title: ABCG2+ L3.6pl, MM-102, replicate 3

city: Oxford

first: Siwei

last: Deng

address: Old Rd, Headington

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

description:
ABCG2+ L3.6pl cells
MM102_rep_3

data_processing:
Raw reads were cleaned using fastp v0.23.2 with default parameters.
Cleaned reads were confirmed high-quality using FastQC v0.11.9.
cleaned reads were mapped to the human genome hg38 using STAR v2.7.3a.
The mapped reads were quantified using featureCounts v2.0.0.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

extract_protocol:
Total RNA was extracted from ABCG2+ L3.6pl tumorspheres with Trizol reagent and purified using Direct-zol RNA miniprep kit according to the manufacturer’s instructions.
Ribosomal RNA was depleted using NEBNEXT rRNA Depletion Kit v2 (Human/Mouse/Rat) (New England Biolabs, cat. E7400S) as per the manufacturer’s instructions. RNA-seq libraries were prepared using NEBNEXT Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, cat. E7760S) according to the manufacturer’s instructions. Fragment size distribution of cDNA libraries was determined using Agilent 4150 TapeStation system (Agilent Technologies). RNA-sequencing of 3 biological replicates per each treatment condition was performed at CD Genomics (New York, USA) using an Illumina NovaSeq6000 S4 sequencing platform.

value: Pancreatic adenosquamous carcinoma

value: Mutation; HGNC; 6407; KRAS; Simple; p.Gly12Asp (c.35G>A); ClinVar=VCV000012582; Zygosity=Unspecified (from parent cell line).

tag: treatment


title: ABCG2+ L3.6pl, MM-102, replicate 2

status: Public on Aug 10 2023

type: SRA

description:
ABCG2+ L3.6pl cells
MM102_rep_2

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype


title: 9sCa: NPCs_Control_BSseq_rep3

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

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

library_source: genomic

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.

molecule: genomic DNA

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.

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.

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

value: WT

tag: library type

value: BSseq

tag: replicate


title: Age120d3

city: Changsha

first: Chen

last: Chen

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

country: China

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.

tag: tissue

value: Backfat tissue

tag: development stage


title: 9sCa: NPCs_Control_BSseq_rep2


title: WT InsMet input rep2

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

country: USA

institute: Salk Institute for Biological Studies

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)

molecule: polyA RNA

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: wild type

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: polyA RNA


title: ABCG2+ L3.6pl, MM-102, replicate 1

description:
ABCG2+ L3.6pl cells
MM102_rep_1


title: 9sCa: NPCs_Control_BSseq_rep1


title: WT Ins input rep2

value: untreated - serum starved


title: Age120d2


title: ABCG2+ L3.6pl, Gemcitabine + MM-102, replicate 3

description:
ABCG2+ L3.6pl cells
MM102_Gem_rep_3

value: Gemcitabine + MM-102


title: Age120d1


title: WT Met input

value: Untreated


title: 9sCa: NPCs_Control_BRD4_rep2

description:
NPCs_Control_BRD4.bw
NPCs_Control_BRD4.genome1.bw
NPCs_Control_BRD4.genome2.bw


title: ABCG2+ L3.6pl, Gemcitabine + MM-102, replicate 1

description:
ABCG2+ L3.6pl cells
MM102_Gem_rep_1

value: Pancreatic adenosquamous carcinoma


title: ABCG2+ L3.6pl, Gemcitabine + MM-102, replicate 2

description:
ABCG2+ L3.6pl cells
MM102_Gem_rep_2

value: Mutation; HGNC; 6407; KRAS; Simple; p.Gly12Asp (c.35G>A); ClinVar=VCV000012582; Zygosity=Unspecified (from parent cell line).


title: WT InsInk input rep2

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


title: 9sCa: NPCs_Control_ATACseq_rep3

description:
NPCs_Control_ATACseq.bw
NPCs_Control_ATACseq.genome1.bw
NPCs_Control_ATACseq.genome2.bw
NPCs_diff.peak.ATAC.RData

value: Female

value: WT

value: ATACseq


title: WT UT input

value: C57BL/6 (F3 generation)


title: Age60d2

value: Backfat tissue


title: ABCG2+ L3.6pl, Gemcitabine, replicate 3

description:
ABCG2+ L3.6pl cells
Gem_rep_3

value: Gemcitabine


title: 9sCa: NPCs_Control_ATACseq_rep2


title: Age60d1


title: hepatocyte_Ampk Ins rep1

data_processing:
Raw RNA sequencing reads in FASTQ files were quality-tested using FASTQC (v0.11.8) (Andrews 2010) and mapped to the mouse reference genome (mm10) with STAR (v2.5.3a) aligner with default parameters (Dobin et al. 2012).
Raw or normalized gene expression levels were quantified across all the exons of RefSeq genes with analyzeRepeats.pl in HOMER (v4.11.1) (Heinz et al. 2010).
Differential expression analysis was performed with raw gene counts using R package, edgeR (v3.26.7) (Robinson et al. 2010), using replicates to compute within-group dispersion and correcting for batch effects. Genes with false discovery rate (FDR) < 0.05 and an absolute fold-change (FC) >= 1.5 were identified as significantly different when comparing two conditions.
Normalized counts were log transformed, filtered, scaled, and centered prior to clustering and heatmap generation with Cluster3 (de Hoon et al. 2004), and visualized with JavaTreeView (Saldanha 2004).
GSEA was carried out with the GenePattern interface, https://genepattern.broadinstitute.org) using preranked lists generated from FDR values, setting gene set permutations to 1000 and using the Hallmark collection in MSigDB version5.0. GO Term and KEGG Pathway analysis were performed with David: http://david.ncifcrf.gov/.
Area-proportional Venn diagrams were plotted using BioVenn (Hulsen et al. 2008). Enrichr: http://amp.pharm.mssm.edu/Enrichr.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized expression table generated with analyzeRepeats.pl. Please see header for specific arguments used.

extract_protocol:
Cells were lysed in qiaxol. RNA was extracted using qiagen RNeasy lipid tissue 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

value: primary hepatocytes

value: 8-16 weeks old

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

tag: pre-treatment


title: ABCG2+ L3.6pl, Gemcitabine, replicate 2

description:
ABCG2+ L3.6pl cells
Gem_rep_2


title: Age60d3


title: hepatocyte_Ampk Ins rep3

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

value: 15 minute pre-treatment with 1nM Insulin


title: BioTASQ_vivo_rep2

city: Nanjing

first: zhenyu

last: luo

state: Jiangsu

address: Xuanwu

department: College of Agricuture

institute: Nanjing Agricultural University

data_processing:
Raw ChIP-seq data were cleaned through trimming adapter contamination and removing low-quality reads using Trim Galore! (version 0.4.4). All cleaned reads were aligned to the MSU v7.0 reference genome using BWA (Burrows-Wheeler Aligner) (mem algorithm, version 0.7.17) with default parameters. Any PCR duplicates were removed using Picard. Reads with mapping quality below ten were excluded using SAMtools (version 1.5, option -q). Only reads with alignment length greater than 50 were used for G4 peak calling and further analyses.
G4 Peak calling was performed using MACS (version 2.1.1) with the following command and parameters: macs2 callpeak -g 3.8e+8 -f BAM --extsize 200 -q 0.05 –nomodel, and the input library was used as control.
The PQS loci file were generate using fastaRegexFinder.py through the rice7 MSU genome

organism: Oryza sativa

source_name: Seedling

growth_protocol: Rice (Oryza. sativa L. spp. japonica) seeds were immerged in tap water at RT in the lab for three days. Uniformly germinated seeds were sowed in the nutrient soil and grown in a greenhouse at a temperature at 28-30 ℃ and a 14 h/10 h light-dark cycle. Two-week-old rice seedlings were collected and cross-linked using 1% of formaldehyde for 10 min under vacuum. The cross-linked seedlings were ground into a fine powder in liquid nitrogen, and stored in -80 ℃ or immediately used for preparation of genomic DNA.

extract_protocol: The fragmented chromatin was diluted in G4DP buffer (10mM Tris-HCl, 5mM EDTA, 150mM KCl, 0.5mM DTT and 0.5% NP-40, pH=7.4) until the final concentration of SDS was below 0.1%. 1/10 volume of supernatant was kept as input. 30 μl of 1 mM BioTASQ was added into diluted chromatin and incubated overnight at 4 °C, then 30 μl of washed M280 Streptavidin Dynalbeads (11206D, Invitrogen) was added and incubated for another 4 h at 4°C. The washed BioTASQ/BioCyTASQ-bound DNA was eluted with 200 μl elution buffer at 65°C for two times with 15 min each, followed by de-crosslinking at 65°C overnight. De-crosslinked G4DPed DNA was extracted using phenol/chloroform followed by cold ethanol precipitation. 30 nm biotin (Sigma, cat, no. 2031) was used as control. Two biological replicates were conducted for BioTASQ/BioCyTASQ and biotin only. All G4DPed DNA was used for the library preparation, which was constructed using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645S). All libraries were sequenced using paired-end mode on Illumina NovaSeq platform

tag: cultivar

value: Nipponbare

value: Seedling

value: two weeks

tag: antibody

value: small-molecular baits BioTASQ

tag: growth

value: vivo


title: ABCG2+ L3.6pl, Gemcitabine, replicate 1

description:
ABCG2+ L3.6pl cells
Gem_rep_1

tag: cell line

tag: cell type

value: Pancreatic adenosquamous carcinoma

value: Mutation; HGNC; 6407; KRAS; Simple; p.Gly12Asp (c.35G>A); ClinVar=VCV000012582; Zygosity=Unspecified (from parent cell line).

tag: treatment


title: BioTASQ_vivo_rep1


title: 9sCa: NPCs_Control_ATACseq_rep1

tag: strain

tag: gender

value: Female

tag: genotype

value: WT


title: ABCG2+ L3.6pl, DMSO, replicate 3

description:
ABCG2+ L3.6pl cells
Ctrl_rep_3

value: DMSO


title: hepatocyte_Ampk InsMet rep1

value: C57BL/6 (F3 generation)

tag: tissue

value: 2mM Metformin for 5h serum-starved


title: 9sCa: ESCs_MSL2KO2_RNAseq_rep3

description:
ESCs_DEseq_basic_DEresults.tsv
ESCs_DEseq_allelic_DEresults.tsv
ESCs_DEgenes_classification.txt

source_name: Embryonic stem cells

tag: library type

value: RNAseq

tag: replicate


title: BioTASQ_vivo_input

tag: age


title: hepatocyte_Ampk InsMet rep2

value: primary hepatocytes

value: 8-16 weeks old

tag: tamoxifen treatment


title: ABCG2+ L3.6pl, DMSO, replicate 2

description:
ABCG2+ L3.6pl cells
Ctrl_rep_2


title: 9sCa: NPCs_Control_BRD4_rep1


title: BioTASQ_vivo_biotin


title: 9sCa: ESCs_MSL2KO2_RNAseq_rep1


title: hepatocyte_Ampk Ins rep2

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

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

value: untreated - serum starved


title: hepatocyte_Ampk InsMet rep3

value: 15 minute pre-treatment with 1nM Insulin


title: ABCG2+ L3.6pl, DMSO, replicate 1

description:
ABCG2+ L3.6pl cells
Ctrl_rep_1


title: 9sCa: ESCs_MSL2KO1_RNAseq_rep3


title: 9sCa: ESCs_MSL2KO1_RNAseq_rep2


title: hepatocyte_Ampk Met rep1

value: Untreated


title: ABCG2+ L3.6pl, PHF5A ChIP, MM-102, replicate 2

description: ABCG2+ L3.6pl cells

data_processing:
Raw reads were cleaned using fastp v0.23.2 with default parameters.
Cleaned reads were confirmed high-quality using FastQC v0.11.9.
Cleaned reads were mapped to the human genome hg38 using Burrows-Wheeler Aligner v0.7.17.
Duplicated reads, reads mapped to ENCODE blacklisted regions, and reads with mapping quality lower than 30 were removed, and only properly paired reads were retained.
BIGWIG tracks were generated using deepTools v3.5.1.
Assembly: hg38
Supplementary files format and content: BIGWIG

extract_protocol:
ChIP lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8, 0.1% sodium deoxycholate, 0.1% SDS and 1% Triton X-100) freshly supplemented with 1x EDTA-free protease inhibitor cocktail
Genomic DNA was quantified with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA) and quality assessed by Tapestation genomic DNA Assay (Agilent Technologies, California, USA). Library preparation was performed using KAPA Hyper Prep kit (Roche, Basel, Switzerland) per manufacturer’s recommendations. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA), and QuantStudio® 5 System (Applied Biosystems, California, USA). Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq S4 (Illumina, California, USA) with a read length configuration of 150 PE for 20M PE reads (10M in each direction) per sample.

tag: chip antibody

value: PHF5A (Proteintech,15554-1-AP)


title: hepatocyte_Ampk Met rep2


title: ABCG2+ L3.6pl, PHF5A ChIP, MM-102, replicate 1

description: ABCG2+ L3.6pl cells


title: Vitro_input

value: Nipponbare

value: Seedling

value: two weeks

value: vitro


title: hepatocyte_Ampk UT rep1


title: hepatocyte_Ampk Met rep3


title: Vitro_biotin


title: ABCG2+ L3.6pl, PHF5A ChIP, DMSO, replicate 2

description: ABCG2+ L3.6pl cells

value: Pancreatic adenosquamous carcinoma

value: Mutation; HGNC; 6407; KRAS; Simple; p.Gly12Asp (c.35G>A); ClinVar=VCV000012582; Zygosity=Unspecified (from parent cell line).


title: 9sCa: ESCs_MSL2KO1_RNAseq_rep1

value: Female


title: 9sCa: ESCs_MSL2KO2_RNAseq_rep2


title: BioTASQ_vitro_rep1

value: small-molecular baits BioTASQ


title: BioCyTASQ_vitro_rep2

value: small-molecular baits BioCyTASQ


title: ABCG2+ L3.6pl, PHF5A ChIP, DMSO, replicate 1

description: ABCG2+ L3.6pl cells

value: DMSO


title: hepatocyte_Ampk UT rep2

value: C57BL/6 (F3 generation)

value: primary hepatocytes

value: 8-16 weeks old


title: BioCyTASQ_vitro_rep1


title: 9sCa: ESCs_Control_RNAseq_rep2

value: WT

value: RNAseq


title: hepatocyte_Ampk UT rep3

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

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

value: untreated - serum starved

value: Untreated


title: 9sCa: ESCs_Control_RNAseq_rep3


title: ABCG2+ L3.6pl, PHF14 ChIP, MM-102, replicate 1

description: ABCG2+ L3.6pl cells

value: PHF14 (Proteintech, 24787-1-AP)


title: liver_Adel Met rep3

source_name: Liver

growth_protocol: Mice maintained on 45% high fat diet,

extract_protocol:
Livers were snap frozen, lysed in qiaxol. RNA was extracted using qiagen RNeasy lipid tissue kit
mRNA-seq libraries were prepared using the TruSeq RNA library preparation kit (version 2)

treatment_protocol: fasted overnight, refed for 1h, and treated with 200 mpk metformin or saline for 4 hours

value: liver

value: 8 month old

tag: Sex

value: male

tag: diet

value: 45% High Fat Diet for 12 weeks

value: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk

tag: fasting treatment

value: Overnight Fast, 1h Refed with high fat diet

tag: metformin treatment

value: 200 mpk Metformin for 4 hours

tag: avertin treatment

value: subLethal dose of avertin 10' prior to collection


title: ABCG2+ L3.6pl, PHF14 ChIP, MM-102, replicate 2

description: ABCG2+ L3.6pl cells

tag: cell line

value: Pancreatic adenosquamous carcinoma

value: Mutation; HGNC; 6407; KRAS; Simple; p.Gly12Asp (c.35G>A); ClinVar=VCV000012582; Zygosity=Unspecified (from parent cell line).


title: Retina.Vascular_T448M

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

data_processing:
CRSP tool (https://github.com/pjiang1105/CRSP)
Using CRSP tool to estimate gene expression values
Using mouse protein database as a reference via applying CRSP tool
Assembly: Mapping and gene expression estimation were not based on a particular genome. It was estimated by CRSP tool via mouse protein database
Supplementary files format and content: tab-delimited text files include TPM and Expected Count values for each Sample

organism: Arvicanthis niloticus

source_name: Whole Retinal Vasculature

extract_protocol:
Total RNAs from 28 Nile grass rat vascular samples were isolated using trizol (ThermoFisher #15596018) and chloroform phase separations followed by the RNeasy mini protocol (Qiagen #74106) with optional on-column DNase digestion (Qiagen #79254). One hundred nanograms of total RNA was used to prepare sequencing libraries.
RNA libraries for RNA-seq were prepared using our lab developed LM-seq protocol

value: Whole Retinal Vasculature

value: Male

tag: acellular capillary density (counts per mm2)

tag: random blood glucose

value: WT

value: No treatment


title: 9sCa: ESCs_Control_RNAseq_rep1

tag: strain

value: Female

value: RNAseq


title: hepatocyte_AATsc Ins rep1

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

tag: treatment

value: untreated - serum starved

tag: pre-treatment

value: 15 minute pre-treatment with 1nM Insulin


title: ABCG2+ L3.6pl, PHF14 ChIP, DMSO, replicate 2

description: ABCG2+ L3.6pl cells

tag: cell type

tag: genotype

value: PHF14 (Proteintech, 24787-1-AP)

value: DMSO


title: liver_Adel Met rep2

tag: tissue

value: liver

value: 8 month old

value: male

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

value: 45% High Fat Diet for 12 weeks

value: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk

value: Overnight Fast, 1h Refed with high fat diet

value: 200 mpk Metformin for 4 hours

value: subLethal dose of avertin 10' prior to collection


title: Retina.Vascular_T447M

value: Whole Retinal Vasculature

value: Male

value: WT

value: No treatment


title: hepatocyte_AATsc Ins rep2

value: C57BL/6 (F3 generation)

value: primary hepatocytes

tag: age

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: ABCG2+ L3.6pl, PHF14 ChIP, DMSO, replicate 1

description: ABCG2+ L3.6pl cells

value: Pancreatic adenosquamous carcinoma

value: Mutation; HGNC; 6407; KRAS; Simple; p.Gly12Asp (c.35G>A); ClinVar=VCV000012582; Zygosity=Unspecified (from parent cell line).

value: PHF14 (Proteintech, 24787-1-AP)

value: DMSO


title: Retina.Vascular_T446M


title: liver_Adel Met rep1

value: liver

value: 8 month old

value: male

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

value: 45% High Fat Diet for 12 weeks

tag: tamoxifen treatment

value: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk

value: Overnight Fast, 1h Refed with high fat diet


title: hepatocyte_AATsc Ins rep3

value: C57BL/6 (F3 generation)

value: 15 minute pre-treatment with 1nM Insulin


title: ABCG2+ L3.6pl, input, MM-102, replicate 2

description: ABCG2+ L3.6pl cells

tag: chip antibody


title: Retina.Vascular_T445F

value: Whole Retinal Vasculature

tag: Sex

value: Female

value: WT

value: No treatment


title: ABCG2+ L3.6pl, input, DMSO, replicate 1

description: ABCG2+ L3.6pl cells

value: Pancreatic adenosquamous carcinoma


title: liver_Adel Sal rep3

tag: diet

value: Saline for 4h

value: subLethal dose of avertin 10' prior to collection


title: hepatocyte_AATsc InsMet rep1

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: 2mM Metformin for 5h serum-starved


title: Retina.Vascular_T430F


title: liver_Adel Sal rep2

value: liver

value: 8 month old

value: male

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

value: 45% High Fat Diet for 12 weeks

tag: fasting treatment


title: hepatocyte_AATsc InsMet rep2

value: C57BL/6 (F3 generation)

value: 15 minute pre-treatment with 1nM Insulin


title: liver_Adel Sal rep1

value: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk

value: Overnight Fast, 1h Refed with high fat diet

tag: metformin treatment


title: ABCG2+ L3.6pl, PHF5A chIP, replicate 2

description: ABCG2+ L3.6pl cells

value: Pancreatic adenosquamous carcinoma

value: Mutation; HGNC; 6407; KRAS; Simple; p.Gly12Asp (c.35G>A); ClinVar=VCV000012582; Zygosity=Unspecified (from parent cell line).

value: PHF5A (Proteintech,15554-1-AP)


title: hepatocyte_AATsc InsMet rep3

value: primary hepatocytes


title: Retina.Vascular_T425M

value: Whole Retinal Vasculature

value: Male

value: WT

value: No treatment


title: Retina.Vascular_T424M


title: liver_AATsc Met rep3

value: liver

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

value: 200 mpk Metformin for 4 hours

tag: avertin treatment

value: subLethal dose of avertin 10' prior to collection


title: ABCG2+ L3.6pl, PHF14 chIP, replicate 2

description: ABCG2+ L3.6pl cells

tag: cell line

value: PHF14 (Proteintech, 24787-1-AP)


title: Retina.Vascular_T420F

value: Female

tag: acellular capillary density (counts per mm2)


title: hepatocyte_AATsc Met rep1

value: C57BL/6 (F3 generation)

value: 8-16 weeks old

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

value: 2mM Metformin for 5h serum-starved

value: Untreated


title: Retina.Vascular_T419F

tag: random blood glucose


title: liver_AATsc Met rep2

tag: strain

value: 8 month old

value: male

value: 45% High Fat Diet for 12 weeks

value: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk

value: Overnight Fast, 1h Refed with high fat diet


title: hepatocyte_AATsc Met rep2

value: primary hepatocytes

tag: treatment


title: hepatocyte_AATsc Met rep3

tag: pre-treatment


title: liver_AATsc Met rep1

value: liver


title: ABCG2+ L3.6pl, PHF14 chIP, replicate 1

description: ABCG2+ L3.6pl cells

tag: cell type

value: Pancreatic adenosquamous carcinoma

value: Mutation; HGNC; 6407; KRAS; Simple; p.Gly12Asp (c.35G>A); ClinVar=VCV000012582; Zygosity=Unspecified (from parent cell line).


title: Retina.Vascular_T414F

value: Whole Retinal Vasculature

tag: genotype

value: WT

value: No treatment


title: hepatocyte_AATsc UT rep1

value: C57BL/6 (F3 generation)

tag: tissue

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

value: untreated - serum starved


title: ABCG2+ L3.6pl, KMT2A ChIP, replicate 2

description: ABCG2+ L3.6pl cells

value: KMT2A (Proteintech, 29278-1-AP)


title: ABCG2+ L3.6pl, KMT2A ChIP, replicate 1

description: ABCG2+ L3.6pl cells


title: ABCG2+ L3.6pl, PHF5A chIP, replicate 1

description: ABCG2+ L3.6pl cells

value: PHF5A (Proteintech,15554-1-AP)


title: Retina.Vascular_T411M

value: Male


title: ABCG2+ L3.6pl, input for PHF5A and PHF14 ChIP, replicate 1

description: ABCG2+ L3.6pl cells


title: liver_AATsc Sal rep2

tag: age

value: 8 month old

value: male

value: Saline for 4h

value: subLethal dose of avertin 10' prior to collection


title: Retina.Vascular_T410F

value: Female


title: liver_AATsc Sal rep1

value: liver

value: 45% High Fat Diet for 12 weeks

tag: tamoxifen treatment

value: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk

value: Overnight Fast, 1h Refed with high fat diet


title: ABCG2+ L3.6pl, input for KMT2A ChIP, replicate 1

description: ABCG2+ L3.6pl cells

value: Pancreatic adenosquamous carcinoma

value: Mutation; HGNC; 6407; KRAS; Simple; p.Gly12Asp (c.35G>A); ClinVar=VCV000012582; Zygosity=Unspecified (from parent cell line).

tag: chip antibody


title: Retina.Vascular_T409F

value: Whole Retinal Vasculature

tag: Sex

value: WT

value: No treatment


title: hepatocyte_Tsc Ins rep1

value: C57BL/6 (F3 generation)

value: primary hepatocytes

value: 8-16 weeks old

value: Tsc2 fl/fl; AlbCreEr

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

value: untreated - serum starved

value: 15 minute pre-treatment with 1nM Insulin


title: hepatocyte_AATsc UT rep3

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

value: Untreated


title: tissue, Tumor_HCC

city: Nanning

first: Deyuan

last: Li

address: 22 Shuangyong Road, Nanning

institute: Guangxi Medical University

data_processing:
Firstly, Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used Bowtie2 and Hisat2 to map reads to the genome of species. Remaining reads (unmapped reads) were still mapped to genome using tophat-fusion. CIRCExplorer2 and CIRIwas used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion. All samples were generated unique circular RNAs. The differentially expressed circRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package–edgeR.
Assembly: GRCH38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: HCC tissue

extract_protocol:
Total RNA was isolated and purified using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.
Approximately 5 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, USA). After removing ribosomal RNAs, the left RNAs were fragmented into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP. An A-base is 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. Single-or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs,The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles 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. The average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed the paired-end sequencing on an Illumina Hiseq 4000 (LC Bio, China) following the vendor's recommended protocol.

tag: disease state

value: hepatocellular carcinoma

value: HCC tissue


title: Retina.Vascular_T408F

value: Female


title: tissue, Normal

source_name: Normal adjacent tissue of HCC

value: Normal adjacent tissue of HCC


title: liver_Tsc Met rep2

value: liver

value: 8 month old

value: male

tag: diet

value: 45% High Fat Diet for 12 weeks

value: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk

tag: fasting treatment

value: Overnight Fast, 1h Refed with high fat diet

value: 200 mpk Metformin for 4 hours

value: subLethal dose of avertin 10' prior to collection


title: Retina.Vascular_T407M

value: Whole Retinal Vasculature

value: Male

value: WT

value: No treatment


title: hepatocyte_Tsc Ins rep2

value: C57BL/6 (F3 generation)

value: primary hepatocytes

value: 8-16 weeks old

value: Tsc2 fl/fl; AlbCreEr

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

value: untreated - serum starved

value: 15 minute pre-treatment with 1nM Insulin


title: liver_Tsc Met rep1

value: liver

value: 8 month old

value: male

tag: metformin treatment

tag: avertin treatment


title: hepatocyte_Tsc Ins rep3


title: liver_AATsc Sal rep3

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

value: 45% High Fat Diet for 12 weeks

value: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk

value: Overnight Fast, 1h Refed with high fat diet

value: Saline for 4h


title: CaBl: HDF_Msl2_ChIP_Rep2

description:
HDF_Msl2_ChIP_peaks.bed
HDF_Msl2_ChIP_peaks.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.
scMultiomics: A unified dataset of both scATAC-seq and scRNA-seq was processed with the count function in cellranger-arc (v2.0.0) (https://support.10xgenomics.com) using the reference mm10-2020-A-2.0.0 (10X). The filtered matrix of WT and MSL2 KO were merged together with Signac (v1.5.0) (131) and Seurat (v4.1.0) (132). The merged dataset was then centered, dimensionally reduced with principal-component analysis using 20 dimensions and embedded with UMAP clustering. Three clustering techniques from Seurat were applied for the merged dataset: independent RNA, independentATAC and WNN method. Chromatin accessibility (TSS +- 200bp) for each gene from the scATAC-seq data was calculated by Signac (v1.5.0) (131) GeneActivities function. Gene counts from all cells were merged together for each gene and compared to the bulk RNA-seq data to calculate pearson correlation.  For allele-specific analysis, the raw fastq files of chromatin accessibility and gene expression were aligned against an N-masked genome (Bowtie2 v2.2.5 (116) for chromatin accessibility data, STAR v2.7.9a (110) for gene expression data) and split into allele-specific BAM files, similar to the analysis of the bulk data. Read headers were then extracted from the allele-specific BAM files and used to create allele-specific fastq files which were subsequently processed using the count function in cellranger-arc (v2.0.0). The workflow to generate the allele-specific fastq files is available under https://github.com/Akhtar-Lab-MPI-IE/multiomePhaser. Note that only the cells identified in the bulk analysis were kept in the allele-specific analysis. Allele-specific gene counts from scRNA-seq data and gene activity from scATAC-seq data were then projected on the UMAP clusters in the featureplot with Seurat (v4.1.0) (132) Featureplot function.
H3K4me3 HiChIP: HiChIP-seq data was processed with MAPS (130) (downloaded from github on May 21th, 2021). In summary, MAPS aligned the FASTQ-files with BWA to a mm10 reference genome. Low mapping quality reads, invalid pairs of alignments and PCR duplicates were filtered sequentially and only valid read pairs were kept for downstream analysis. Filtered reads were binned at 10 kb size to generate the chromatin contact matrix. MAPS normalizes chromatin contact frequencies anchored at genomic regions at the merged H3K4me3 peaks to identify long-range chromatin interactions at 10 kb resolution. A binomial test was then used to determine significant chromatin interactions with FDR corrected p-value cutoff of 0.01.
Assembly: 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.

source_name: Primary human dermal fibroblasts

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.
scMultiomics: WT and MSL2 KO NPCs were harvested using Accutase (Sigma), resuspended in fresh medium, and placed on ice. Viability was estimated using trypan blue and a hemocytometer. Nuclei were prepared according to 10x Genomics guidelines (manual CG000365 revB) using the recipes indicated in the manual with few modifications. In brief, cell pellets were resuspended in 1X cell lysis buffer supplemented with RNase A inhibitor (Sigma 3335399001), incubated for 8 minutes on ice, and then washed twice with a wash buffer (supplemented with RNase A inhibitor). Nuclei were resuspended in a diluted nuclei buffer (supplemented with RNase inhibitors) and filtered through a 40 mm tip strainer (Flowmi Cell Strainer, H13680-0040, Bel-Art). Nuclei were quantified using a hemocytometer and adjusted to 3220 nuclei/ml. 5 ml of diluted nuclei were subsequently used for the transposase reaction.
H3K4me3 HiChIP: HiChIP was performed as previously described (108) with slight modifications. In brief, 5 million WT and MSL2 KO cells were fixed with 1% formaldehyde for 15 minutes at room temperature, followed by 5 minutes quenching with 0.2M glycine. Fixed cell pellets were resuspended in a cold lysis buffer (10 mM Tris, pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630 with proteinase inhibitor). Nuclei isolation was performed by sonication using a Covaris E220 for 30 secs according to the following settings: 75 peak power, 200 cycles per burst, 3% duty factor, temperature 4°C. Successful nuclei isolation was confirmed using a bright-field microscope. Nuclei were then resuspended in 50 µl 0.5% of SDS and incubated at 37 degrees for 10 min. Permeabilization was quenched by adding a master mix containing 25 µl 10% Triton X-100 , 135 µl water, 25 µl 10X CutSmart Buffer, and 4 µl MboI enzyme (25U/µl, New England Biolabs), followed by digestion for 2 hours at 37 degrees in a thermomixer, shaking at 800 rpm. Biotin fill-in was performed by the addition of 10mM each of dATP, dGTP, dTTP, biotin14-dCTP (Thermo Fisher Scientific), and 25 units of Klenow, and incubation at 25 degrees for 1 hour in a thermomixer, shaking at 600 rpm. Proximity ligation was performed at room temperature in 1× T4 DNA ligase buffer (New England Biolabs), 0.1mg/ml BSA, 1% Triton X-100 and 4,000 U T4 DNA Ligase (New England Biolabs). The nuclei were harvested and then resuspended in 1ml chromatin shearing buffer (10mM Tris, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 1% Triton X-100, 0.5% sodium deoxycholate, protease inhibitors). Chromatin shearing was performed by sonication using Covaris E220 for 20 minutes with the following settings: 104 peak power, 200 cycles per purst, 3% duty factor. The samples were centrifuged at 10,000g for 10 minutes, and the supernatant was collected. Chromatin immunoprecipitation was performed overnight by the addition of 5ug of H3K4me3 antibody (Diagenode) to the sheared chromatin. The next day, 40 µl per sample of Magnetic Dynabeads G were reclaimed using a magnet, washed twice with chromatin shearing buffer, and then added to the immunoprecipitation samples and left rotating for 3 hours in a cold room. After incubation, the beads were washed with chromatin shearing buffer three times, LiCl buffer once (10mM Tris, pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% IGEPAL CA-630, 0.1% sodium deoxycholate), and TE buffer twice (10mM Tris, pH 8.0, 0.1mM EDTA). To elute DNA, washed beads were resuspended in elution buffer (10mM Tris, pH 8.0, 350mM NaCl, 1% SDS) with 10μg RNase A and 20μg proteinase K, and were incubated at 37 degrees for 1 hour and then at 65 degrees overnight. DNA was purified using the Zymo DNA Clean & Concentrator kit. Biotin pull-down was performed using Dynabeads MyOne Streptavidin T1 beads, and libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer’s instructions (New England Biolabs, #E7645).

tag: gender

value: Male

value: WT

tag: library type

tag: replicate


title: liver_Tsc Sal rep2

tag: strain

value: C57BL/6 (F3 generation)

value: subLethal dose of avertin 10' prior to collection


title: hepatocyte_AATsc UT rep2

value: primary hepatocytes

value: 8-16 weeks old

tag: treatment

tag: pre-treatment

value: Untreated


title: Retina.Vascular_T404F

value: Whole Retinal Vasculature

value: Female

tag: acellular capillary density (counts per mm2)

tag: random blood glucose

tag: genotype

value: No treatment


title: hepatocyte_Tsc InsMet rep1

tag: tissue

tag: age

value: Tsc2 fl/fl; AlbCreEr

tag: tamoxifen treatment

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

value: 2mM Metformin for 5h serum-starved

value: 15 minute pre-treatment with 1nM Insulin


title: CaBl: HDF_Msl2_ChIP_Rep1


title: Retina.Vascular_T401F

tag: Sex


title: liver_Tsc Sal rep1

value: liver

value: 8 month old

value: male

tag: diet

value: 45% High Fat Diet for 12 weeks

value: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk


title: liver_AA Met rep3

value: C57BL/6 (F3 generation)

value: Raptor - S722A; S792A

tag: fasting treatment

value: Overnight Fast, 1h Refed with high fat diet

value: 200 mpk Metformin for 4 hours


title: CaBl: HDF_Kansl3_ChIP_Rep2

description:
HDF_Kansl3_ChIP_peaks.bed
HDF_Kansl3_ChIP_peaks.bw

value: Male

value: WT


title: Retina.Vascular_T398F

value: Whole Retinal Vasculature

value: Female


title: liver_Tsc Met rep3

value: Tsc2 fl/fl; AlbCreEr

tag: metformin treatment

value: subLethal dose of avertin 10' prior to collection


title: hepatocyte_Tsc InsMet rep3

value: primary hepatocytes

value: 8-16 weeks old

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

value: 2mM Metformin for 5h serum-starved


title: liver_AA Met rep2

value: liver

value: 8 month old

value: male

tag: avertin treatment


title: hepatocyte_Tsc InsMet rep2

value: C57BL/6 (F3 generation)

value: 15 minute pre-treatment with 1nM Insulin


title: hepatocyte_Tsc Met  rep3

value: Untreated


title: liver_AA Met rep1

value: Raptor - S722A; S792A

value: 45% High Fat Diet for 12 weeks

value: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk

value: Overnight Fast, 1h Refed with high fat diet

value: 200 mpk Metformin for 4 hours


title: Retina.Vascular_T397F

value: Whole Retinal Vasculature

value: Female

value: WT

value: No treatment


title: hepatocyte_Tsc Met rep1

value: primary hepatocytes

value: 8-16 weeks old

value: Tsc2 fl/fl; AlbCreEr

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


title: CaBl: HDF_Input_Rep1

tag: gender

value: Male


title: CaBl: HDF_IgG_ChIP_Rep2

description:
HDF_IgG_ChIP_peaks.bed
HDF_IgG_ChIP_peaks.bw

tag: library type


title: CaBl: HDF_Input_Rep2

tag: replicate


title: liver_AA Sal rep3

tag: strain

value: C57BL/6 (F3 generation)

value: liver

value: 8 month old

value: male

value: Saline for 4h

value: subLethal dose of avertin 10' prior to collection


title: Retina.Vascular_T399F

tag: treatment


title: CaBl: HDF_Kansl3_ChIP_Rep1


title: liver_AA Sal rep2

value: Raptor - S722A; S792A

value: 45% High Fat Diet for 12 weeks

value: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk

value: Overnight Fast, 1h Refed with high fat diet


title: hepatocyte_Tsc UT rep1

value: untreated - serum starved

tag: pre-treatment

value: Untreated


title: CaBl: HDF_IgG_ChIP_Rep1

value: WT


title: Retina.Vascular_T392F

value: Whole Retinal Vasculature

value: Female

tag: acellular capillary density (counts per mm2)

value: No treatment


title: liver_WT Met rep3

value: wild type

value: 200 mpk Metformin for 4 hours


title: hepatocyte_Tsc UT rep2

value: C57BL/6 (F3 generation)

value: primary hepatocytes

value: 8-16 weeks old

value: Tsc2 fl/fl; AlbCreEr

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


title: Kasumi1 shHIF2a rep3

city: Milan

first: Rosa

last: Bernardi

address: via Olgettina 60

country: Italy

institute: San Raffaele Scientific Institute

data_processing:
Read quality was determined using FastQC and low-quality sequences were trimmed using the software BBDuck.
Reads were aligned to the human reference genome (GRCh38) using the BWA MEM software with standard parameters.
Uniquely mapped reads were selected with MarkDuplicates from Picard Tools.
Further filtering was done on reads mapping in regions present in the ENCODE hg38 blacklist.
ATAC peaks were called uing MACS with standar parameters (FDR <0.05)
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: Cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum, and 100IU/ml penicillin plus 100mg/ml streptomycin antibiotics. Selection of silenced cells was obtained by addinding 2 micrograms/ml puromicine to the medium.

extract_protocol:
A total of 60000 cells were lysed with digitonin and tagmented with an engineered Tn5 transposase at 37°C for 30 minutes, a protocol optimized for blood cells. Tagmented DNA was purified using the MinElute Reaction Cleanup kit and then amplified by PCR. Before the sequencing, fragments with a 1-5 kb size range were removed by magnetic separation with AMPure XP beads.
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.

tag: cell line

tag: cell type

value: Acute Myeloid Leukemia

tag: shRNA


title: liver_AA Sal rep1

tag: tissue

value: liver

tag: age

value: 8 month old

value: male

tag: genotype

value: Raptor - S722A; S792A

value: 45% High Fat Diet for 12 weeks

value: Saline for 4h

value: subLethal dose of avertin 10' prior to collection


title: Retina.Vascular_T389M

value: Whole Retinal Vasculature

tag: Sex

value: Male

tag: random blood glucose

value: WT


title: Kasumi1 shHIF2a rep2


title: liver_WT Met rep2

value: wild type

tag: diet

tag: tamoxifen treatment

value: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk

tag: fasting treatment

value: Overnight Fast, 1h Refed with high fat diet

tag: metformin treatment

value: 200 mpk Metformin for 4 hours


title: hepatocyte_Tsc UT rep3

value: C57BL/6 (F3 generation)

value: primary hepatocytes

value: 8-16 weeks old

value: Tsc2 fl/fl; AlbCreEr

value: untreated - serum starved

value: Untreated


title: Retina.Vascular_T370M

value: No treatment


title: Kasumi1 shHIF2a rep1

value: Acute Myeloid Leukemia


title: Retina.Vascular_T396F

value: Female


title: liver_WT Met rep1

value: liver

value: 8 month old

value: male

value: 45% High Fat Diet for 12 weeks

tag: avertin treatment

value: subLethal dose of avertin 10' prior to collection


title: hepatocyte_Tsc Met rep2

tag: strain

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

value: 2mM Metformin for 5h serum-starved


title: Kasumi1 shCTRL rep3

value: shCTRL


title: hepatocyte_AA Ins rep2

value: C57BL/6 (F3 generation)

value: Raptor - S722A; S792A

tag: treatment

value: 15 minute pre-treatment with 1nM Insulin


title: Retina.Vascular_T353M

value: Whole Retinal Vasculature

value: Male

value: WT


title: hepatocyte_AA Ins rep3

value: primary hepatocytes

value: 8-16 weeks old

value: untreated - serum starved

tag: pre-treatment


title: liver_WT Sal rep3

value: liver

value: wild type

value: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk

value: Overnight Fast, 1h Refed with high fat diet

value: Saline for 4h


title: Retina.Vascular_T393F

value: Female

tag: acellular capillary density (counts per mm2)

value: No treatment


title: Retina.Vascular_T348M


title: liver_WT Sal rep2

value: 8 month old

value: male

value: 45% High Fat Diet for 12 weeks

value: subLethal dose of avertin 10' prior to collection


title: Retina.Vascular_T391M

value: Whole Retinal Vasculature


title: Kasumi1 shCTRL rep2

tag: cell line

value: Acute Myeloid Leukemia

value: shCTRL


title: Kasumi1 shCTRL rep1

tag: cell type


title: hepatocyte_AA InsMet rep1

value: C57BL/6 (F3 generation)

value: primary hepatocytes

value: Raptor - S722A; S792A

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

value: 2mM Metformin for 5h serum-starved

value: 15 minute pre-treatment with 1nM Insulin


title: liver_WT Sal rep1

value: liver

value: wild type

value: Treated with Tamoxifen 3x after 7 weeks on HFD to delete Tsc2 and Ampk

value: Overnight Fast, 1h Refed with high fat diet


title: hepatocyte_AA Ins rep1

value: 8-16 weeks old

value: untreated - serum starved


title: hepatocyte_AA InsMet rep2


title: Kasumi1shEPASp10ATRA

data_processing:
Base-calling was performed on NovaSeq 6000 Illumina machine, obtaining 30 million single end reads per sample on average
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.32)
The remaining reads were aligned to the reference human genome GRCh38, using STAR aligner (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using featureCounts (version1.16) and annotated according to Gencode basic annotations (Gencode version 28)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

source_name: Acute Myeloid Leukemia cell line

growth_protocol: Cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum, and 100IU/ml penicillin plus 100mg/ml streptomycin antibiotics. Selection of silenced cells was obtained by addinding puromicine to the medium: 2mg/ml (Kasumi1), and 6mg/ml (HL60).

extract_protocol:
total RNA from a minimum of 1x10^6 up to 3x10^6 cells were isolated with QIAGEN RNeasy Plus Micro Kit according to the manufacturer’s instructions. After isolation, total RNA was treated with DNAse I (Sigma) accordingly to the manufacturer's instructions.
Libraries were generated with the TruSeq stranded mRNA protocol. This protocol allows unbiased 5’/3’ library preparation starting from 100 ng of total RNA. Libraries were barcoded, pooled and sequenced on an Illumina Nova-Seq 6000 sequencing system.

treatment_protocol: Two replicates of shCTRL, shHIF1a and shHIF2a Kasumi1 cells were treated for 24 hours with ATRA 1mM.

value: Acute Myeloid Leukemia cell line

tag: fab subtype

tag: main genetic lesions

value: 1mM ATRA 24 hours


title: Stab-con-13-5-3

city: Hamilton

first: Darreb

last: Bridgewater

state: Ontario

address: 1280 Main Street West

country: Canada

institute: McMaster University

data_processing:
Raw sequence data were exported to FASTQ format and were filtered based on quality scores.
Next the reads were mapped to  the UCSC/mm10 reference version using HISAT2.
The counts were obtained by using ht-seq count with the “intersection-strict” option.
Counts were transformed with TMM transformation and then normalized with VOOM.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data file contains a matrix containing data from all samples.

extract_protocol:
Embryonic kidneys were micro-dissected using Dumont #5 INOX surgical forceps in cold phosphate-buffered saline (PBS) pH 7.4 under a Leica EZ4D microscope and were washed in cold PBS immediately after microdissection. Kidney explants were dissociated using 0.3% Collagenase (Sigma Aldrich) for 10 minutes at 37°C. Kidneys were then triturated through a 25-gauge needle to make a single-cell suspension, and then washed 3 times in cold PBS supplemented with 2% fetal bovine serum. Before sorting, cells were run through a 40μm strainer (ThermoFisher Scientific). Cells were sorted into PBS (if undergoing second sort) or directly into Qiagen’s RLT Lysis Buffer.
Sequencing of samples was performed using the Illumina HiSeq system (Illumina, San Diego).

tag: strain background

value: wild-type

tag: developmental stage

tag: tissue

value: kidney

value: stromal cells


title: Stab-con-13-5-2

tag: genotype


title: Kasumi1shEPASp8ATRA


title: Kasumi1shEPASp10

value: untreated


title: Stab-con-13-5-1


title: hepatocyte_AA Met rep2

value: C57BL/6 (F3 generation)

value: primary hepatocytes

tag: age

value: Untreated


title: Kasumi1shEPASp8


title: hepatocyte_AA Met rep3

value: Raptor - S722A; S792A

tag: tamoxifen treatment

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

value: 2mM Metformin for 5h serum-starved


title: Stab-con-12-5-3


title: Kasumi1shHIF1p10ATRA


title: hepatocyte_AA UT rep1


title: MRSL_Control

type: RNA

city: Blacksburg

first: Irving

middle: Coy

last: Allen

state: VA

address: 205 Duck Pond Dr.

department: Biomedical Sciences and Pathobiology

institute: Virginia-Maryland College of Veterinary Medicine

description: Clariom S Affymetrix and ThermoFisher

hyb_protocol: Performed by ThermoFisher ClariomS services

data_processing: CHP data provided by ThermoFisher ClariomS services. Researchers analysed data using the Transcriptome Analysis Console (ThermoFisher, Applied Biosystems)

label: Biotin

source_name: HeLa RNA MRSL vendor control

growth_protocol: Tissue samples were obtained during clinically indicated EGD procedures. Biopsies were collected from endoscopically visible areas of active inflammation and healthy mucosa in subjects and controls, respectively. Samples were stored in RNAlater (Qiagen) in -80C freezer until extraction. During the same procedure a separate sample was collected for clinical diagnostic purposes. Definitive diagnosis of EOE was made using clinical, endoscopic, and histologic metrics per current guidelines (Dellon, 2018). Control samples were included after endoscopic and histologic confirmation that the tissue was confirmed to be normal.

extract_protocol: Qiagen AllPrep kit per manufacturer's protocols

tag: disease state

tag: tissue type


title: Stab-con-12-5-2


title: Stab-con-12-5-1


title: Stab-13-5-3

value: beta-catSO


title: Kasumi1shHIF1p8ATRA


title: hepatocyte_AA InsMet rep3

value: 15 minute pre-treatment with 1nM Insulin


title: C276

description: Clariom S Affymetrix and ThermoFisher

scan_protocol: Performed by ThermoFisher ClariomS services

source_name: Control 276

value: Control

value: Esophagus


title: C160

description: Clariom S Affymetrix and ThermoFisher

source_name: Control 160

label_protocol: Performed by ThermoFisher ClariomS services


title: C280

description: Clariom S Affymetrix and ThermoFisher

source_name: Control 280


title: hepatocyte_AA UT rep3

value: 8-16 weeks old

value: untreated - serum starved


title: Kasumi1shHIF1p8

value: Acute Myeloid Leukemia cell line


title: hepatocyte_AA UT rep2


title: Kasumi1shHIF1p10


title: hepatocyte_AA Met rep1


title: C200

description: Clariom S Affymetrix and ThermoFisher

source_name: Control 200


title: Stab-13-5-2


title: hepatocyte_WT Ink rep1

value: wild type

value: 0.1uM INK-128 for 5h serum-starved


title: Kasumi1shCTRLp10ATRA

value: 1mM ATRA 24 hours


title: hepatocyte_WT Ink rep2


title: C169

description: Clariom S Affymetrix and ThermoFisher

source_name: Control 169


title: C180

description: Clariom S Affymetrix and ThermoFisher

source_name: Control 180


title: C194

description: Clariom S Affymetrix and ThermoFisher


title: C102

description: Clariom S Affymetrix and ThermoFisher

source_name: Control 102


title: hepatocyte_WT Ink rep3

source_name: Primary Hepatocytes


title: C212

description: Clariom S Affymetrix and ThermoFisher

source_name: Control 212


title: Kasumi1shCTRLp10

value: untreated


title: hepatocyte_WT Ins rep1

value: C57BL/6 (F3 generation)


title: Kasumi1shCTRLp8


title: Stab-12-5-1

value: kidney

value: stromal cells


title: Stab-13-5-1


title: Stab-12-5-2


title: HL60shEPASp4

value: c-myc amplicons, tp53 deleted


title: HL60shEPAS1p6


title: hepatocyte_WT Ins rep3

value: primary hepatocytes

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


title: hepatocyte_WT Ins rep2


title: Kasumi1shCTRLp8ATRA


title: K-O-con-13-5-2

value: wild-type


title: K-O-con-13-5-3


title: Stab-12-5-3

value: beta-catSO


title: hepatocyte_WT InsInk

value: 15 minute pre-treatment with 1nM Insulin


title: HL60shHIF1p4


title: hepatocyte_WT Ins rep4


title: K-O-con-12-5-3


title: K-O-con-13-5-1


title: C251

description: Clariom S Affymetrix and ThermoFisher

source_name: Control 251

value: Control

value: Esophagus


title: E81

description: Clariom S Affymetrix and ThermoFisher

source_name: EoE 81

value: EoE


title: E278

description: Clariom S Affymetrix and ThermoFisher

source_name: EoE 278


title: C211

description: Clariom S Affymetrix and ThermoFisher

source_name: Control 211


title: hepatocyte_WT InsMet rep1

value: 8-16 weeks old

value: 2mM Metformin for 5h serum-starved


title: C193

description: Clariom S Affymetrix and ThermoFisher

source_name: Control 193


title: HL60shCTRLp6

value: Acute Myeloid Leukemia cell line


title: HL60shCTRLp4


title: HL60shHIF1p6


title: hepatocyte_WT InsMet rep2

value: wild type


title: K-O-con-12-5-2


title: G72T

city: Ithaca

first: David

last: Sannino

state: New York

address: 123 Wing Drive

department: Microbiology

institute: Cornell University

data_processing:
DNA removed with TURBO DNA-free kit
rRNA depleted with Illumina Ribo-Zero Gold rRNA Removal Kit
Reads were processed using Trimmomatic v 0.36
Remaining rRNA was bioinformatically removed
Reads were mapped to the draft genome using bwa mem
Assembly: Ca. Epulopiscium viviparus' draft genome, Genbank accession number CP117982
Supplementary files format and content: excel sheet containing the FPKMs of the genes for each sample

organism: Candidatus Epulonipiscium viviparus

source_name: from Naso tonganus gut

growth_protocol: Naso tonganus samples were caught via spearfishing, kept on ice, and guts were dissected.

extract_protocol:
All were extracted using QIAGEN Rneasy kit, except for G72T, which was extracted using Trizol
Cornell University Genomics Facility

value: from Naso tonganus gut

value: bacterial population

value: Naso tonganus in evening


title: BioTASQ_vitro_rep2

source_name: Seedling

tag: cultivar

value: Nipponbare

value: Seedling

value: two weeks

tag: antibody

value: small-molecular baits BioTASQ

tag: growth

value: vitro


title: hepatocyte_WT InsMet rep3

tag: strain

value: C57BL/6 (F3 generation)

value: primary hepatocytes

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

tag: treatment

tag: pre-treatment


title: G195

tag: cell type


title: K-O-13-5-3

value: beta-catSD

value: kidney

value: stromal cells


title: K-O-13-5-2


title: hepatocyte_WT Met rep2

value: 8-16 weeks old

value: 2mM Metformin for 5h serum-starved

value: Untreated


title: hepatocyte_WT Met rep1

value: wild type


title: G191

value: from Naso tonganus gut

value: bacterial population

value: Naso tonganus caught in mid morning


title: hepatocyte_WT Met rep3


title: K-O-13-5-1


title: E266

description: Clariom S Affymetrix and ThermoFisher

source_name: EoE 266

value: EoE

value: Esophagus


title: G146


title: K-O-12-5-3


title: G145


title: hepatocyte_WT UT Rep1

value: untreated - serum starved


title: E88

description: Clariom S Affymetrix and ThermoFisher

source_name: EoE 88


title: E285

description: Clariom S Affymetrix and ThermoFisher

source_name: EoE 285


title: K-O-con-12-5-1

value: wild-type


title: E238

description: Clariom S Affymetrix and ThermoFisher

source_name: EoE 238


title: E208

description: Clariom S Affymetrix and ThermoFisher

source_name: EoE 208


title: E109

description: Clariom S Affymetrix and ThermoFisher

source_name: EoE 109


title: E282

description: Clariom S Affymetrix and ThermoFisher

source_name: EoE 282


title: K-O-12-5-2


title: hepatocyte_WT UT rep2

value: C57BL/6 (F3 generation)


title: E60

description: Clariom S Affymetrix and ThermoFisher

source_name: EoE 60


title: hepatocyte_WT UT rep3

source_name: Primary Hepatocytes

value: primary hepatocytes


title: K-O-12-5-1


title: G64Q

value: Naso tonganus caught in early morning


title: E139

description: Clariom S Affymetrix and ThermoFisher

source_name: EoE 139


title: G140


title: BY4741, dAP, dataset1, MNase-seq

status: Public on Aug 09 2023

city: Beijing

first: Youyang

last: Sia

address: Haidian district

institute: Tsinghua University

data_processing:
Pair-end sequencing reads were trimmed by Trimmomatic and were mapped to sacCer3 reference genome using Bowtie2.
Reads in the range of 120-180bp were selected, and those mapped to repetitive rRNA locus (chrXII: 451275–469084) were excluded.
SAMtools was used to remove possible PCR duplicates.
An equal number of reads (13,480,875 reads, 3,615,621 reads, and 5,266,074reads for dataset1, dataset2 and dataset3, respectively) was randomly selected for each sample
Nucleosome positions were identified using algorithm as described for GeneTrack.
Assembly: sacCer3
Supplementary files format and content: bigWig, guassian smoothed peak

organism: Saccharomyces cerevisiae

growth_protocol: 30℃, YPD, mid-log phase

extract_protocol:
Cells were harvested and converted to spheroplasts using 0.25 mg ml–1 zymolase100T (MP Biomedicals cat#320932). Spheroplasts were digested with micrococcal nuclease (NEB M0247S) at concentrations of 600/1200/2400 gel unit/ml. Samples were treated with proteinase K (25 μg ml–1, Tiangen RT403) 30 mins at 65 °C to remove protein. Phenol:chloroform was used to extract the DNA. We incubated the sample with RNase A (100 μg ml–1, Tiangen RT405) to remove RNA.
DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB #E7645S)

tag: cell line


title: BY4741, dIoc3, dataset3, MNase-seq


title: BY4741, dH4, dataset2, MNase-seq


title: BY4741, dH4, dataset3, MNase-seq


title: BY4741, dAP, dataset2, MNase-seq


title: BY4741, dAP, dataset3, MNase-seq


title: BY4741, dH4, dataset1, MNase-seq


title: BY4741, WT3, dataset2, MNase-seq

value: WT


title: BY4741, WT3, dataset1, MNase-seq


title: BY4741, WT2, dataset2, MNase-seq


title: E51

description: Clariom S Affymetrix and ThermoFisher

source_name: EoE 51


title: BY4741, WT3, dataset3, MNase-seq


title: BY4741, WT2, dataset3, MNase-seq


title: BY4741, WT1, dataset2, MNase-seq


title: BY4741, WT2, dataset1, MNase-seq


title: BY4741, WT1, dataset3, MNase-seq


title: BY4741, dIoc3, dataset2, MNase-seq


title: BY4741, dIoc3, dataset1, MNase-seq


title: BY4741, WT1, dataset1, MNase-seq


title: cortex, MEK-3, experiment

city: Shanghai

first: Guoping

last: Liu

address: 138 Yi Xue Yuan Road

institute: Fudan University

data_processing:
scRNA-Seq: High quality sequences (clean reads) were obtained by removing low quality sequences and joints. The clean reads were then processed with Cell Ranger software to obtain quantitative information on gene expression.
RNA-Seq: Gene expression levels were reported as fragments per kilobase of exon per million fragments mapped (FPKM).
RNA-Seq: Genes with a p value <0.05 were considered would be called as differentially expressed.
Assembly: mm10

source_name: cortex

extract_protocol:
scRNA-Seq: Briefly, mouse embryos were dissected out and immediately submerged in fresh ice-cold Hanks balanced salt solution (Gibco 12175-095). The cortex was then cut into pieces and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit (Miltenyi Biotec, catalog no. 130-092-628) according to the manufacturer’s instructions.
scRNA-Seq: The Chromium dropletbased sequencing platform (10X Genomics) was used to generate scRNA-Seq libraries, following the manufacturer’s instructions (manual document part number: CG00052 Rev C). The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina NovaSeq 6000 or Illumina Hiseq4000.
RNA-Seq: The E14.5 cortex tissues from Rosa-fgf8/Rosa-mek1dd mice and littermate controls were dissected.
RNA-Seq: Total RNA was isolated using an RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol. RNA-seq libraries were prepared according to the Illumina HiSeq 4000 protocol. The gene expression level was reported with fragments per kilobase of exon model per million mapped reads (FPKM)

value: cortex

value: MEK-OE


title: cortex, MEK-4, experiment


title: cortex, FGF8, experiment-27


title: cortex, MEK-1, experiment


title: cortex, MEK-2, experiment


title: cortex, FGF8, experiment-23


title: cortex, FGF8, experiment-11


title: cortex, FGF8, experiment-12


title: cortex, FGF8, experiment-21


title: cortex, control-5


title: cortex, control-3


title: cortex, control-2


title: Ti-SeMet

city: Changchun

first: Tongjian

last: Zhao

address: 1266 Fujin Road

institute: School of Pharmaceutical Sciences, Jilin University

data_processing:
Hisat2 for sequence alignment
Stringtie tools for transcript assembly, transcript abundance estimation, gene structure optimization
Samtools tools for related file processing
Assembly: mm9
Supplementary files format and content: Xls file include expression  values for each sample

source_name: calvaria

extract_protocol:
TRIzol (Thermo Fisher, 15596018) was used to separate and purify total RNA from the samples, following the manufacturer's instructions. The quantity and purity of the total RNA were assessed using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the integrity of RNA was evaluated using Bioanalyzer 2100 (Agilent, CA, USA).
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: calvaria

value: preosteoblast

value: Wild type

value: stimulated with 10μg/cm² Ti particles and 5μM Se-Met for 24h


title: Ti-MC

value: stimulated with 10μg/cm² Ti particles for 24h


title: B-MC

value: no special treatment


title: cortex, control-1


title: MPE macrohpages, IL-10−/− mice B1

first: Xin-Yu

last: Shi

address: 8 Gongti Nanlu

department: Department of Respiratory and Critical Care Medicin

institute: Beijing Chao-Yang Hospital

data_processing:
The final libraries were quantified using KAPA Library Quantification kit (KAPA Biosystems, South Africa) and an Agilent 2100 Bioanalyzer.
After quantitative reverse transcription-polymerase chain reaction (RT-qPCR) validation, libraries were subjected to paired-end sequencing with pair end 150-base pair reading length on an Illumina HiSeq sequencer (Illumina).
Assembly: Mus_musculus.GRCm38.dna.toplevel.modified.fa
Supplementary files format and content: tab-delimited text files include RPKM values for each sample.

source_name: MPE macrohpages

growth_protocol: Ten days after injection of MC38 cells, mice were euthanized by CO2 asphyxiation, and MPE samples were collected and then centrifuged at 400 × g for 6 minutes.

extract_protocol:
MPE macrophages were isolated using Anti-F4/80 MicroBeads (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of macrophages was > 90%, which was confirmed by flow cytometry, and cells were cultured in DMEM with 10% FBS for further use.
Libraries for sequencing were constructed with NEB Next Ultra RNA Library Prep Kit for Illumina (NEB). Poly(A) tailed mRNA molecules were enriched from 1 μg total RNA with NEB Next Poly(A) mRNA Magnetic Isolation Module (NEB) kit.

treatment_protocol: The cell pellets of MPE were resuspended in PBS, and mononuclear cells were isolated by Ficoll-Hypaque gradient centrifugation (Pharmacia, Uppsala, Sweden) within 1 hour.

value: MPE macrohpages


title: MPE macrohpages, IL-10−/− mice B3


title: MPE macrohpages, WT mice A2


title: MPE macrohpages, IL-10−/− mice B2


title: cortex, SMOM2,experiment

description: 10x Genomics

library_source: transcriptomic single cell

value: Rosa SMOM2


title: MPE macrohpages, WT mice A3


title: Renal tissue derived from METTL3fl/fl, wt mouse with UUO model

city: Hefei

first: Wei-Jian

last: Ni

state: Anhui

address: No. 17 Lujiang Road

department: Anhui Provincial Hospital, The First Affiliated Hospital of USTC

institute: University of Science and Technology of China

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Mouse mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 6 samples were retained for further “m6A quantity” analyses. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities.

source_name: Renal cortex of UUO-7d mice

label_protocol: "IP" and "Sup" RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

growth_protocol: METTL3fl/fl, wt and METTL3fl/fl, cre T mice were routinely reared to 22-24 g after they reached 8 weeks of age.

extract_protocol: Total RNAs were immunoprecipitated with anti-N6-methyladenosine(m6A) antibody. The immunoprecipitated "IP" fraction contained enriched m6A methylated RNAs, and the supernatant " Sup" fraction contained unmodified RNAs.

treatment_protocol: For the unilateral ureteral ligation-induced UUO kidney fibrosis model, mice received permanent ligation of the free ureter in the left kidney under aseptic and anesthetic conditions, while sham-operated mice received the free ureter but not ligation under equivalent conditions. Seven days after surgery, mice were sacrificed under anesthesia to obtain renal cortical tissue.

value: Gene knockout mice on C57BL/6 background

value: 8 week

tag: gender

value: male

tag: type

value: IP enriched m6A methylated RNAs

value: supernatant unmodified RNAs


title: Renal tissue derived from METTL3fl/fl, cre T mouse with UUO model


title: Renal tissue of the onilateral ureteral ligation (UUO) mice (model) 2

source_name: Renal cortex of UUO mice

growth_protocol: Mice were routinely reared to 22-24 g after they reached 8 weeks of age.


title: Renal tissue of the onilateral ureteral ligation (UUO) mice (model) 3


title: Renal tissue of the sham-operated mice 3

source_name: Renal cortex of sham-operated mice


title: Renal tissue of the onilateral ureteral ligation (UUO) mice (model) 1


title: Renal tissue of the sham-operated mice 1


title: cortex, control-4


title: Renal tissue of the sham-operated mice 2


title: TrueLeaf_batch_11_Litva_F1

first: Wenwen

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

data_processing:
Quality control was conducted using fastp version 0.20.0.
Read mapping was performed using the aligner HISAT2 v2.1.0.
The read counts mapped to each gene were quantified using featureCounts.
Potential batch effects were corrected using the ComBat-seq function in the sva software package.
Transcript per million (TPM) gene expression was calculated by normalizing gene length and library size followed by TMM normalization.
Assembly: TAIR10 Arabidopsis Col-0 reference genome
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample
Supplementary files format and content: Matrix table with TPM value for every gene and every sample

organism: Arabidopsis thaliana

source_name: True leaf

growth_protocol: The plants were grown on MS plates containing 1% sucrose under long-day condition (16-h light at 22°C and 8-h dark at 18°C) after surface-sterilization followed by 7-day stratification of the seeds.

extract_protocol:
flash frozen in liquid nitrogen, and RNA was extracted using an RNeasy Plant Mini Kit (Qiagen), followed by on-column DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: True leaf

tag: developmental stage

value: 15 DAS (days after sowing)

tag: batch

value: Col-0 x Litva F1


title: TrueLeaf_batch_11_Le-0_F1

tag: tissue

tag: genotype

value: Col-0 x Le-0 F1


title: TrueLeaf_batch_11_Pu2-23_F1

value: Col-0 x Pu2-23 F1


title: TrueLeaf_batch_11_Ts-1_F1

value: Col-0 x Ts-1 F1


title: TrueLeaf_batch_11_Si-0_F1

value: Col-0 x Si-0 F1


title: TrueLeaf_batch_11_Ob-0_F1

value: Col-0 x Ob-0 F1


title: TrueLeaf_batch_11_Kyoto_F1

value: Col-0 x Kyoto F1


title: TrueLeaf_batch_11_ICE119_F1

value: Col-0 x ICE119 F1


title: TrueLeaf_batch_10_Sha_F1

value: Col-0 x Sha F1


title: TrueLeaf_batch_10_Pog-0_F1

value: Col-0 x Pog-0 F1


title: TrueLeaf_batch_10_Rd-0_F1

value: Col-0 x Rd-0 F1


title: TrueLeaf_batch_11_Ber_F1

value: Col-0 x Ber F1


title: TrueLeaf_batch_10_Old-1_F1

value: Col-0 x Old-1 F1


title: TrueLeaf_batch_10_Hn-0_F1

value: Col-0 x Hn-0 F1


title: TrueLeaf_batch_10_Pu2-7_F1

value: Col-0 x Pu2-7 F1


title: MPE macrohpages, WT mice A1

value: WT

value: MPE macrohpages


title: TrueLeaf_batch_10_Stw-0_F1

value: True leaf

value: 15 DAS (days after sowing)

value: Col-0 x Stw-0 F1


title: TrueLeaf_batch_09_Pt-0_F1

value: Col-0 x Pt-0 F1


title: TrueLeaf_batch_09_Kro-0_F1

value: Col-0 x Kro-0 F1


title: TrueLeaf_batch_10_Mer-6_F1

value: Col-0 x Mer-6 F1


title: TrueLeaf_batch_09_Lm-2_F1

value: Col-0 x Lm-2 F1


title: TrueLeaf_batch_09_Ler-1_F1

value: Col-0 x Ler-1 F1


title: TrueLeaf_batch_09_HR-5_F1

value: Col-0 x HR-5 F1


title: TrueLeaf_batch_09_Ha-0_F1

value: Col-0 x Ha-0 F1


title: TrueLeaf_batch_09_Fei-0_F1

value: Col-0 x Fei-0 F1


title: TrueLeaf_batch_09_Dr-0_F1

value: Col-0 x Dr-0 F1


title: TrueLeaf_batch_08_Tottarp-2_F1

value: Col-0 x Tottarp-2 F1


title: TrueLeaf_batch_09_Kar-1_F1

value: Col-0 x Kar-1 F1


title: TrueLeaf_batch_08_Knox-18_F1

value: Col-0 x Knox-18 F1


title: TrueLeaf_batch_08_Hovdala-2_F1

value: Col-0 x Hovdala-2 F1


title: TrueLeaf_batch_08_ICE29_F1

value: Col-0 x ICE29 F1


title: TrueLeaf_batch_09_Jl-3_F1

value: True leaf

value: Col-0 x Jl-3 F1


title: TrueLeaf_batch_08_ICE150_F1

value: 15 DAS (days after sowing)

value: Col-0 x ICE150 F1


title: TrueLeaf_batch_08_El-0_F1

value: Col-0 x El-0 F1


title: TrueLeaf_batch_08_Cerv-1_F1

value: Col-0 x Cerv-1 F1


title: TrueLeaf_batch_08_Bla-1_F1

value: Col-0 x Bla-1 F1


title: TrueLeaf_batch_07_Tscha-1_F1

value: Col-0 x Tscha-1 F1


title: TrueLeaf_batch_07_Sp-0_F1

value: Col-0 x Sp-0 F1


title: TrueLeaf_batch_07_TDr-1_F1

value: Col-0 x TDr-1 F1


title: TrueLeaf_batch_07_Bch-1_F1

value: Col-0 x Bch-1 F1


title: TrueLeaf_batch_07_Baa-1_F1

value: Col-0 x Baa-1 F1


title: TrueLeaf_batch_07_No-0_F1

value: Col-0 x No-0 F1


title: TrueLeaf_batch_07_Je-0_F1

value: Col-0 x Je-0 F1


title: TrueLeaf_batch_07_Bl-1_F1

value: Col-0 x Bl-1 F1


title: TrueLeaf_batch_07_ICE163_F1

value: Col-0 x ICE163 F1


title: TrueLeaf_batch_06_Rou-0_F1

value: Col-0 x Rou-0 F1


title: TrueLeaf_batch_06_ICE102_F1

value: True leaf

value: Col-0 x ICE102 F1


title: TrueLeaf_batch_06_Nw-0_F1

value: 15 DAS (days after sowing)

value: Col-0 x Nw-0 F1


title: TrueLeaf_batch_06_Pla-0_F1

value: Col-0 x Pla-0 F1


title: TrueLeaf_batch_06_Nemrut-1_F1

value: Col-0 x Nemrut-1 F1


title: TrueLeaf_batch_06_Koch-1_F1

value: Col-0 x Koch-1 F1


title: TrueLeaf_batch_06_Nok-3_F1

value: Col-0 x Nok-3 F1


title: TrueLeaf_batch_05_Zal-1_F1

value: Col-0 x Zal-1 F1


title: TrueLeaf_batch_08_Da1-12_F1

value: Col-0 x Da1-12 F1


title: TrueLeaf_batch_05_Wl-0_F1

value: Col-0 x Wl-0 F1


title: TrueLeaf_batch_05_Ws-2_F1

value: Col-0 x Ws-2 F1


title: TrueLeaf_batch_05_Westkar-4_F1

value: Col-0 x Westkar-4 F1


title: TrueLeaf_batch_05_Rubezhnoe-1_F1

value: Col-0 x Rubezhnoe-1 F1


title: TrueLeaf_batch_05_Yeg-1_F1

value: Col-0 x Yeg-1 F1


title: TrueLeaf_batch_05_RRS-7_F1

value: Col-0 x RRS-7 F1


title: TrueLeaf_batch_06_Pna-17_F1

value: Col-0 x Pna-17 F1


title: TrueLeaf_batch_04_Chat-1_F1

value: True leaf

value: Col-0 x Chat-1 F1


title: TrueLeaf_batch_05_Ey15-2_F1

value: 15 DAS (days after sowing)

value: Col-0 x Ey15-2 F1


title: TrueLeaf_batch_05_Ak-1_F1

value: Col-0 x Ak-1 F1


title: TrueLeaf_batch_04_Pro-0_F1

value: Col-0 x Pro-0 F1


title: TrueLeaf_batch_05_Bay-0_F1

value: Col-0 x Bay-0 F1


title: TrueLeaf_batch_04_TueWa1-2_F1

value: Col-0 x TueWa1-2 F1


title: TrueLeaf_batch_04_Er-0_F1

value: Col-0 x Er-0 F1


title: TrueLeaf_batch_03_Ta-0_F1

value: Col-0 x Ta-0 F1


title: TrueLeaf_batch_04_Ka-0_F1

value: Col-0 x Ka-0 F1


title: TrueLeaf_batch_04_Vind-1_F1

value: Col-0 x Vind-1 F1


title: TrueLeaf_batch_04_Kl-5_F1

value: Col-0 x Kl-5 F1


title: TrueLeaf_batch_03_Van-0_F1

value: Col-0 x Van-0 F1


title: TrueLeaf_batch_03_Tuescha9_F1

value: Col-0 x Tuescha9 F1


title: TrueLeaf_batch_04_HKT2.4_F1

value: Col-0 x HKT2.4 F1


title: TrueLeaf_batch_04_Me-0_F1

value: Col-0 x Me-0 F1


title: TrueLeaf_batch_03_Vie-0_F1

value: True leaf

value: Col-0 x Vie-0 F1


title: TrueLeaf_batch_03_Ven-1_F1

value: 15 DAS (days after sowing)

value: Col-0 x Ven-1 F1


title: TrueLeaf_batch_04_Ga-0_F1

value: Col-0 x Ga-0 F1


title: TrueLeaf_batch_03_TueV-13_F1

value: Col-0 x TueV-13 F1


title: TrueLeaf_batch_02_Wei-0_F1

value: Col-0 x Wei-0 F1


title: TrueLeaf_batch_03_Tu-0_F1

value: Col-0 x Tu-0 F1


title: TrueLeaf_batch_02_Ra-0_F1

value: Col-0 x Ra-0 F1


title: TrueLeaf_batch_03_Uk-1_F1

value: Col-0 x Uk-1 F1


title: TrueLeaf_batch_02_Uod-1_F1

value: Col-0 x Uod-1 F1


title: TrueLeaf_batch_02_C24_F1

value: Col-0 x C24 F1


title: TrueLeaf_batch_02_Per-1_F1

value: Col-0 x Per-1 F1


title: TrueLeaf_batch_02_Com-1_F1

value: Col-0 x Com-1 F1


title: TrueLeaf_batch_02_Kin-0_F1

value: Col-0 x Kin-0 F1


title: TrueLeaf_batch_01_Bs-1_F1

value: Col-0 x Bs-1 F1


title: TrueLeaf_batch_01_Gel-1_F1

value: Col-0 x Gel-1 F1


title: TrueLeaf_batch_02_Abd-0_F1

value: True leaf

value: Col-0 x Abd-0 F1


title: TrueLeaf_batch_01_La-0_F1

value: 15 DAS (days after sowing)

value: Col-0 x La-0 F1


title: TrueLeaf_batch_01_Is-0_F1

value: Col-0 x Is-0 F1


title: TrueLeaf_batch_01_Gu-0_F1

value: Col-0 x Gu-0 F1


title: TrueLeaf_batch_11_Col-0


title: TrueLeaf_batch_01_Bor-4_F1

value: Col-0 x Bor-4 F1


title: TrueLeaf_batch_11_Pu2-23


title: TrueLeaf_batch_11_Ts-1