bigwig files are created with deepTools bamCoverage (v3.3.2) (Ramirez et al., 2014), using size factor calculated by deepTools multiBamSummary (v3.3.2).
BSseq: Raw fastq files were aligned against the ‘N-masked’ genome and deduplicated using Bismark (v0.22.3) (Krueger and Andreas, 2011). Resulting Alignments were allele-separated using SNPsplit with flags '--paired' and '--bisulfite'. Relevant quality metrics (conversion rates, genome coverage and GC bias) were calculated using MethylDackel version 0.6.0 (https://github.com/dpryan79/MethylDackel) and DeepTools (v3.5.0). Allele-specific differentially CpG methylated sites between MSL2 KO and WT or between allele2 and allele1 were called with DSS version 2.34.0.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files: log2 ratio or subtract value over the input sample (merged replicates) . bed: peak calling from MACS2 (merged replicates). RData: differential peak calling result from CSAW and differential CpG methylation sites from DSS. tsv: differential expression analysis from DESeq2. txt: Differentially expression genes further classification into five cateogories.

molecule: total RNA

organism: Mus musculus

source_name: Neural progenitor cells

growth_protocol: Male mouse ES cells, obtained from Anne Ferguson-Smith (University of Cambridge), were cultured in NDiff 227 medium (Takara) supplemented with LIF (Millipore), 2i inhibitors (PD0325901 and CHIR99021, Stemgent). Female mouse ES cells, obtained from Edith Heard (EMBL Heidelberg), were cultured in KnockOut-DMEM (KO-DMEM, Gibco) supplemented with 15% KnockOut Serum Replacement (KOSR, Gibco), GlutaMAX (Gibco), non-essential amino acids (Gibco), sodium pyruvate (Gibco), 2-Mercaptoethanol (Gibco), LIF, and 2i inhibitors. Male and female ES cells were differentiated into NPCs as previously described (Conti et al. 2005; Splinter et al. 2011). In brief, 1 million male or female ES cells were plated on 0.1% gelatin-coated plates in N2B27 medium, consisting of 1:1 DMEM/F-12 (Gibco) and Neurobasal medium (Gibco), supplemented with B27 (Gibco), GlutaMAX, 2-Mercaptoethanol, Apo-transferrin (Sigma), bovine serum albumin (Sigma), insulin (Sigma), putrescine (Sigma), progesterone (Sigma), and sodium selenite (Sigma). After 7 days, cells were dissociated and 3 million cells were plated on non-adherent culture dishes in the presence of 10ng/ml epidermal growth factor (EGF, Peprotech) and 10ng/ml basic fibroblast growth factor (FGF, Peprotech) to induce formation of embryoid bodies. After 3 days, the embryoid bodies were transferred to gelatin-coated plates to allow the expansion of NPCs.

treatment_protocol: For the MSL2 knockout generation, two guide RNAs (gRNAs) were cloned into a PX-459 derivative (pSpCas9(BB)-2A-Puro) plasmid (Addgene 62988), and a split puromycin resistance or GFP-positive approach for selection was used (Flemr and Bühler 2015). Male and female ES cells and NPCs were transfected using Lipofectamine 3000 (Invitrogen) according to the manufacturer's instructions. After 48 hours, the cells were sorted based on their GFP expression status using a MoFlo XDP Cell Sorter (Beckman Coulter). Genomic DNA from single clones was isolated by resuspending cells in lysis buffer (10 mM Tris pH 8.0, 0.5 mM Ethylenediaminetetraacetic acid (EDTA), 0.5% Triton X-100) supplemented with Proteinase K (Thermo Scientific), and incubated at 55°C for 1 hour. Genomic DNA was collected after centrifugation at 16,000 g for 10 minutes. Polymerase chain reaction (PCR) was carried out using the 2X PCR Master Mix (Qiagen) at a final volume of 10μL. Successful knockout was verified using CloneJet PCR Cloning (Thermo Scientific) and BigDye Direct Sanger Sequencing (Thermo Scientific) kits according to the manufacturer’s instructions.

tag: strain

tag: gender

value: Female

tag: genotype

tag: library type

tag: replicate


title: DIRECT-K562-5


title: Mouse embyronic stem cells in 2D cell culture

type: RNA

city: Zhunan, Miaoli County

first: Chia-Chi

last: Chang

address: 35 Keyan Road

department: Institute of Cellular and System Medicine

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: Samples were hybridized with Mouse Gene 2.0 ST Array (Affymetrix) and scanned at the NHRI Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: The data were analyzed using Affymetrix Expression Console™ Software (version 1.4) default analysis settings and RMA (Robust Multi-Array) summarization and normalization options.

label: biotin

source_name: mESC, 72 h after 2D culture

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Plus cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: mESC are cultured in DMEM with 10% FBS, 10^3 U/mL LIF, 100µM NEAA, 1mM sodium pyruvate, 2mM L-glutamine, 71.4µM b-mercaptoethanol, 100 U/ml antibiotics. Cells were sub-cultured at the dilution of 1:10 to 1:20 at 80-90% conﬂuence.

extract_protocol: RNA was isolated with the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions. Inclusion of 1 U/ µL of the RiboLock RNase Inhibitor (Thermo) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with RQ1 RNase-Free DNasee (Peomega) to remove trace amounts of genomic DNA.

treatment_protocol: 2D culture condition: seeded 10^6 cells on cell culture dish for 3 days.

value: Embryonic stem cell

tag: culture condition


title: Mouse lung adenocarcinoma cell line in 3D cell culture

source_name: LLC, 72 h after 3D culture

growth_protocol: LLC are cultured in DMEM with 10% FBS, 100 U/ml antibiotics. Cells were sub-cultured at the dilution of 1:3 to 1:4 at 80-90% conﬂuence.

treatment_protocol: 3D culture condition: 10cm culture dishes were coated with 1% agarose to prevent cell adhesion and seeded 10^6 cells /agarose coated dish for 3 days.

value: Lung cancer cell


title: Mouse stromal cell line in 2D cell culture

source_name: M210B4, 72 h after 2D culture

growth_protocol: M210B4 are cultured in RPMI-1640 with 10% FBS, 100 U/ml antibiotics. Cells were sub-cultured at the dilution of 1:3 to 1:4 at 80-90% conﬂuence.

value: (C57BL/6J X C3H/HeJ)F1 mouse

value: Stromal cell


title: Mouse stromal cell line in 3D cell culture

source_name: M210B4, 72 h after 3D culture


title: Mouse embyronic stem cells in 3D cell culture

source_name: mESC, 72 h after 3D culture


title: shKRAS_1_S18

city: Pamplona

first: Silvestre

last: Vicent

state: Outside the US or Canada

address: 55 PIO XII Ave

department: Oncology

country: Spain

institute: Center for Applied Medical Research (CIMA)

data_processing:
The quality of the samples was verified using FastQC v0.11.3 software.
FASTQ files were mapped to hg19 human assembly using STAR v2.5.2b with default parameters.
featureCounts v1.5.0 software and Gencode v19 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: H358 cell line

growth_protocol: Cells were grown in RPMI1640 (10% FBS and 1% antibiotics)

extract_protocol:
RNA was processed using Trizol and cleaned using Qiagen columns. RNA quality was analysed using Experion™ (Bio-Rad) and only RNAs with RQI>7 were included in the experiment.
Library construction was done as reported in Jaitin, D.A., et al., Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science, 2014. 343(6172): p. 776-9.
Low input RNA-seq (mars-seq)

treatment_protocol: Cells were infected with 3 different shRNAs (GFPsh, FOSL1sh or KRASsh) for 2 days, then selected with puromycin for 3 days. Upon expansion of selected cells, shRNAs were induced by addition of 1 ug/ml doxycycline for 4 days, then trypsinized and plated for 24 h before RNA was harvested

value: shKRAS


title: 9sCa: NPCs_MSL2KO1_labeledTTseq_rep1


title: RKO, ATAC

city: Tokyo

first: Kiyoshi

last: Yamaguchi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Clinical Genome Research

country: Japan

institute: The University of Tokyo

description: 60-bp SE

library_source: genomic

data_processing:
Reads were aligned to the human genome (hg19) using Bowtie2 (v2.4.1).
Peak calling was performed using MACS3 (v3.0.0b3) with the significance cut-off q-value < 0.1.
Assembly: hg19
Supplementary files format and content: peaks.xls

molecule: genomic DNA

source_name: RKO

growth_protocol: SKBR3 and HCT116 cells were cultured in McCoy’s 5A medium, T47D in RPMI medium, RKO in DMEM containing 10% fetal bovine serum and antibiotic/antimycotic solution at 37°C under a humidified atmosphere containing 5% CO2.

extract_protocol:
Tagmentation reaction and purification of DNA were performed using ATAC-Seq Kit (cat# 53150, Active motif, Carlsbad, CA), according to the manufacturer's directions.
Libraries were also prepared using the ATAC-Seq Kit.

value: RKO

value: Colorectal cancer

value: WT


title: T47D, ATAC

description: 60-bp SE

value: Breast cancer


title: DIRECT-K562-3


title: HCT116, ATAC

description: 60-bp SE


title: 9sCa: NPCs_MSL2KO1_RNAseq_rep3

description:
NPCs_MSL2KO1_RNAseq.bw
NPCs_MSL2KO1_RNAseq.genome1.bw
NPCs_MSL2KO1_RNAseq.genome2.bw

data_processing:
RNAseq and TTseq: The data are processed via snakePipes mRNA-seq pipeline (developing branch) (Bhardwaj et al., 2019). SnakePipes removed adapters and low quality bases (< Q20) using TrimGalore (v0.6.5) with parameters '-q 20 --trim-n'. The trimmed reads are aligned with STAR (v2.7.4) (Dobin et al., 2013) to an ‘N-masked’ genome, which is a version of the mouse reference genome mm10 where all the polymorphicsites (SNPs) for Mus musculus CAST/EiJ and Mus musculus C57BL/6 (or 129S1/SvImJ) are masked by ambiguity nucleobase ‘N’ (Keane et al., 2011). The mapped reads are then passed to SNPSplit (0.3.4) (Krueger and Andrews, 2016) to generate allele-specific BAM files by separating the alignment into two distinct alleles (CAST/EiJ and C57BL/6 or 129S1/SvImJ) based on SNPs information downloaded from Mouse Genome Database (Keane et al., 2011). The aligned reads of standard and allele specific level are counted separately on Gencode GTF (m9) via featureCounts (v2.0.0) (Yang et al., 2014).
ChIPseq: The data are processed via snakePipes DNA-mapping and ChIP-seq pipeline (developing branch) (Bhardwaj et al., 2019). Adapters and low quality bases (< Q20) are removed using TrimGalore (v0.6.5) with parameters '-q 20 --trim-n'. For all samples, reads are then mapped to the ‘N-masked’’ genome with Bowtie2 (2.3.5) (Langmead and Salzberg, 2012). Reads mapped on blacklisted regions from Encode Consortium are discarded. Duplicated reads are also filtered with Picard MarkDuplicates (1.65) (https://broadinstitute.github.io/picard/). In the end, only properly paired mapped reads and reads with mapping quality over 3 are kept for further analysis. SNPSplit (0.3.4) (Krueger and Andrews, 2016) is then used to generate allele-specific BAM files and deepTools (v3.3.2) (Ramirez et al., 2014) is used to check data quality. In the ChIP-seq part, peak calling is performed with MACS2 (v2.2.6) (Zhang et al., 2008) with options [--qvalue 0.001]. It is done with input as control on total and allele specific ChIP-seq signals respectively. CSAW (v1.20.0) (Lun and Smyth, 2015) is additionally used to calculate log2FC on peak regions between MSL2 KO and WT or between allele2 and allele1. Bigwig files are created with deepTools bamCompare (v3.3.2) (Ramirez et al., 2014), using input normalization method and log2ratio and subtract option.
ATACseq: The data are processed via snakePipes DNA-mapping and ATAC-seq pipeline (developing branch) (Bhardwaj et al., 2019). In the DNA-mapping part, adapters and low quality bases (< Q20) are removed using TrimGalore (v0.6.5) with parameters '-q 20 --trim-n'. For all samples, reads are then mapped to the ‘N-masked’’ genome with Bowtie2 (v2.3.5) (Langmead and Salzberg, 2012). Reads mapped on blacklisted regions from Encode Consortium are discarded. Duplicated reads are also filtered with Picard MarkDuplicates (v1.65) (https://broadinstitute.github.io/picard/). In the end, only properly paired mapped reads and reads with mapping quality over 3 are kept for further analysis. SNPSplit (0.3.4) (Krueger and Andrews, 2016) is then used to generate allele-specific BAM files and deepTools (v3.3.2) (Ramirez et al., 2014) is used to check data quality. In the ATAC-seq part, the BAM files are filtered to include only properly paired reads with appropriate fragment sizes (<150 bases). To identify open/accessible regions, peak calling is done with MACS2 (v2.2.6) (Zhang et al., 2008) with options [--qvalue 0.001], on total and allele-specific ATAC-seq signal respectively. CSAW (v1.20.0) (Lun and Smyth, 2015) is additionally used to calculate log2FC on peak regions between MSL2 KO and WT or between allele2 and allele1. Bigwig files are created with deepTools bamCoverage (v3.3.2) (Ramirez et al., 2014), using size factor calculated by deepTools multiBamSummary (v3.3.2).
BSseq: Raw fastq files were aligned against the ‘N-masked’ genome and deduplicated using Bismark (v0.22.3) (Krueger and Andreas, 2011). Resulting Alignments were allele-separated using SNPsplit with flags '--paired' and '--bisulfite'. Relevant quality metrics (conversion rates, genome coverage and GC bias) were calculated using MethylDackel version 0.6.0 (https://github.com/dpryan79/MethylDackel) and DeepTools (v3.5.0). Allele-specific differentially CpG methylated sites between MSL2 KO and WT or between allele2 and allele1 were called with DSS version 2.34.0.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files: log2 ratio or subtract value over the input sample (merged replicates) . bed: peak calling from MACS2 (merged replicates). RData: differential peak calling result from CSAW and differential CpG methylation sites from DSS. tsv: differential expression analysis from DESeq2. txt: Differentially expression genes further classification into five cateogories.

value: RNAseq


title: DIRECT-K562-2


title: SKBR3, ATAC

description: 60-bp SE


title: shGFP_3_S25

value: shGFP


title: Cord blood mononuclear cells (CBPMCs) from symptomatic COVID+ human #9

city: PARIS 14EME ARRONDISSEMENT

first: Qui Trung

last: NGO

address: 24 rue du Faubourg Saint Jacques

country: France

institute: Institut Cochin (U1016 Inserm/UMR8104 CNRS/UMR-S8104)

description: sCOV 9

data_processing:
Fastq files were aligned using STAR algorithm (version 2.7.6a), on the Ensembl release 101 reference
Reads were then count using RSEM (v1.3.1) and the statistical analyses on the read counts were performed with R (version 3.6.3) and the DESeq2 package (DESeq2_1.26.0) to determine the proportion of differentially expressed genes between two conditions
We used the standard DESeq2 normalization method (DESeq2’s median of ratios with the DESeq function), with a pre-filter of reads and genes
Canonical pathways and upstream regulators analyses were performed using Ingenuity Pathway Analysis (IPA, Qiagen)
Assembly: Ensembl release 101, Homo sapiens GRCh38
Supplementary files format and content: txt files represent expected_count, TPM, FPKM values

source_name: Cord blood

extract_protocol:
Cord blood mononuclear cells were lysed and total RNA was extracted using MACHEREY-NAGEL NucleoSpin RNA extraction kit
RNA libraries for RNA-seq were prepared using NEBNext polyA + Ultra II Library Prep Kit following manufacturer's protocols.

tag: tissue

value: Cord blood

value: Cord blood mononuclear cells (CBPMCs)

tag: disease state

value: Symptomatic COVID+


title: shGFP_2_S22


title: DIRECT-K562-1


title: 9sCa: NPCs_MSL2KO1_RNAseq_rep2


title: Cord blood mononuclear cells (CBPMCs) from symptomatic COVID+ human #8

description: sCOV 8


title: 9sCa: NPCs_MSL2KO1_RNAseq_rep1


title: shGFP_1_S19


title: HDF cells, succinic acid+UVA, 3

city: Chengdu

first: Yu

last: Li

state: Sichuan

address: Guoxue Alley, No.37

department: Dermatology and venereology

institute: West China Hospital, Sichuan University

data_processing:
Quality control. Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis .
Reads mapping. The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
Expression analysis. We used HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Differential expression analysis. The difference expression of genes was analyzed by DESeq (v1.38.3) and bi-directional clustering analysis of all different genes of samples were performed by R language Pheatmap (v1.0.12) software package.
Enrichment analysis. New transcript analysis. Differential variable shear analysis. SNP and InDel analysis. Transcription factor family analysis.Exon difference analysis. Interaction Analysis of Differential Gene Protein Network
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: skin, dermis

growth_protocol: Human dermal fibroblasts (HDFs), derived from human skin specimens, were cultured with DMEM containing 10% FBS and 1% penicillin/streptomycin and 250 ng/mL amphotericin B in a 37 °C and 5% CO2 incubator. For all experiments, cells were used between 5 and 15 passages.

extract_protocol:
RNA was harvest using Invitrogen TRIzol method. 0.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using

treatment_protocol: HDFs were pretreated with 1 mg/mL Maifuyin (Mageline Biology Tech Co., Ltd) and 1 mg/mL succinic acid (Aladdin) for 24 hours. HDFs were washed twice with PBS, then resuspended in PBS and subjected to 2 J/cm2 UVA irradiation or untreated (control). Then,HDFs were incubated with new serum-free medium for 3 h. Next, cells were washed twice with PBS and mRNAs were isolated from cell cultures using the Trizol method.

value: skin, dermis

value: HDFs

value: human dermal fibroblast

value: succinic acid+UVA


title: 9sCa: NPCs_MSL2KO1_Pol2_rep2

description:
NPCs_MSL2KO1_Pol2.bw
NPCs_MSL2KO1_Pol2.genome1.bw
NPCs_MSL2KO1_Pol2.genome2.bw

value: Female


title: shFOSL1_3_S23


title: Cord blood mononuclear cells (CBPMCs) from symptomatic COVID+ human #7

description: sCOV 7


title: HDF cells, succinic acid+UVA, 2


title: Cord blood mononuclear cells (CBPMCs) from symptomatic COVID+ human #6

description: sCOV 6


title: shFOSL1_2_S20


title: Cord blood mononuclear cells (CBPMCs) from symptomatic COVID+ human #5

description: sCOV 5


title: HDF cells, succinic acid+UVA, 1


title: 9sCa: NPCs_MSL2KO1_Pol2_rep1


title: HDF cells, Maifuyin+UVA, 3

value: Maifuyin+UVA


title: shFOSL1_1_S17


title: 9sCa: NPCs_MSL2KO1_MSL2_rep2

description:
NPCs_MSL2KO1_MSL2.bw
NPCs_MSL2KO1_MSL2.genome1.bw
NPCs_MSL2KO1_MSL2.genome2.bw


title: Cord blood mononuclear cells (CBPMCs) from symptomatic COVID+ human #3

description: sCOV 3


title: HDF cells, Maifuyin+UVA, 1


title: Tram_2

data_processing:
The quality of the samples was verified using FastQC v0.11.5 software.
FASTQ files were mapped to hg38 human assembly using STAR v2.5.3a with default parameters.
featureCounts v1.6.0 software and Gencode v28 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: H1792 cell line treated with Trametinib (MEKi) for 16 hours

growth_protocol: H1792 were grown in 10% FBS-supplemented RPMi1640

extract_protocol:
RNA was processed using Trizol and cleaned using Qiagen columns. RNA quality was analysed using Experion™ (Bio-Rad) and only RNAs with RQI>7 were included in the experiment.
Library construction was done as reported in Jaitin, D.A., et al., Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science, 2014. 343(6172): p. 776-9; Low input RNA-seq (mars-seq)

treatment_protocol: Cells were treated with 0.5 uM trametinib and 0.625 uM lestaurtinib for 16 hours


title: Tram_3


title: 9sCa: NPCs_MSL2KO1_MSL2_rep1


title: HDF cells, Maifuyin+UVA, 2


title: 9sCa: NPCs_MSL2KO1_MOF_rep1

description:
NPCs_MSL2KO1_MOF.bw
NPCs_MSL2KO1_MOF.genome1.bw
NPCs_MSL2KO1_MOF.genome2.bw
NPCs_MSL2KO1_MOF_peaks.bed


title: Tram_1


title: 9sCa: NPCs_MSL2KO1_MOF_rep2


title: HDF cells, UVA, 3

value: UVA


title: 9sCa: NPCs_MSL2KO1_KANSL3_rep2

description:
NPCs_MSL2KO1_KANSL3.bw
NPCs_MSL2KO1_KANSL3.genome1.bw
NPCs_MSL2KO1_KANSL3.genome2.bw
NPCs_MSL2KO1_KANSL3_peaks.bed


title: Cord blood mononuclear cells (CBPMCs) from symptomatic COVID+ human #1

description: sCOV 1


title: Lest_3

source_name: H1792 cell line treated with Lestaurtinib (multikinase FLT3i) for 16 hours


title: Cord blood mononuclear cells (CBPMCs) from asymptomatic COVID+ human #3

description: aCOV 3

value: Asymptomatic COVID+


title: 9sCa: NPCs_MSL2KO1_KANSL3_rep1


title: Lest_2


title: HDF cells, UVA, 1


title: Lest_1


title: 9sCa: NPCs_MSL2KO1_KANSL1_rep2

description:
NPCs_MSL2KO1_KANSL1.bw
NPCs_MSL2KO1_KANSL1.genome1.bw
NPCs_MSL2KO1_KANSL1.genome2.bw
NPCs_MSL2KO1_KANSL1_peaks.bed


title: Cord blood mononuclear cells (CBPMCs) from asymptomatic COVID+ human #2

description: aCOV 2


title: Cord blood mononuclear cells (CBPMCs) from symptomatic COVID+ human #4

description: sCOV 4


title: HDF cells, control, 3

value: control


title: Cord blood mononuclear cells (CBPMCs) from asymptomatic COVID+ human #1

description: aCOV 1


title: 9sCa: NPCs_MSL2KO1_KANSL1_rep1


title: CTL_3

source_name: H1792 cell


title: 9sCa: NPCs_MSL2KO1_Input4_rep2

description: Same batch as H4K5ac, H4K12ac


title: HDF cells, control, 2


title: Cord blood mononuclear cells (CBPMCs) from COVID- human #5

description: CTL 5

value: COVID-


title: Cord blood mononuclear cells (CBPMCs) from COVID- human #3

description: CTL 3


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, TCR, tube6B

city: San Diego

first: Ashu

last: Sethi

state: CA

address: 9420 Athena Circle

department: Health Sciences

country: USA

institute: La Jolla Institute for Immunology

description:
polyA RNA
10x Genomics

library_source: transcriptomic single cell

data_processing:
Data processing was done using Cell Ranger software v5.0.0.
The illumina barcode demultiplexing was performed using mkfastq
Alignment with reference GRCh38 (GENCODE v32/Ensembl 98) and gene counting were done using Multi program
R package Seurat was used for downstream clustering and UMAP analysis
Seurat's function MultiSeqDemux was used for hashtag demultiplexing and singlet assignment
Assembly: GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: seurat metadata

source_name: Blood

extract_protocol:
For single cell RNA-seq assays, we used the 10x Genomics platform. For each patient sample, the maximum amount of CM+ memory T cells and 15,000 CM- cells were collected in low retention and sterile ice-cold 1.5 mL tubes containing 500 μL of PBS - FBS (1:1 volume) completed with RNase inhibitor (1:100). Each experiment of 12 patients generated 4 tubes where each combined the CM- fraction of 3 subjects with the CM+ fraction of 3 different subjects. Approximately 50,000 sorted cells per tube were processed and loaded on the 10X Chromium Controller (10X Genomics). We used a 5’mRNA capture chemistry (5’ 10X v2 chemistry) and performed cDNA amplification and library preparation for gene expression, feature barcoded surface antibodies, and TCR according to manufacturer's protocol.
Final libraries were quality checked for fragment size by capillary electrophoresis (Fragment analyzer), and quantity by fluorescence assay (Picogreen) before pooling and sequencing on a NovaSeq 6000 (200 cycle S4 kit v1.5; Illumina, San Diego, CA, USA) to a depth of > 25,000 reads/cell for GEX, > 5,000 reads/cell for hashtag oligo libraries, and >5,000 reads/cell for TCR libraries.

treatment_protocol: PBMC stimulated with cow milk epitope pool (M111) for 6 hours and then sorted for CD4 memory T cells either positive for  CD154, CD137, both (Positive) or none (Negative)

value: Blood

value: CD4 memory T cells

value: Cow milk epitope pool


title: Cord blood mononuclear cells (CBPMCs) from COVID- human #2

description: CTL 2


title: Cord blood mononuclear cells (CBPMCs) from symptomatic COVID+ human #2

description: sCOV 2


title: EndoC,HNF1A,CUT&RUN

city: cleveland

first: Peidong

last: Gao

state: Ohio

address: 10900 Euclid Avenue

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Using the default settings of bowtie2 v2.2.6 to align the paired-end raw reads.
Next, we use samtools v1.3.1 to sort and extract uniquely mapped reads.
Then we remove PCR duplications with the default parameter by using picard v1.93, and MACS2 v2.2.7.1 was used to call peaks.
After having the non-duplicated sorted bam file we converted bam files to bedgraph files using bedtools v 2.25 (bamtobed,genomecov).
Finally we use bedGraphToBigWig to convert bedGraph to bigWig file then upload to UCSC for track graphing.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

growth_protocol: EndoC-βH3 cells were cultured on 10cm TPP plates (Sigma #Z707686) as described1. Plates were first coated with ECM solution (10ml of DMEM (Gibco #11960044), 100ul ECM gel (Sigma #E1270), 20ul fibronectin (Sigma #F1141), 100ul Streptomycin-Penicillin (Gibco #15140122), 5ml per 10cm dish) for 1hr at 37°C before use. Cells were cultured in DMEM (Sigma #D6046) with 2% BSA fraction V (Sigma #10775835001), 50uM 2-mercaptoethanol (Gibco #31350010), 10mM Nicotinamide (Sigma #481907), 5.5ug/ml Transferrin (Sigma #T8158), 6.7ng/ml sodium selenite (Sigma #214485), and Penicillin/Streptomycin (Gibco #15140122). Before use, cells were treated with 1uM tamoxifen (Selleck #S7827) 2x/week for 21 days. Successful excision of the immortalizing transgene was confirmed by observing the cell morphology.

extract_protocol:
CUTANA™ ChIC / CUT&RUN Assays
CUTANA™ CUT&RUN Library Prep Kit, primer set two

value: Beta cell

value: tamoxifen 21 days


title: Cord blood mononuclear cells (CBPMCs) from COVID- human #4

description: CTL 4

value: Cord blood

value: Cord blood mononuclear cells (CBPMCs)


title: 9sCa: NPCs_MSL2KO1_Input4_rep1

description: Same batch as H4K5ac, H4K12ac


title: 9sCa: NPCs_MSL2KO1_Input2_rep2

description: Same batch as MSL2, DNMT3A, DNMT3B


title: CTL_2


title: HDF cells, control, 1

value: skin, dermis

value: WT


title: WT mice, vehicle treated, rep5

city: South San Francisco

first: Brad

middle: A

last: Friedman

address: 1 DNA Way

department: Neuroinformatics

institute: Genentech, Inc.

data_processing:
The fastq sequence files for all RNA-seq samples were filtered for read quality (keeping reads where at least 70% of the cycles had Phred scores ≥ 23), and ribosomal RNA contamination. The remaining reads were aligned to the mouse reference genome (GRCm38) using the GSNAP alignment tool
These steps, and the downstream processing of the resulting alignments to obtain read counts were implemented in the Bioconductor package HTSeqGenie.
Differential gene expression analysis was performed with voom+limma
Genome_build: GRCm38
Supplementary_files_format_and_content: .rData file containing summarizedExperiment of raw-counts, with row and column metadata

source_name: Bulk tissue: whole brain hemisphere

growth_protocol: TPL2 kinase-deficient mice carrying D270A mutation were generated in-house. All TPL2-KD mice were homozygous for the TPL2-D270A mutation. Cohorts were produced with all genotypes as littermates.

extract_protocol:
RNA was extracted from samples using Qiagen RNeasy Plus Mini Kit. Concentration of RNA samples was determined using NanoDrop 8,000 (Thermo Scientific) and RNA integrity was determined by Fragment Analyzer (Advanced Analytical Technologies). 0.5 μg of total RNA was used as an input material for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). Library size was confirmed using a Fragment Analyzer (Advanced Analytical Technologies). Library concentrations were determined by qPCR-based using a Library quantification kit (KAPA).
The libraries were multiplexed and then sequenced on Illumina HiSeq2500 (Illumina) to generate 30 M of single end 50 base pair reads per library.

treatment_protocol: ~3-month-old WT or TPL2-KD mice were injected with PBS vehicle control or LPS (10 mg/kg) (n =5 per condition). 24 hours later, mice were perfused with cold PBS and the mouse hemi brains were immediately sub-dissected and preserved in RNAlater.

value: Vehicle

tag: sampleID


title: CTL_1


title: HDF cells, UVA, 2

value: HDFs

value: human dermal fibroblast


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube6B

description:
polyA RNA
10x Genomics


title: WT mice, vehicle treated, rep4


title: 9sCa: NPCs_MSL2KO1_Input2_rep1

description: Same batch as MSL2, DNMT3A, DNMT3B

value: Female


title: Cord blood mononuclear cells (CBPMCs) from COVID- human #1

description: CTL 1


title: 9sCa: NPCs_MSL2KO1_Input1_rep2

description: Same batch as NRF1, BRD4, KANSL1, KANSL3, MOF, Pol2


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube6B

description:
protein
10x Genomics


title: 9sCa: NPCs_MSL2KO1_Input1_rep1


title: Human H1

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

data_processing:
RSEM: Reads were mapped to the human genome using Bowtie 0.12.8 (Langmead et al. 2009) allowing up to 2-mismatches. The gene expression values are estimated by RSEM tool
CRSP: we used CRSP tool to estimate the gene expression values without mapping to human genome or reference genes. The purpose is to compare our CRSP tool (without genome mapping) with RSEM tool (gold-standarded method).
Genome_build: hg19
Supplementary_files_format_and_content: H1_PairedEnd.RSEM.results: Gene expression values output from RSEM tool
Supplementary_files_format_and_content: H1_PairedEnd.CRSP.results: Gene expression values output from CRSP tool (without relying on human genome or gene annotations)

source_name: Human H1 ES cells

growth_protocol: Human ES (H1) cells

extract_protocol: Illumina truSeq Protocol

treatment_protocol: No treatment

value: ES cell line


title: WT mice, vehicle treated, rep2


title: WT mice, vehicle treated, rep3


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, TCR, tube6A

description:
polyA RNA
10x Genomics


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, TCR, tube5B

description:
polyA RNA
10x Genomics


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube6A

description:
polyA RNA
10x Genomics


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube5B

description:
polyA RNA
10x Genomics


title: WT mice, LPS treated, rep3

value: LPS


title: D16-1T-H

city: Shanghai

first: qiudong

last: zhao

address: 225 Changhai Road

department: Tumor Immunology and Gene Therapy Center

institute: Shanghai Eastern Hepatobiliary Surgery Hospital

description: 10x Genomics

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 30%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: Rnor_6.0 (Ensembl release 93)
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

organism: Rattus norvegicus

source_name: tumor

extract_protocol:
Each sample was placed in a sterile Petri dish on ice. Fat, fibrous and necrotic areas were removed, and the tissue was subsequently minced to smaller pieces of less than 3 mm. Samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with collagenase Ⅱ (Worthington) for 60 min at 37°C, with agitation. Subsequently, the sample was filtered using a 70-mm nylon mesh (Miltenyi #130-095-823). 10 ml of this cell suspension was counted by Trypan Blue to determine the concentration of live cells. The sample was then centrifuged at 300g and 4℃ for 5 min, and the supernatant was discarded. The cell pellet was resuspended in 1 ml freezing media (Gibco) for long term cryopreservation in liquid nitrogen. Throughout the dissociation procedure, cells were maintained on ice whenever possible, and the entire procedure was completed in less than 1 hr.
Cryopreserved single-cell suspensions were promptly thawed and prepared as outlined by the 10x Genomics Single Cell 30 v3 Reagent Kit user guide.

value: tumor

tag: Sex

value: male

value: DEN

tag: time

value: 16 week


title: 9sCa: NPCs_MSL2KO1_H4K5ac_rep2

description:
NPCs_MSL2KO1_H4K5ac.bw
NPCs_MSL2KO1_H4K5ac.genome1.bw
NPCs_MSL2KO1_H4K5ac.genome2.bw

source_name: Neural progenitor cells


title: WT mice, LPS treated, rep5


title: WT mice, vehicle treated, rep1


title: 9sCa: NPCs_MSL2KO1_H4K16ac_rep1

description:
NPCs_MSL2KO1_H4K16ac.bw
NPCs_MSL2KO1_H4K16ac.genome1.bw
NPCs_MSL2KO1_H4K16ac.genome2.bw


title: D12-1-H

description: 10x Genomics

source_name: liver

value: liver

value: 12 week


title: 9sCa: NPCs_MSL2KO1_H4K5ac_rep1


title: 9sCa: NPCs_MSL2KO1_H4K16ac_rep2


title: D12-2-H

description: 10x Genomics


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube5B

description:
protein
10x Genomics

value: Blood

value: CD4 memory T cells

value: Cow milk epitope pool


title: 9sCa: NPCs_MSL2KO1_H4K12ac_rep2

description:
NPCs_MSL2KO1_H4K12ac.bw
NPCs_MSL2KO1_H4K12ac.genome1.bw
NPCs_MSL2KO1_H4K12ac.genome2.bw


title: D16-1P-H

description: 10x Genomics


title: WT mice, LPS treated, rep2


title: D8-1-H

description: 10x Genomics

value: 8 week


title: 9sCa: NPCs_MSL2KO1_H4K12ac_rep1


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube6A

description:
protein
10x Genomics


title: WT mice, LPS treated, rep4

value: WT


title: D4-1-H

description: 10x Genomics

value: 4 week


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, TCR, tube5A

description:
polyA RNA
10x Genomics


title: WT mice, LPS treated, rep1


title: 9sCa: NPCs_MSL2KO1_H3-4_rep2

description: Same batch as H4K5ac, H4K12ac


title: TPL2KD mice, vehicle treated, rep4

value: Vehicle

value: TPL2 KD


title: Nor-1-H

description: 10x Genomics

value: normal

value: 0 week


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube5A

description:
polyA RNA
10x Genomics


title: rna_C57_Kupffer_AMLN_30weeks_rep4

city: La Jolla

first: Hunter

last: Bennett

state: California

address: 9500 Gilman Drive, MC 0651

department: Dept. of Cellular & Molecular Medicine

institute: University of California, San Diego

description:
f0_tpm.txt
f0_tpm.txt

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the strain specific genome, mm10 was used for C57BL/6J (Link et al., 2018). MMARGE was used to shift strain specific alignment to the mm10 genome. STAR was used with default parameters was used to map RNA-seq experiments (Dobin et al., 2013). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
Each experiment was quantified using the “analyzeRepeats” script of HOMER. To generate a table of raw read counts, the parameters -count exons -condenseGenes - noadj were used. To generate a table of TPM values, the parameters -count exons  -tpm were used. Differentially expressed genes were identified using raw sequencing read counts by DESeq2 (Love et al., 2014) analysis through the “getDifferentialExpression” HOMER command. Gene ontology analysis was performed using Metascape (Tripathi et al., 2015).
CB6F1/J data was mapped to both the C57BL/6J and BALB/cJ genome, strain specific mappings were shifted to the reference genome using MMARGE shift (Link et al., 2018). Finally, perfectly aligned reads overlying strain specific mutations were isolated using MMARGE allele specific reads command. As such, the processed data matrices for f1 data include two entries per sample, one initially aligned to the C57BL/6J genome and one initially aligned to the BALB/cJ genome, both then shifted to the mm10 genome.
Assembly: mm10
Supplementary files format and content: Tab delimited text files of the folllowing: Table of unnormalized read counts RNA-seq and table of TPM values for RNA-Seq

molecule: polyA RNA

source_name: Kupffer Cells, C57BL/6J, AMLN 30 weeks

extract_protocol:
extract protocol, non-parenchymal cells (Kupffer cells, Stellate cells, liver sinusoidal endoethelial cells)
Mice were humanely euthanized by exposure to CO2 and liver non-parenchymal cells processed for fluorescence activated cell sorting of Kupffer cells, with modifications from published methodology (Seidman et al., 2020; Sakai et al., 2019). In brief, livers were retrograde perfused for 3 min at a rate of 5-7 ml/min through the inferior vena cava with HBSS without Ca++ or Mg++ supplemented with 0.5 mM EGTA, 0.5 mM EDTA, and 20 mM HEPES. Perfusions were then switched to 40 ml of a digestion buffer, held at 37C, comprised of HBSS with Ca++ and Mg++ supplemented with 0.033 mg/ml of Liberase TM (Roche), 20 μg/ml DNaseI (Worthington), and 20 mM HEPES. Livers were then excised, minced, and digested for an additional 20 minutes in vitro at 37C with gentle rotation in 20 ml of fresh digestion buffer. The perfusion and digestion steps were performed in the presence of 1 μM flavopiridol to offset transcriptional changes associated with digestion. After tissue digestion, cells were passed through a 70-micron cell strainer and hepatocytes removed by 2 low-speed centrifugation steps at 50 X G for 2 min. Nonparenchymal cells in the supernatant were further separated from debris by pelleting for 15 min at 600 X G in 50 ml of 20% isotonic Percoll (Sigma Aldrich) at room temperature. Cells were then washed from Percoll containing buffer and suspended in 10 ml 28% OptiPrep (Sigma Aldrich) and carefully underlaid beneath 3 ml of wash buffer. The resulting gradient was centrifuged at 1,400 X G for 25 minutes at 4C with no break and cells enriched at the interface were saved and subjected to isotonic erythrocyte lysis. Enriched non-parenchymal cells were then washed, suspended in PBS, then stained for 10 minutes with Zombie NIR (BioLegend) and purified anti-CD16/32 (93, BioLegend) to label dead cells and block Fc receptors. Cells were then immunolabeled with specific antibodies of interest, washed, and sorted using a Beckman Coulter MoFlo Astrios EQ configured with spatially separated 355 nm, 405 nm, 488 nm, 561 nm, and 642 nm lasers.
extract protocol, hepatocyes
Hepatocytes were prepared by perfusion digestion in a retrograde fashion through the inferior vena cava to the portal vein. In brief, livers were blanched with clearing buffer, then digested with a collagenase solution at 39C. Livers were perfused for 18 minutes at 5 ml/min. The perfusion and digestion steps were performed in the presence of 1 mM flavopiridol to offset transcriptional changes associated with digestion. After digestion, individual livers were gently dissociated using forceps in Medium 199 supplemented with 5% FBS and penicillin/streptomycin/gentamycin. Crude hepatocyte preps were carefully strained through a 100-micron strainer into and isolated using a Percoll gradient.
extract protocol, BMDMs
Mice were humanely euthanized by exposure to CO2 and bone marrow from femur, tibia, and iliac bones was isolated as described previously (Link et al., 2018). Bone marrow cells were seeded innon- tissue culture plates in m-CSF enriched media. After an additional 4-5 days of culture, non-adherent cells were washed off with room temperature PBS, and adherent macrophages were obtained by scraping.
Performed as published previously (Gosselin et al., 2017; Oishi et al., 2016). Isolated cells were pelleted and put into 150 μl lysis/Oligo d(T) Magnetic Beads binding buffer and stored at -80°C until processing. mRNAs were enriched by incubation with Oligo d(T) Magnetic Beads (NEB, S1419S) and then fragmented/eluted by incubation at 94°C for 9 min. Poly A enriched mRNA was fragmented, in 2x Superscript III first-strand buffer with 10mM DTT (Invitrogen), by incubation at 94°C for 9 minutes, then immediately chilled on ice before the next step. The 10 μL of fragmented mRNA, 0.5 μL of Random primer (Invitrogen), 0.5 μL of Oligo dT primer (Invitrogen), 0.5 μL of SUPERase-In (Ambion), 1 μL of dNTPs (10 mM) and 1 μL of DTT (10 mM) were heated at 50°C for three minutes. At the end of incubation, 5.8 μL of water, 1 μL of DTT (100 mM), 0.1 μL Actinomycin D (2 μg/μL), 0.2 μL of 1% Tween-20 (Sigma) and 0.2 μL of Superscript III (Invitrogen) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads according to manufacturer's instruction and eluted with 10 μL nuclease-free water. The RNA/cDNA double-stranded hybrid was then added to 1.5 μL of Blue Buffer (Enzymatics), 1.1 μL of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 μL of RNAse H (5 U/μL), 1.05 μL of water, 1 μL of DNA polymerase I (Enzymatics) and 0.15 μL of 1% Tween-20. The mixture was incubated at 16°C for 1 hour. The resulting dUTP-marked dsDNA was purified using 28 μL of Sera-Mag Speedbeads (Thermo Fisher Scientific), diluted with 20% PEG8000, 2.5M NaCl to final of 13% PEG, eluted with 40 μL EB buffer (10 mM Tris-Cl, pH 8.5) and frozen at -80°C. The purified dsDNA (40 μL) underwent end repair by blunting, A-tailing and adapter ligation as previously described (Heinz et al., 2010) using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 9-14 cycles, size selected by gel extraction, quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and sequenced on a Hi-seq 4000 or a NextSeq 500 (Illumina, San Diego, CA) according to the manufacturer's instructions.

treatment_protocol: For in vivo LPS experiments male mice were fasted overnight and treated for 2 hours by intraperitoneal injection of 0.1 mg/kg E. coli O114:B4 lipopolysaccharide. Control mice were equivalently fasted but uninjected. For in vitro BMDM LPS experiments macrophages were treated with 100 ng/ml Kdo2-lipid A (Avanti lipids), a highly purified E. coli lipopolysaccharide or an equivalent volume of PBS.

tag: source

value: Sorted non-parenchymal cells

value: Kupffer cell

value: AMLN Diet 30 weeks


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube5A

description:
protein
10x Genomics


title: 9sCa: NPCs_MSL2KO1_H3-2_rep2

description: Same batch as MSL2, DNMT3A, DNMT3B

value: Female


title: TPL2KD mice, vehicle treated, rep3


title: rna_C57_Kupffer_AMLN_30weeks_rep3

description:
f0_tpm.txt
f0_raw.txt


title: rna_C57_Kupffer_AMLN_30weeks_rep2

description:
f0_tpm.txt
f0_raw.txt


title: TPL2KD mice, vehicle treated, rep2


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, TCR, tube4B

description:
polyA RNA
10x Genomics


title: 9sCa: NPCs_MSL2KO1_H3-4_rep1

description: Same batch as H4K5ac, H4K12ac


title: rna_C57_Kupffer_AMLN_30weeks_rep1

description:
f0_tpm.txt
f0_raw.txt


title: TPL2KD mice, LPS treated, rep4

value: LPS


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube4B

description:
protein
10x Genomics


title: rna_C57_Kupffer_NSG_rep2

description:
f0_tpm.txt
f0_raw.txt

source_name: Recruited Kupffer Cells, C57BL/6J, NSG Transplant

value: NSG Transplant


title: rna_C57_Kupffer_NSG_rep3

description:
f0_tpm.txt
f0_raw.txt


title: 9sCa: NPCs_MSL2KO1_H3-1_rep2


title: 9sCa: NPCs_MSL2KO1_H3-2_rep1

description: Same batch as MSL2, DNMT3A, DNMT3B


title: 9sCa: NPCs_MSL2KO1_H3-1_rep1


title: TPL2KD mice, LPS treated, rep2


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, TCR, tube4A

description:
polyA RNA
10x Genomics


title: 9sCa: NPCs_MSL2KO1_DNMT3B_rep2

description:
NPCs_MSL2KO1_DNMT3B.bw
NPCs_MSL2KO1_DNMT3B.genome1.bw
NPCs_MSL2KO1_DNMT3B.genome2.bw


title: 9sCa: NPCs_MSL2KO1_DNMT3A_rep2

description:
NPCs_MSL2KO1_DNMT3A.bw
NPCs_MSL2KO1_DNMT3A.genome1.bw
NPCs_MSL2KO1_DNMT3A.genome2.bw


title: TPL2KD mice, LPS treated, rep3


title: 9sCa: NPCs_MSL2KO1_DNMT3B_rep1


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube4A

description:
protein
10x Genomics


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube4A

description:
polyA RNA
10x Genomics


title: rna_C57_Kupffer_NSG_rep1

description:
f0_tpm.txt
f0_raw.txt


title: rna_BALB_Kupffer_NSG_rep3

description:
f0_tpm.txt
f0_raw.txt

source_name: Recruited Kupffer Cells, BALB/cJ, NSG Transplant

value: BALB/cJ


title: Ampk InsMet  poly rep2

first: April

middle: Elizabeth

last: Williams

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
Library strategy: Ribosome profiling
First, adapter trimming was performed with cutadapt (v1.14).
Next, reads were mapped with STAR (v2.4.0i) against a database of repetitive elements, with mapping reads discarded from further analysis.
Remaining reads were then mapped to the mouse genome (mm10) with STAR (v2.4.0i)
Stranded reads mapping to GENCODE (vM20) genes were quantified with featureCounts (subread-1.6.4). Mitochondrial genes were discarded, and only genes with at least 0.5 reads per million across all datasets were kept for further analysis.
Differential expression in polysome versus input was quantified with edgeR (v3.26.8) with dispersion = 0.06 estimated from the subset of experiments with multiple replicates.
Genome_build: mm10
Supplementary_files_format_and_content: EdgeR output files (*.txt.gz*) contain gene identifier, log(fold-change in polysome versus input), log(counts per million), and p-value (polysome versus input)

source_name: Primary Hepatocytes

growth_protocol: Primary hepatocytes were isolated from mice 8-16 weeks of age following Tamoxifen treatment to induce deletion of Tsc2 and AMPK, cells were plated in serum for 3-4 hours then moved to serum free media for 16h prior to treatment

extract_protocol:
Cells were snap frozen, lysed in polysome buffer, put through sucrose gradient and fractionated (ribosome associated only), RNA isolated using Trizol LS and zymo direct-zol RNA purification kit
mRNA-seq libraries were prepared using the TruSeq RNA library preparation kit (version 2)

treatment_protocol:
Cells in serum-free media were treated with metformin or Ink in the presence or absence of Insulin 15' pretreatment
Cells were treated with cyclohexamide 10' prior to collection

value: C57BL/6 (F3 generation)

value: primary hepatocytes

tag: age

value: 8-16 weeks old

value: Ampka1 fl/fl; Ampka2 fl/fl; AlbCreER

tag: tamoxifen treatment

value: Tamoxifen treatment 3x 14-17 days prior to hepatocyte isolation

tag: metformin treatment

value: 2mM Metformin for 2h serum-starved

tag: insulin treatment

value: 15 minute pre-treatment with 1nM Insulin

tag: rna fraction

value: polysome fractionated samples


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube4B

description:
polyA RNA
10x Genomics

value: Blood

tag: cell type

value: CD4 memory T cells

tag: treatment

value: Cow milk epitope pool


title: TPL2KD mice, vehicle treated, rep1

tag: strain

value: Vehicle

tag: genotype

value: TPL2 KD


title: TPL2KD mice, LPS treated, rep1


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, TCR, tube3B

description:
polyA RNA
10x Genomics


title: 9sCa: NPCs_MSL2KO1_DNMT3A_rep1

tag: gender

value: Female

tag: library type

tag: replicate


title: rna_BALB_Kupffer_NSG_rep2

description:
f0_tpm.txt
f0_raw.txt

value: Sorted non-parenchymal cells

value: Kupffer cell


title: Ampk InsMet  poly rep1

tag: tissue


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube3B

description:
polyA RNA
10x Genomics


title: 9sCa: NPCs_MSL2KO1_BSseq_rep2

description:
NPCs_MSL2KO1_BSseq.bw
NPCs_MSL2KO1_BSseq.genome1.bw
NPCs_MSL2KO1_BSseq.genome2.bw

value: BSseq


title: rna_BALB_Kupffer_NSG_rep1

description:
f0_tpm.txt
f0_raw.txt

value: BALB/cJ

value: NSG Transplant


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube3B

description:
protein
10x Genomics


title: Ampk Ins  poly rep1

value: C57BL/6 (F3 generation)

value: primary hepatocytes

value: 8-16 weeks old

value: untreated - serum starved


title: rna_C57_Hepatocyte_Control_rep2

description:
f0_tpm.txt
f0_raw.txt

source_name: Hepatocytes, C57BL/6J, Control

value: Purified hepatocytes

value: Hepatocyte

value: Control


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube3A

description:
protein
10x Genomics

value: Blood

value: CD4 memory T cells


title: Ampk Ins  poly rep2

value: Ampka1 fl/fl; Ampka2 fl/fl; AlbCreER

value: Tamoxifen treatment 3x 14-17 days prior to hepatocyte isolation

value: 15 minute pre-treatment with 1nM Insulin

value: polysome fractionated samples


title: rna_BALB_Hepatocyte_Control_rep2

description:
f0_tpm.txt
f0_raw.txt

source_name: Hepatocytes, BALB/cJ, Control


title: 9sCa: NPCs_MSL2KO1_BRD4_rep2

description:
NPCs_MSL2KO1_BRD4.bw
NPCs_MSL2KO1_BRD4.genome1.bw
NPCs_MSL2KO1_BRD4.genome2.bw

value: Female


title: AATsc InsMet  poly rep2

value: Raptor - S722A; S792A; Tsc2 fl/fl; AlbCreEr

value: 2mM Metformin for 2h serum-starved


title: 9sCa: NPCs_MSL2KO1_ATACseq_rep3

description:
NPCs_MSL2KO1_ATACseq.bw
NPCs_MSL2KO1_ATACseq.genome1.bw
NPCs_MSL2KO1_ATACseq.genome2.bw

value: ATACseq


title: Ampk Met  poly

value: C57BL/6 (F3 generation)

value: Untreated


title: rna_C57_Hepatocyte_Control_rep1

description:
f0_tpm.txt
f0_raw.txt


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube3A

description:
polyA RNA
10x Genomics

value: Cow milk epitope pool


title: Ampk UT  poly

value: primary hepatocytes

value: 8-16 weeks old

value: untreated - serum starved


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube2B

description:
polyA RNA
10x Genomics


title: rna_BALB_Hepatocyte_Control_rep1

description:
f0_tpm.txt
f0_raw.txt

value: Purified hepatocytes

value: Hepatocyte

value: BALB/cJ

value: Control


title: 9sCa: NPCs_MSL2KO1_BRD4_rep1


title: AATsc InsMet  poly rep1

value: Tamoxifen treatment 3x 14-17 days prior to hepatocyte isolation


title: rna_AJ_Hepatocyte_Control_rep2

description:
f0_tpm.txt
f0_raw.txt

source_name: Hepatocytes, A/J, Control

value: A/J


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube2B

description:
protein
10x Genomics

value: Blood

value: CD4 memory T cells


title: 9sCa: NPCs_MSL2KO1_ATACseq_rep1

value: Female


title: 9sCa: NPCs_MSL2KO1_BSseq_rep1

value: BSseq


title: rna_C57_Hepatocyte_Control_rep3

description:
f0_tpm.txt
f0_raw.txt


title: AATsc Ins  poly rep2

value: Raptor - S722A; S792A; Tsc2 fl/fl; AlbCreEr

value: 15 minute pre-treatment with 1nM Insulin

value: polysome fractionated samples


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, TCR, tube3A

description:
polyA RNA
10x Genomics

value: Cow milk epitope pool


title: rna_AJ_Hepatocyte_Control_rep1

description:
f0_tpm.txt
f0_raw.txt


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, TCR, tube2A

description:
polyA RNA
10x Genomics


title: rna_C57_Stellate_Control_rep3

description:
f0_tpm.txt
f0_raw.txt

source_name: Stellate Cells, C57BL/6J, Control

value: Sorted non-parenchymal cells

value: Stellate cell


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, TCR, tube2B

description:
polyA RNA
10x Genomics


title: AATsc Ins  poly rep1

value: C57BL/6 (F3 generation)

value: primary hepatocytes

value: 8-16 weeks old

value: untreated - serum starved


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube2A

description:
protein
10x Genomics


title: rna_C57_Stellate_Control_rep2

description:
f0_tpm.txt
f0_raw.txt

value: Control


title: 9sCa: NPCs_MSL2KO1_ATACseq_rep2

value: ATACseq


title: AATsc Met  poly

value: Tamoxifen treatment 3x 14-17 days prior to hepatocyte isolation

value: 2mM Metformin for 2h serum-starved

value: Untreated


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube2A

description:
polyA RNA
10x Genomics

value: Blood

value: CD4 memory T cells


title: rna_C57_Stellate_Control_rep1

description:
f0_tpm.txt
f0_raw.txt


title: 9sCa: NPCs_Control_labeledTTseq_rep1

value: Female

value: WT

value: labeledTTseq


title: 9sCa: NPCs_Control_labeledTTseq_rep2


title: 9sCa: NPCs_Control_RNAseq_rep3

description:
NPCs_Control_RNAseq.bw
NPCs_Control_RNAseq.genome1.bw
NPCs_Control_RNAseq.genome2.bw
NPCs_DEseq_basic_DEresults.tsv
NPCs_DEseq_allelic_DEresults.tsv
NPCs_DEgenes_classification.txt

value: RNAseq


title: Tsc InsMet  poly rep1

value: Tsc2 fl/fl; AlbCreEr

value: 15 minute pre-treatment with 1nM Insulin

value: polysome fractionated samples


title: 9sCa: NPCs_Control_unlabeledTTseq_rep1

value: unlabeledTTseq


title: rna_BALB_Stellate_Control_rep4

description:
f0_tpm.txt
f0_raw.txt

source_name: Stellate Cells, BALB/cJ, Control

value: Sorted non-parenchymal cells

value: Stellate cell

value: BALB/cJ


title: rna_BALB_Stellate_Control_rep3

description:
f0_tpm.txt
f0_raw.txt

value: Control


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, TCR, tube1B

description:
polyA RNA
10x Genomics

value: Cow milk epitope pool


title: AATsc UT  poly

value: C57BL/6 (F3 generation)

value: primary hepatocytes

value: 8-16 weeks old

value: Raptor - S722A; S792A; Tsc2 fl/fl; AlbCreEr

value: Tamoxifen treatment 3x 14-17 days prior to hepatocyte isolation

value: untreated - serum starved


title: Tsc InsMet  poly rep2

value: 2mM Metformin for 2h serum-starved


title: 9sCa: NPCs_Control_RNAseq_rep2

value: Female

value: WT

value: RNAseq


title: 9sCa: NPCs_Control_unlabeledTTseq_rep2


title: rna_BALB_Stellate_Control_rep2

description:
f0_tpm.txt
f0_raw.txt


title: 9sCa: NPCs_Control_RNAseq_rep1


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, TCR, tube1A

description:
polyA RNA
10x Genomics

value: Blood

value: CD4 memory T cells


title: Tsc Ins  poly rep1

value: Tsc2 fl/fl; AlbCreEr

value: 15 minute pre-treatment with 1nM Insulin

value: polysome fractionated samples


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube1B

description:
polyA RNA
10x Genomics


title: 9sCa: NPCs_Control_Pol2_rep2

description:
NPCs_Control_Pol2.bw
NPCs_Control_Pol2.genome1.bw
NPCs_Control_Pol2.genome2.bw


title: Tsc Met Poly

value: Untreated


title: rna_BALB_Stellate_Control_rep1

description:
f0_tpm.txt
f0_raw.txt

value: Sorted non-parenchymal cells

value: Stellate cell

value: BALB/cJ

value: Control


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube1A

description:
polyA RNA
10x Genomics

value: Cow milk epitope pool


title: rna_AJ_Stellate_Control_rep4

description:
f0_tpm.txt
f0_raw.txt

source_name: Stellate Cells, A/J, Control

value: A/J


title: 9sCa: NPCs_Control_Pol2_rep1


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube1A

description:
protein
10x Genomics


title: Tsc UT  poly

value: C57BL/6 (F3 generation)

value: primary hepatocytes

value: 8-16 weeks old

value: Tamoxifen treatment 3x 14-17 days prior to hepatocyte isolation

value: untreated - serum starved


title: rna_AJ_Stellate_Control_rep3

description:
f0_tpm.txt
f0_raw.txt


title: Tsc Ins  poly rep2


title: AA InsMet  poly rep2

value: Raptor - S722A; S792A

value: 2mM Metformin for 2h serum-starved


title: 9sCa: NPCs_Control_MSL2_rep2

description:
NPCs_Control_MSL2.bw
NPCs_Control_MSL2.genome1.bw
NPCs_Control_MSL2.genome2.bw
NPCs_Control_MSL2_peaks.bed

value: Female

value: WT


title: AA InsMet  poly rep1

value: 15 minute pre-treatment with 1nM Insulin

value: polysome fractionated samples


title: CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube1B

description:
protein
10x Genomics

value: Blood

value: CD4 memory T cells


title: 9sCa: NPCs_Control_MOF_rep2

description:
NPCs_Control_MOF.bw
NPCs_Control_MOF.genome1.bw
NPCs_Control_MOF.genome2.bw
NPCs_Control_MOF_peaks.bed


title: 9sCa: NPCs_Control_MSL2_rep1


title: dHL60_DMEMF12_Rep3

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

data_processing:
BCL Convert Conversion Software v3.9.3 (Illumina) was used to generate de-multiplexed Fastq files
Trimmed using Cutadap v3.5, mapped using STAR v2.7.10a
Features counted using featureCounts function from the Rsubread Bioconductor package
TMM method of edgeR used to create Log2 expression values
Limma and voom technique used to fit linear models
Assembly: GRCh38.v40
Supplementary files format and content: Tab-delimited text file contains raw counts

growth_protocol: HL-60 cells were maintained in IMDM supplemented with 10% HI FBS. Before treatment, HL-60 cells were differentiated into neutrophil-like cells (dHL-60 cells) by growing them for 4 days in IMDM supplemented with 2% HI FBS, 1.3% DMSO, 10 µg/ml insulin, 5.5 µg/ml transferrin, and 6.7 ng/ml sodium selenite.

extract_protocol:
RNA was extracted from dHL-60 cells using the RNeasy Mini Kit (Qiagen #74104) with the RNase-Free DNase Set (Qiagen #79254) to remove any residual DNA. Quality control (RNA-integrity number (RIN))
poly-A enrichment

treatment_protocol: dHL-60 cells were lysed immediately for the time 0 samples. For the treatments, dHL-60 cells were treated for 30 minutes with either recombinant TGF-β1, tumor-conditioned media from the MCF10CA1a cell line (M4), or one of the corresponding media controls (IMDM or DMEM/F12).

tag: cell line

value: promyeoloblasts differentiated into neutrophil-like cells


title: AA Ins  poly rep2


title: rna_AJ_Stellate_Control_rep1

description:
f0_tpm.txt
f0_raw.txt

value: Sorted non-parenchymal cells

value: Stellate cell

value: Control


title: rna_AJ_Stellate_Control_rep2

description:
f0_tpm.txt
f0_raw.txt

value: A/J


title: dHL60_M4_TCM_Rep3


title: 9sCa: NPCs_Control_MOF_rep1


title: AA Ins  poly rep1

value: C57BL/6 (F3 generation)

value: primary hepatocytes


title: rna_C57_LSEC_Control_rep4

description:
f0_tpm.txt
f0_raw.txt

source_name: Liver Sinusoidal Endothelial Cells, C57BL/6J, Control

value: Liver Sinusoidal Endothelial cell


title: dHL60_IMDM_Rep3

value: IMDM


title: rna_C57_LSEC_Control_rep3

description:
f0_tpm.txt
f0_raw.txt


title: AA Met  poly

value: 8-16 weeks old

value: Raptor - S722A; S792A

value: Tamoxifen treatment 3x 14-17 days prior to hepatocyte isolation

value: Untreated


title: 9sCa: NPCs_Control_KANSL3_rep2

description:
NPCs_Control_KANSL3.bw
NPCs_Control_KANSL3.genome1.bw
NPCs_Control_KANSL3.genome2.bw
NPCs_Control_KANSL3_peaks.bed

value: Female

value: WT


title: dHL60_t0_Rep3


title: dHL60_TGFb_Rep3

value: TGFb


title: rna_C57_LSEC_Control_rep2

description:
f0_tpm.txt
f0_raw.txt


title: AA UT  poly

value: untreated - serum starved

value: polysome fractionated samples


title: 9sCa: NPCs_Control_KANSL1_rep2

description:
NPCs_Control_KANSL1.bw
NPCs_Control_KANSL1.genome1.bw
NPCs_Control_KANSL1.genome2.bw
NPCs_Control_KANSL1_peaks.bed


title: dHL60_M4_TCM_Rep2

value: promyeoloblasts differentiated into neutrophil-like cells


title: dHL60_DMEMF12_Rep2


title: 9sCa: NPCs_Control_KANSL3_rep1


title: WT InsInk  poly rep2

value: wild type

value: 0.1uM INK-128 for 2h serum-starved

value: 15 minute pre-treatment with 1nM Insulin


title: 9sCa: NPCs_Control_KANSL1_rep1


title: rna_BALB_LSEC_Control_rep4

description:
f0_tpm.txt
f0_raw.txt

source_name: Liver Sinusoidal Endothelial Cells, BALB/cJ, Control

value: Sorted non-parenchymal cells

value: BALB/cJ

value: Control


title: WT Ink  poly

value: C57BL/6 (F3 generation)

value: primary hepatocytes


title: dHL60_IMDM_Rep2

value: IMDM


title: 9sCa: NPCs_Control_Input4_rep2

description: Same batch as H4K5ac, H4K12ac


title: dHL60_TGFb_Rep2


title: WT InsMet  poly rep2

value: 8-16 weeks old

value: Tamoxifen treatment 3x 14-17 days prior to hepatocyte isolation

value: 2mM Metformin for 2h serum-starved


title: dHL60_t0_Rep2

value: Untreated


title: rna_BALB_LSEC_Control_rep2

description:
f0_tpm.txt
f0_raw.txt

value: Liver Sinusoidal Endothelial cell


title: WT InsMet  poly rep1


title: rna_BALB_LSEC_Control_rep1

description:
f0_tpm.txt
f0_raw.txt


title: 9sCa: NPCs_Control_Input2_rep2

description: Same batch as MSL2, DNMT3A, DNMT3B

value: Female

value: WT


title: rna_AJ_LSEC_Control_rep4

description:
f0_tpm.txt
f0_raw.txt

source_name: Liver Sinusoidal Endothelial Cells, A/J, Control

value: A/J


title: 9sCa: NPCs_Control_Input2_rep1

description: Same batch as MSL2, DNMT3A, DNMT3B


title: dHL60_DMEMF12_Rep1

value: promyeoloblasts differentiated into neutrophil-like cells


title: WT Ins  poly rep2

value: wild type

value: untreated - serum starved

value: polysome fractionated samples


title: rna_C57_LSEC_Control_rep1

description:
f0_tpm.txt
f0_raw.txt

value: Sorted non-parenchymal cells


title: 9sCa: NPCs_Control_Input1_rep2


title: rna_AJ_LSEC_Control_rep3

description:
f0_tpm.txt
f0_raw.txt

value: Control


title: WT InsInk  poly rep1

value: C57BL/6 (F3 generation)

value: 0.1uM INK-128 for 2h serum-starved

value: 15 minute pre-treatment with 1nM Insulin


title: WT Ins  poly rep1

value: primary hepatocytes

value: 8-16 weeks old


title: WT Met  poly

value: Tamoxifen treatment 3x 14-17 days prior to hepatocyte isolation

value: 2mM Metformin for 2h serum-starved


title: dHL60_IMDM_Rep1

value: IMDM


title: rna_BALB_LSEC_Control_rep3

description:
f0_tpm.txt
f0_raw.txt

value: Liver Sinusoidal Endothelial cell

value: BALB/cJ


title: 9sCa: NPCs_Control_H4K5ac_rep2

description:
NPCs_Control_H4K5ac.bw
NPCs_Control_H4K5ac.genome1.bw
NPCs_Control_H4K5ac.genome2.bw

value: Female

value: WT


title: 9sCa: NPCs_Control_Input1_rep1


title: rna_AJ_LSEC_Control_rep1

description:
f0_tpm.txt
f0_raw.txt

value: A/J


title: WT UT poly

data_processing:
First, adapter trimming was performed with cutadapt (v1.14).
Next, reads were mapped with STAR (v2.4.0i) against a database of repetitive elements, with mapping reads discarded from further analysis.
Remaining reads were then mapped to the mouse genome (mm10) with STAR (v2.4.0i)
Stranded reads mapping to GENCODE (vM20) genes were quantified with featureCounts (subread-1.6.4). Mitochondrial genes were discarded, and only genes with at least 0.5 reads per million across all datasets were kept for further analysis.
Differential expression in polysome versus input was quantified with edgeR (v3.26.8) with dispersion = 0.06 estimated from the subset of experiments with multiple replicates.
Genome_build: mm10
Supplementary_files_format_and_content: EdgeR output files (*.txt.gz*) contain gene identifier, log(fold-change in polysome versus input), log(counts per million), and p-value (polysome versus input)

value: wild type

value: untreated - serum starved

value: Untreated


title: 9sCa: NPCs_Control_Input4_rep1

description: Same batch as H4K5ac, H4K12ac


title: 9sCa: NPCs_Control_H4K5ac_rep1


title: dHL60_M4_TCM_Rep1

value: promyeoloblasts differentiated into neutrophil-like cells


title: Ampk InsMet input rep2

value: C57BL/6 (F3 generation)

value: Ampka1 fl/fl; Ampka2 fl/fl; AlbCreER

value: polyA RNA


title: dHL60_t0_Rep1


title: rna_C57_Kupffer_Control_rep2

description:
f0_tpm.txt
f0_raw.txt

source_name: Kupffer Cells, C57BL/6J, Control

value: Sorted non-parenchymal cells

value: Kupffer cell

value: Control


title: rna_C57_Kupffer_Control_rep1

description:
f0_tpm.txt
f0_raw.txt


title: Ampk Ins input rep2

value: primary hepatocytes

value: 8-16 weeks old

value: Tamoxifen treatment 3x 14-17 days prior to hepatocyte isolation

value: 15 minute pre-treatment with 1nM Insulin


title: Kasumi1, input, shHIF2a

city: Milan

first: Rosa

last: Bernardi

address: via Olgettina 60

country: Italy

institute: San Raffaele Scientific Institute

data_processing:
Base-calling was performed on NovaSeq 6000 Illumina machine
ChIP-seq reads were trimmed using BBDuk from BBTools suite version 37.36 with suggested settings (ktrim=r k=23 mink=11 hdist=1)
ChIP-seq reads were aligned to the UCSC hg38 genome using BWA-MEM version 0.7.12-r1039 . Uniquely mapped reads were selected with MarkDuplicates from Picard Tools version 1.104
Filtering was done on reads mapping in regions present in the ENCODE hg38 blacklist and regions flagged as not primary alignment or with mapping quality score less than 15
H3K27me3 peaks were detected using MACS2 v2.2.7.1
bigWig files were generated using bamCoverage from Deeptools
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: Cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum, and 100 IU/ml penicillin plus 100 mg/ml streptomycin antibiotics. Silenced cells were selected by adding 2 micrograms/ml puromycin to the medium.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using the Diagenode Bioruptor 300.
Library were sequenced using Illumina High throughput Sequencing technology. Samples were loaded on NovaSeq 6000 and sequenced in paried-end mode, generating 100 nt length reads in order to obtain approximately 40M reads. Libraries were validated using the High Sensitivity D5000 ScreenTape (Agilent Technologies).

value: Acute Myeloid Leukemia (AML)

tag: chip antibody


title: Kasumi1, input, shCTRL

value: shCTRL


title: dHL60_TGFb_Rep1

tag: time

value: TGFb


title: 9sCa: NPCs_Control_H4K16ac_rep2

description:
NPCs_Control_H4K16ac.bw
NPCs_Control_H4K16ac.genome1.bw
NPCs_Control_H4K16ac.genome2.bw

extract_protocol:
RNAseq: Total RNA was extracted using the Direct-zol RNA Miniprep Plus Kit (Zymo Research) according to the manufacturers’ instructions. Maxima First Strand cDNA Synthesis Kit (Thermo Scientific) was used to synthesize cDNA from total RNA according to the manufacturers’ instructions. Quantitative reverse transcription PCR was carried out on Roche LightCycler II using the Faststart SYBR Green Master (Rox) mix (Roche) at a final volume of 10μL.
TT-seq: In brief, 10 million NPCs were incubated with N2B27 medium supplemented with 500 uM 4- thiouridine (4sU, Sigma) for 5 minutes at 37°C. Total RNA was isolated, fragmented using Bioruptor Plus for 1 minute (30s ON, 30s OFF, high setting), and incubated with Biotin-HPDP (Thermo Scientific) for 2 hours. MyOne C1 Streptavidin magnetic beads (Thermo Scientific) were used to immunoprecipitate labelled RNA before elution in 5% beta-mercaptoethanol (Roth). FInal RNA was cleaned up using the Oligo Clean and Concentrator Kit (Zymo Research) according to the manufacturer’s instructions. Libraries were prepared from 100 ng of high quality RNA using the Ovation Universal RNA-Seq System (Nugen) according to the manufacturer’s instructions.
ChIPseq: MSL2 WT and KO NPCs were covered with 1% formaldehyde in culture media on the plate and incubated at room temperature (RT) on a rocking plate for 10 min. Media was removed and cells were washed twice with 1xPBS supplemented with 1x protease inhibitor cocktail (Roche). Cells were scraped off the plate, collected in ice-cold 1xPBS and centrifuged at 500g for 5 minutes. After an additional 1xPBS wash, cell pellets were stored at -80°C until usage. Nuclei were isolated using the NEXSON based nuclei isolation protocol. Cell pellets were thawed on ice and resuspended in ice cold 1ml of lysis buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% Igepal, 1x protease inhibitor cocktail). The cell suspension was then transferred into 1ml milliTUBE (Covaris) and sonicated in Covaris instrument (E220) for 30 sec at peak power 75W, duty factor 2% and 200 cycles/burst. Nuclei were pelleted at 1000g at 20°C for 5min. The cytoplasmic fraction in the supernatant was discarded and nuclear pellets were carefully resuspended in 0.5% SDS and incubated at room temperature for 10min. Sample was diluted 1:5 in the digestion buffer (Final concentration: 1.1% Triton, 1x CutSmart buffer, nuclease free H2O, 1x protease inhibitor cocktail). Chromatin of up to 1 million nuclei were digested in 250ul digestion buffer with Cvik1 (5U/100.000 cells, New England Biolabs) at 20°C for 16hrs, shaking at 800rpm. After the chromatin digestion, the nuclei were pelleted for 5min at 1000g and washed in cold nuclei wash solution (10mM Tris-HCl pH 8, 0.25% Triton, 0.2mg/ml BSA) and stored on ice. To confirm the enzymatic chromatin shearing efficiency, 5% of the nuclei solution was incubated together with a decrosslinking solution consisting of 2ul proteinase K, 1ul RNaseA and 4ul 5M NaCl at 37°C for 30min followed by a 2hr incubation at 65°C. DNA was purified using MinElute PCR purification kit (Qiagen) and analyzed on a Agilent Tapestation system (G2964AA) using the Agilent D1000 Screentape reagents.
ATACseq: In brief, nuclei of 50,000 cells per replicate were isolated in 50 μl of cold ATAC resuspension buffer (0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin (Promega)) by incubating on ice for 3 minutes. After lysis, 1 ml of cold ATAC resuspension buffer containing 0.1% Tween-20 (without NP-40 or digitonin) was added, and nuclei were then centrifuged at 500g for 10 minutes. Transposition was carried out using 50 μl of transposition mix (25 μl 2X TD buffer (Illumina), 2.5 μl transposase (Illumina), 16.5 μl 1X PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) at 37°C for 30 minutes in a thermomixer with shaking at 1000 rpm. Transposed DNA was collected using Zymo DNA Clean and Concentrator (Zymo Research) according to the manufacturer's instructions, and added to the PCR mix containing 25 μl of NEBNext Master Mix (New England Biolabs) and 5 μl of Index adapters (Illumina). Libraries were amplified using the following PCR program: 72°C for 5 minutes, 98°C for 30 seconds, then 10 cycles of: 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. Library quality was analyzed using the Fragment analyzer (Agilent Technologies) prior to sequencing.
BSseq: Bisulfite-Seq was performed using the NEBNext Enzymatic Methyl-seq Kit (E7120S) according to the manufacturer’s instructions. In brief, genomic DNA (gDNA) was extracted from wild-type and MSL2 knockout NPCs using the QIAamp DNA Mini kit (Qiagen) according to the manufacturer’s instructions.Subsequently, 50ng of high quality gDNA was sheared for 120 seconds using an E220 Covaris to obtain fragments between around 300 base pairs in length. Following end prep and EM-seq adapter ligation, DNA was oxidised and denatured using sodium hydroxide. Libraries were amplified for 6 PCR cycles, and sequenced with 2x100bp paired-end reads on an Illumina NovaSeq6000 sequencer.

value: Female

value: WT


title: rna_AJ_LSEC_Control_rep2

description:
f0_tpm.txt
f0_raw.txt

tag: source

value: Liver Sinusoidal Endothelial cell

value: A/J


title: Ampk Met input

value: C57BL/6 (F3 generation)

tag: age

value: 2mM Metformin for 2h serum-starved

value: Untreated


title: Kasumi1, H3K27me3, shHIF2a rep3


title: rna_BALB_Kupffer_Control_rep2

description:
f0_tpm.txt
f0_raw.txt

source_name: Kupffer Cells, BALB/cJ, Control

value: Sorted non-parenchymal cells

value: BALB/cJ


title: Ampk UT input

value: Ampka1 fl/fl; Ampka2 fl/fl; AlbCreER

tag: tamoxifen treatment

value: untreated - serum starved

value: polyA RNA


title: 9sCa: NPCs_Control_H4K16ac_rep1

source_name: Neural progenitor cells


title: 9sCa: NPCs_Control_H4K12ac_rep2

description:
NPCs_Control_H4K12ac.bw
NPCs_Control_H4K12ac.genome1.bw
NPCs_Control_H4K12ac.genome2.bw


title: Kasumi1, H3K27me3, shHIF2a rep2


title: rna_AJ_Kupffer_Control_rep2

description:
f0_tpm.txt
f0_raw.txt

source_name: Kupffer Cells, A/J, Control

value: Kupffer cell

value: Control


title: AATsc InsMet input rep2

value: primary hepatocytes

value: 8-16 weeks old

value: Raptor - S722A; S792A; Tsc2 fl/fl; AlbCreEr

value: Tamoxifen treatment 3x 14-17 days prior to hepatocyte isolation

tag: metformin treatment

value: 15 minute pre-treatment with 1nM Insulin


title: rna_AJ_Kupffer_Control_rep1

description:
f0_tpm.txt
f0_raw.txt


title: 9sCa: NPCs_Control_H4K16ac_rep3

value: Female

value: WT


title: AATsc Ins input rep2

value: C57BL/6 (F3 generation)

tag: insulin treatment


title: Age360d3

city: Changsha

first: Chen

last: Chen

address: No. 8 Changlang Road, Furong District, Changsha City, Hunan Province

institute: Hunan Institute of Animal & Veterinary Science

data_processing:
After removing ribosomal RNAs, the left RNAs were fragmented into short fragments using divalent cations under high temperature.
The cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution.
An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA
Adapters are ligated to the fragments, and size selection (300-600bp) was performed with AMPureXP beads.
After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR, and paired-end sequencing was performed.
Assembly: Sus scrofa reference genome (V11.1, Ensembl V96)
Supplementary files format and content: 4_genes_fpkm_expression file includes genomic location, raw counts and FPKM values of genes in each sample.

organism: Sus scrofa

source_name: Backfat tissue

extract_protocol:
Approximately 5 μg of total RNA was used to eliminate ribosomal RNA according to the Ribo-ZeroTM rRNA removal Kit (Illumina, USA), and the ribo-minus RNA was used for construction of sequencing libraries.
The 2×150 bp paired-end sequencing (PE150) was executed. Cutadapt was initially applied to obtain clean data, and Hisat2 software was used to map clean reads to the Sus scrofa reference genome (V11.1, Ensembl V96), and the mapped reads were assembled using StringTie.

value: Backfat tissue

tag: development stage


title: 9sCa: NPCs_Control_H4K12ac_rep1


title: Kasumi1, H3K27me3, shCTRL rep3

tag: cell type

value: Acute Myeloid Leukemia (AML)

value: shCTRL


title: Kasumi1, H3K27me3, shCTRL rep2

tag: treatment


title: AATsc Met input

tag: strain

value: 2mM Metformin for 2h serum-starved

value: Untreated

tag: rna fraction


title: rna_BALB_Kupffer_Control_rep1

description:
f0_tpm.txt
f0_raw.txt

value: Sorted non-parenchymal cells

value: BALB/cJ


title: AATsc UT input

tag: genotype

value: untreated - serum starved

value: polyA RNA


title: 9sCa: NPCs_Control_H3-4_rep1

description: Same batch as H4K5ac, H4K12ac

tag: gender

tag: library type


title: 9sCa: NPCs_Control_H3-4_rep2

description: Same batch as H4K5ac, H4K12ac

tag: replicate


title: Age360d2

tag: tissue


title: Age360d1


title: 9sCa: NPCs_Control_H3-2_rep2

description: Same batch as MSL2, DNMT3A, DNMT3B


title: 9sCa: NPCs_Control_H3-2_rep1

description: Same batch as MSL2, DNMT3A, DNMT3B


title: Tsc Ins input rep2

value: primary hepatocytes

value: Tsc2 fl/fl; AlbCreEr


title: Age300d2


title: SCC-9 cells, KO2_IP

city: guangzhou

first: xun

last: chen

state: guangdong

address: Linyuanxi Road 55

institute: Sun yat-sen University

data_processing:
The fastp tool (https://github.com/OpenGene/fastp) was used to remove the low   quality reads and trim adaptors . Sequence quality of IP and input samples was  verified using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)   and RseQC (http://rseqc.sourceforge.net/) .
Clean reads were then mapped to the reference genome Homo sapiens (Version: v101) using HISAT2 (http://daehwankimlab.github.io/hisat2)
m6A peak calling and analysis of   differentially methylated peaks were performed by R package exomePeak2   (https://bioconductor.org/packages/release/bioc/html/exomePeak2.html) , and   peaks were annotated by intersection with gene architecture using R package   5  ANNOVAR (http://www.openbioinformatics.org/annovar/)
The MEME   (http://meme-suite.org) (30) and HOMER (http://homer.ucsd.edu/homer/motif) were   used for de novo and known motif finding, followed by localization of the motif with   respect to peak summit. The expression level of all transcripts and genes from input   libraries was analyzed through calculating FPKM (total exon fragments/mapped reads   (millions) × exon length (kb)) using StringTie (https://ccb.jhu.edu/software/stringtie)  (31). The R package edgeR (https://bioconductor.org/packages/edgeR) (32) was used   to identify differentially expressed transcripts and genes, and the threshold was set to  |log2fold change (FC)|≥1 and p value < 0.05.
The differentially expressed genes and differentially methylated coding genes were subjected to Gene Oncology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis
Supplementary files format and content: bigwig

source_name: oral

growth_protocol: SCC-9 and SCC-9 GPX8 KO cells were maintained in DMEM medium, supplemented with 10% FBS (GIBCO, Australia), 100 U/mL penicillin G and 100 μg/mL streptomycin, in a humidified atmosphere of 5% CO2 at 37 ◦C. About 5×107 cells were harvested for MeRIP-seq and RNA-seq.

extract_protocol:
total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and quantified. RNA integrity was evaluated by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) and fragmentedinto about 100nt using Magnesium RNA Fragmentation Module (NEB, USA). The RNA fragments weredivided into two portions, one was kept as input and the otherwas used to enrich m6A-methylated RNA fragments by immunoprecipitation with m6A-specific antibody (Synaptic Systems, Germany).
Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol
MeRIP-seq

value: oral

tag: cell line

value: squamous cells

value: GPX8 knockout

tag: rip antibody

value: m6A-specific antibody


title: Tsc InsMet input rep2

value: 8-16 weeks old

value: Tamoxifen treatment 3x 14-17 days prior to hepatocyte isolation

value: 15 minute pre-treatment with 1nM Insulin


title: SCC-9 cells, KO1_IP


title: Age300d3

value: Backfat tissue


title: Tsc Met input

value: C57BL/6 (F3 generation)


title: 9sCa: NPCs_Control_H3-1_rep2

first: Asifa

last: Akhtar

address: Stuebeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

description: Same batch as NRF1, BRD4, KANSL1, KANSL3, MOF, Pol2

value: Female

value: WT


title: Age300d1


title: Kasumi1, H3K27me3, shCTRL rep1

value: Acute Myeloid Leukemia (AML)

value: shCTRL

tag: chip antibody


title: 9sCa: NPCs_Control_H3-1_rep1


title: Tsc UT input

tag: age

value: untreated - serum starved

value: Untreated


title: Age240d3


title: SCC-9 cells, KO1_input


title: AA InsMet input rep2

value: primary hepatocytes

value: Raptor - S722A; S792A

tag: tamoxifen treatment

value: 2mM Metformin for 2h serum-starved

value: polyA RNA


title: SCC-9 cells, NC2_IP

value: oral

value: squamous cells


title: 9sCa: NPCs_Control_DNMT3B_rep2

description:
NPCs_Control_DNMT3B.bw
NPCs_Control_DNMT3B.genome1.bw
NPCs_Control_DNMT3B.genome2.bw


title: Age240d2


title: AA Ins input rep2

value: 8-16 weeks old

tag: metformin treatment


title: 9sCa: NPCs_Control_DNMT3B_rep1


title: AA Met input

value: Tamoxifen treatment 3x 14-17 days prior to hepatocyte isolation

tag: insulin treatment


title: Age240d1

tag: development stage


title: Kasumi1, H3K27me3, shHIF2a rep1

tag: cell type


title: SCC-9 cells, NC1_IP

value: m6A-specific antibody


title: SCC-9 cells, NC2_input


title: SCC-9 cells, KO2_input

value: GPX8 knockout


title: 9sCa: NPCs_Control_DNMT3A_rep2

description:
NPCs_Control_DNMT3A.bw
NPCs_Control_DNMT3A.genome1.bw
NPCs_Control_DNMT3A.genome2.bw


title: 9sCa: NPCs_Control_BSseq_rep4

description:
NPCs_Control_BSseq.bw
NPCs_Control_BSseq.genome1.bw
NPCs_Control_BSseq.genome2.bw
NPCs_diff.peak.BS.RData

value: BSseq


title: Age180d3

value: Backfat tissue


title: SCC-9 cells, NC1_input

value: WT


title: AA UT input

value: C57BL/6 (F3 generation)


title: 9sCa: NPCs_Control_DNMT3A_rep1

value: Female


title: WT Ink input

value: wild type

value: 0.1uM INK-128 for 2h serum-starved


title: Age180d1


title: Age180d2