title: NeuN+ nuclei from the septal area of adult C57BL6/J mice [snRNA-seq]

city: Shanghai

first: Xiaofei

last: Yu

address: 2005 Songhu Rd

institute: Fudan University

data_processing:
base calling using Illumina Bcl2fastq
alignment against an intron-to-exon converted reference using 10X cellranger V3
downstream analysis including QC filtering and other statistical analysis using Seurat V3.1
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for each gene in each cell

source_name: septal neuron nuclei

extract_protocol:
Nuclei were prepared as reported before with modifications. Specifically, septal tissues were dissected from 10 mice, pooled together, and stored in 1mL of ice-cold Brain Homogenization Buffer [10 mM Tricine-KOH pH8, 25 mM KCl, 5mM MgCl2, 250 mM Sucrose and 0.1% Triton X-100), supplemented with 0.5 U/mL SUPERase•In (ThermoFisher, AM2696), 0.5 U/mL RNase Inhibitor (ThermoFisher, AM2682) and 2x EDTA-free Halt protease inhibitor cocktail (ThermoFisher, 87786)]. Samples were transferred into a cold Wheaton 1mL glass homogenizer and ground by 10 strokes with the “Loose” pestle, followed by 14 strokes with the “Tight” pestle. Homogenate was then filtered with a 40um cell strainers and underlaid with 1mL 20% iodixanol in a clear ultracentrifuge tube. Sample was centrifuged at 10,000 g for 20 min at 4 oC with low acceleration/deceleration setting. Nuclei was resuspended in 500uL Staining Buffer (1x DPBS, 0.5% BSA, 0.1% Triton X-100, 0.05% NP-40, 0.5 U/mL SUPERase•In, 0.5 U/mL RNase Inhibitor, 2x EDTA-free Halt protease inhibitor cocktail) and stained with anti-NeuN-AF647 (Abcam, ab190565, 1:500) and Hoechst 33342 (ThermoFisher, H3570, 1:500) at 4 oC for 30 minutes.  Nuclei was washed once with Staining Buffer, spun down at 1000g for 5 minutes and resuspended in Nuclei FACS Buffer (1x DPBS, 0.5% BSA, 0.5U/mL SUPERase•In, 0.5U/mL RNase Inhibitor, 2x EDTA-free Halt protease inhibitor cocktail). NeuN+ nuclei were collected with a BD FACSAria cell sorter, inspected with a Countess automated cell counter, and loaded into a 10x Genomics Chromium controller.
RNA libraries were prepared with Chromium Single Cell 3' Reagent Kits (V2) according to the manufacturer's instruction

tag: strain

tag: sample

value: NeuN+ nuclei

value: septal tissue


title: Arabidopsis,ATXR3, rep2

status: Public on Sep 23 2024

type: SRA

city: Davis

first: Satoyo

last: Oya

state: CA

address: 1 Shields Ave, Plant_ Enviro Sci, RM 1210, 387 N Quad (MS11665)

department: Plant Sciences

country: USA

institute: UC Davis

library_source: genomic

data_processing:
The exact codes for trimming and mapping are provided at https://github.com/Satoyo08/seven_ATXRs. For ChIP-seq against 3xFLAG-tagged H3K4-ATX(R)s, pair-end files were trimmed by trimmomatic with the following option; ILLUMINACLIP:$adaptor:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36. Trimmed reads were mapped to TAIR10 genome by bowtie2 without option. The browser track files were generated by deeptools bamCoverage -b [bamfile] -o [outputfilename] --normalizeUsing RPKM --outFileFormat bedgraph then by converted to bw file by ucsctools/bedGraphToBigWig. For ChIP-seq against histone, read 1 file was mapped to TAIR10 genome by bowtie with the following options; -M 1 -3 80 --best --chunkmbs 200. The bam files were converted to bw by deeptools bamCoverage without option.
Assembly: TAIR10
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 15 dai seedling

growth_protocol: seedling grown on MS media under 22°C Long day condition

extract_protocol:
ChIP-seq targeting histone modifications and epitope-tagged proteins were carried out based on Inagaki, S. et al., Nat Plants (2021)  with some modifications. Briefly, approximately 1.5 g frozen seedlings were ground into a fine powder in liquid nitrogen and suspended in 25 ml of nuclei isolation buffer. The buffer for histone modifications was 10mM HEPES pH7.6, 1M sucrose, 5mM KCl, 5mM MgCl2, 5mM EDTA, 1 % formaldehyde, 0.1 % β-mercaptoethanol, 0.6 % Triton X-100, supplemented with 1 tablet/50 ml cOmplete proteinase inhibitor and 1 mM Pefabloc SC (Roche)). The buffer for epitope-tagged proteins additionally contains 0.1 mM spermine, 0.5 mM spermidine and 1.5 mM ethylene glycol bis(succinimidyl succcinate) (EGS; ThermoFisher) and 0.3 % IGEPAL CA-630 was used instead of 0.6 % Triton X-100. The suspension was incubated for 10 minutes in RT to crosslink, quenched by adding glycine to 130 mM, filtered through a 40 µm nylon cell strainer, and pelleted by centrifugation at 3,000 rpm at 4°C for 10 min. The pellet was resuspended in 300 µl of nuclei isolation buffer and layered on top of 500 µl of nuclei separation buffer (10 mM HEPES pH 7.6, 1 M sucrose, 5 mM KCl, 5 mM MgCl2, 5 mM EDTA pH 8.0, 15 % Percoll) and pelleted by centrifugation at 3,000 × g for 5 min at 4 °C. The pellet was directly resuspended in 950 µl RIPA buffer without Triton-X (50mM Tris-HCl pH7.8, 150 mM NaCl, -1mM EDTA, 0.1% SDS, 0.1% Sodium deoxycholate and cOmplete proteinase inhibitor). The suspension was sonicated using picoruptor (Diagenode) with the following settings: water bath; 4 °C, 30 sec ON and 30 sec OFF, 7 cycles for histone modifications, and 5 cycles for epitope-tagged protein. The sonicated chromatin was then supplemented with Triton-X to 1.0 %, then centrifuged at 13,000 g for 3 min, and the supernatant was diluted with RIPA buffer and aliquoted. The chromatin solution was incubated with 1-2 μg of antibodies overnight at 4 °C. Antibodies used are : H3 antibody (ab1791; Abcam) and others with H3K4 methylation-specific antibodies (H3K4me1 (ab8895; Abcam), H3K4me2 (ab32356; Abcam), H3K4me3 (ab8580; Abcam) and FLAG (F1804; SIGMA). Then the antibody-chromatin mix was incubated for 2 h at 4 °C with Dynabeads Protein G magnetic beads. For histone modifications, the incubated beads were washed once with 1 ml of RIPA buffer, twice with 1 ml of High-salt RIPA buffer (RIPA buffer with 500 mM NaCl), once with 1 ml of LiCl buffer (10 mM Tris–HCl, pH 7.8, 1 mM EDTA, 0.25 M LiCl, 1% IGEPAL CA-630, 1% sodium deoxycholate) and once with 1 ml of TE buffer (10 mM Tris–HCl, pH 7.8, 1 mM EDTA), each time rotating for 10 min in 4 °C. For epitope-tagged proteins, beads were washed once with RIPA buffer, medium salt RIPA buffer (RIPA buffer with 300 mM NaCl), high salt RIPA buffer, and TE buffer. DNA was eluted from the beads and reverse-crosslinked by adding 100 μl of elution buffer (10 mM Tris–HCl, pH 7.8, 0.3 M NaCl, 5 mM EDTA, 0.5% SDS) and incubating overnight at 65 °C. The DNA samples were then treated with RNase A (Nippon Gene) for 30 min and with Proteinase K (ThermoFisher) for 2 h at 37 °C, and purified using the Monarch PCR & DNA Cleanup Kit (NEB).
ChIP-seq libraries were made with a ThruPlex kit as directed in manufacture’s protocol  and dual size-selected using SPRI select beads to enrich 200 – 500 bp fragments.

tag: tissue

value: 15 dai seedling

tag: genotype

value: Express 3x FLAG-tagged ATXR3 under native promoter in the atxr3 mutant background


title: SCRmus_Sox2-SCR_dCTCF_Sox2_rep2

city: Illkirch

first: Tom

last: Sexton

address: 1 rue Laurent Fries

country: France

institute: IGBMC (Institute of Genetics and Molecular and Cellular Biology)

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq
Individual 4C-seq experiments were demultiplexed according to bait primer sequence using sabre, with two mismatches permitted (-m 2)
Reads were aligned using Bowtie (v1.0.0) with the settings -a -m 1 --best --strata
Mapped reads were filtered and mapped to DpnII restriction fragments with the 4See utilities described in Ben Zouari et al. 4See: a flexible browser to explore 4C data. Front. Genet. 10: 1372.
Assembly: mm10
Supplementary files format and content: Cis files, containing a header and two columns (restriction fragment midpoint coordinate, counts), the input format for 4See (Ben Zouari et al. 4See: a flexible browser to explore 4C data. Front. Genet. 10: 1372.)
Library strategy: 4C-seq

organism: Mus musculus musculus x Mus musculus castaneus

source_name: Embryonic stem cells

growth_protocol: Mouse F1 ESCs (M. musculus129 × M. castaneus, female cells obtained from Barbara Panning) and derivatives were cultured on 0.1% gelatin-coated plates in ES medium (DMEM containing 15% FBS, 0.1 mM MEM nonessential amino-acids, 1 mM sodium pyruvate, 2 mM GlutaMAX, 0.1 mM 2-mercaptoethanol, 1000 U/mL LIF, 3 µM CHIR99021 [GSK3β inhibitor; Biovision], and 1 µM PD0325901 [MEK inhibitor; Invitrogen]), which maintains ESCs in a pluripotent state in the absence of a feeder layer.

extract_protocol:
Cells were fixed with 2% paraformaldehyde in 10% FBS in PBS for 10 min at 23°C. The fixation was quenched with cold glycine at a final concentration of 125 mM, then cells were washed with PBS and permeabilized on ice for 1 h with 10 mM Tris-HCl, pH 8, 100 mM NaCl, 0.1% NP-40, and protease inhibitors. Nuclei were resuspended in DpnII restriction buffer at 10 million nuclei/mL concentration, and 5 million nuclei aliquots were further permeabilized by treatment for 1 h with 0.4% SDS at 37°C, then incubating for a further 1 h with 3.33% Triton X-100 at 37°C. Nuclei were digested overnight with 1500 U DpnII at 37°C, then washed twice by centrifuging and resuspending in T4 DNA ligase buffer. In situ ligation was performed in 400 μL T4 DNA ligase buffer with 20,000 U T4 DNA ligase overnight at 23°C. DNA was purified by reverse cross-linking with an overnight incubation at 65°C with proteinase K, followed by RNase A digestion, phenol/chloroform extraction, and isopropanol precipitation. The DNA was digested with 5 U/μg Csp6I at 37°C overnight, then re-purified by phenol/chloroform extraction and isopropanol precipitation. The DNA was then circularized by ligation with 200 U/μg T4 DNA ligase under dilute conditions (3 ng/μL DNA), and purified by phenol/chloroform extraction and isopropanol precipitation. For musculus-specific 4C profiles, samples of the DNA were digested with AvaII, cutting specifically at the region between the Csp6I site and the non-reading primer annealing site on the castaneus allele. 100 ng aliquots of treated DNA were then used as template for PCR with bait-specific primers containing Illumina adapter termini. PCR reactions were pooled, primers removed by washing with 1.8× AMPure XP beads, then quantified on a Bioanalyzer (Agilent) before sequencing with a HiSeq 4000 (Illumina).
4C PCR products are quantified in a Bioanalyzer, and pooled in equimolar quantities for direct cluster generation on an Illumina HiSeq4000

treatment_protocol: For differentiation, ESCs were passaged onto laminin-511-coated 35 mm glass bottom petri dishes and switched to DMEM (4.5 g/L glucose) supplemented with 2 mM GlutaMAX, 10% FBS, 0.1 mM MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol without LIF or 2i inhibitors. After 24 h (d1), the medium was changed daily and supplemented with 5 µM retinoic acid for a further 48 h (d2 and d3).

tag: cell line

value: Embryonic stem cells

value: F1 with insertion of ANCH1 into SCR-proximal region of musculus allele, and ANCH3 into Sox2 promoter-proximal region of musculus allele; homozygous deletion of CTCF motif at Sox2

tag: treatment


title: WT2

country: China

library_source: transcriptomic

data_processing:
HISAT2 (v 2.1.0) RNA-sequencing alignment software was used for  for mapping next-generation sequencing reads to mouse genome with following parameters: -3 30.
SAMtools (v 1.3) was used for filtering and sorting mapped reads with following parameters: samtools view -q 5; samtools sort -T -n.
HTSeq (v 0.9.1) was used for counting reads in features with following parameters: --mode=union --stranded=no.
Data was normalized with R (v 4.0.5) and Limma-Voom (v 3.46.0) and log2-transformed
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with normalized gene counts for each gene in each sample

molecule: total RNA

organism: Mus musculus

source_name: Brain septal tissue

extract_protocol:
Brains were dissected and immediately immersed into ice-cold Dissection Buffer (1x HBSS, 2.5 mM HEPES pH7.4, 4 mM NaHCO3 and 35 mM Glucose). Tissues from 4-5 mice were pooled and transferred into Teflon-glass homogenizer with Homogenization Buffer [10 mM HEPES pH7.4, 150 mM KCl, 5 mM MgCl2, 0.5 mM DTT, 0.5 U/mL SUPERase•In (ThermoFisher, AM2696), 0.5 U/mL RNase Inhibitor (ThermoFisher, AM2682) and 2x EDTA-free Halt protease inhibitor cocktail (ThermoFisher, 87786)]. Tissues were then dounced 12 strokes or until no visible clumps of tissue could be seen. Lysate was then transferred into a new RNase-free microcentrifuge tube and cleared by centrifuging at 2000g at 4 oC for 10 minutes. Clear supernatant was then supplemented with 0.6% NP-40 and 18 mM DHPC and incubated on ice for 2 minutes. Samples were centrifuged again at 16,000g for at 4C for 10 minutes and clear supernatant was collected into new microcentrifuge tubes. RNA was extracted with a RNeasy Micro Kit (Qiagen, 74004) RNA quality was determined by a Bioanalyzer 2000 (Agilent) and samples with RIN>9 were used to prepare sequencing libraries.
Library were constructed with the SMARTer Ultralow Input RNA for Illumina Sequencing Kit and sequenced on an Illumina HiSeq2500 platform, following the manufacturers' instructions.

treatment_protocol: Mice were treated by 30-minute restraint stress with DecapiCones for 3 days and sacrificed 1.5 hours after the last restraint.

value: WT

value: Brain septal tissue

tag: batch

value: experiment 2


title: Arabidopsis,ATX5, rep2

value: Express 3x FLAG-tagged ATX5 under native promoter in the atx5 mutant background


title: N2.5

city: Montreal

first: Alain

last: Pacis

state: QC

address: 1010 Sherbrooke #1800

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Adapters and low-quality sequences (Phred score <30) were trimmed using Trimmomatic. The resulting reads were aligned to the C. elegans reference genome WBcel235 assembly using STAR. Read counts were obtained using HTSeq with parameters -m intersection-nonempty -stranded=reverse. For all downstream analyses, we excluded lowly expressed genes (average read count <10 across all samples). Raw counts were normalized using the edgeR’s TMM algorithm125 and transformed to log2-counts per million (log2CPM) using the voom function in the limma R package. To assess differences in gene expression, we fitted a linear model using the lmfit function with parameter method = "robust". Nominal p-values were corrected for multiple testing using the Benjamini-Hochberg method. Gene set enrichment analysis based on pre-ranked gene list by t-statistic was performed using the R package fgsea (http://bioconductor.org/packages/fgsea/)
Assembly: WBcel235
Supplementary files format and content: RNA-seq raw counts matrix are tab-delimited text files, with the genes in rows and the samples in columns.

organism: Caenorhabditis elegans

source_name: Strain N2

growth_protocol: ~50,000 synchronized L1s were hatched in 2-3 15-cm NGM plates with 2mL OP50 lawn and grown at 16C to gravidity and until embryos are laid on the plates.

extract_protocol:
Embryos were harvested with standard bleaching procedure, flash-frozen in liquid N2, and kept at -80C until RNA extraction. Embryo pellets were Dounce-homogenized and RNA was extracted using phenol(Trizol)/chloroform, treated with Turbo DNase, and pure RNA was extracted using chloroform/isopropanol and dissolved in water. RNA with RIN >8 was used for library preparation. Four independent biological replicates (denoted .2, .3, .4, .5) were used.
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina Cat#20020599) following manufacturer's protocol.

treatment_protocol: Each genotype was grown in parallel and no treatment was applied.

value: Strain N2

tag: cell type

value: Mixed-stage embryos


title: Escherichia coli control, not irradiated sample: replicate R1

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

country: Germany

institute: Quantitative Biology Center (QBiC)

description:
Sample UC L- R1
QPDAM051A6_EC-00-1

data_processing:
The Nextflow-based nf-core pipeline nf-core/rnaseq (version 1.4.2; https://github.com/nf-core/rnaseq) was used for the RNA-Seq bioinformatic analysis.
As part of this workflow, FastQC (version v0.11.8) was used to determine the quality of the FASTQ files (Andrews, 2010). Subsequently, adapter trimming was conducted with Trim Galore (version 0.6.4) (Krueger and Andrews, 2012). STAR aligner (version 2.6.1, (Dobin et al., 2012)) was used to map the reads that passed the quality control against the latest assembly (E. coli-strain K-12, DH10B (Build EB1)), downloaded from NCBI. The RNA-Seq data quality control was performed with RSeQC (version 3.0.1) (Wang et al., 2012) and read counting of the features (e.g. genes) with featureCounts (version 1.6.4) (Liao et al., 2014). An aggregation of the quality control for the RNA-Seq analysis was performed with MultiQC (version 1.7; http://multiqc.info/) (Ewels et al., 2016).
The analysis of the differential gene expression was performed in the R language (version 3.5.1) using DESeq2 (version 1.22) through the nextflow based workflow qbic-pipelines/rnadeseq (https://github.com/qbic-pipelines/rnadeseq, version 1.3.2). Table 1 shows the experimental groups that were compared. Genes were considered differentially expressed (DE) genes when the Benjamini-Hochberg multiple testing adjusted p-value (Benjamini and Hochberg, 1995) was smaller than 0.05 (padj ≤ 0.05).
Genes were further filtered for biological relevance if the log2 Fold Change (FC) in expression between the two considered groups  was above the threshold of 1.0 and less than -1.0.
EcoCyc database was used for pathway analysis (Keseler et al., 2017). All DE genes were included, and enrichment was calculated using Fisher'’s exact test and Benjamini-Hochberg multiple testing (p ≤ 0.05).
Assembly: E. coli-strain K-12, DH10B (Build EB1)), downloaded from NCBI
Supplementary files format and content: Raw counts as standard output from the featureCounts step of the nf-core pipeline nf-core/rnaseq (version 1.4.2; https://github.com/nf-core/rnaseq)  workflow, showing raw read count values for each gene as row in each sample as separate column.

organism: Escherichia coli

source_name: bacterial cell culture

growth_protocol: Gram-negative Escherichia coli (DSM 1103; ATCC 25922) was obtained from the German Collection of Microorganisms and Cell Cultures GmbH (DSMZ; Braunschweig, Germany) and was used as reference strain in this study. E. coli was grown in Tryptic Soy Broth (TSB) and on Mueller-Hinton (MH) agar plates. Planktonic cultures (5 mL) were grown aerobically overnight at 37 °C. Afterwards, suspensions were harvested by centrifugation (ROTINA 420 R, Hettich Lab Technology, Tuttlingen, Germany) and resuspended in TSB yielding an optical density (OD) of 2.0, as measured by means of a spectrophotometer at 600 nm (Ultrospec 3300 pro; Amersham Biosciences, Amersham, United Kingdom).

extract_protocol:
RNA extraction and sequencing were performed by the NGS Competence Center Tübingen (NCCT), the sequencing partner of the Quantitative Biology Center (QBiC), University of Tübingen, Germany. RNA of all samples was isolated with the RNeasy® Mini-Kit (Qiagen, Hilden, Germany). RNA extraction was followed by DNase I treatment in solution using the DNase I recombinant Kit (Roche, Basel, Switzerland) and purification and concentration of RNA using the RNA Clean & Concentrator-5 Kit (Zymo Research, Freiburg, Germany).
Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus Kit (Illumina, San Diego, CA, USA) with 100 ng total RNA. Sequencing was performed on the Illumina NextSeq 500 using a High Output Kit (version 2.5; 75 cycles) with 1% PhiX spike-in (Illumina, San Diego, CA, USA).

treatment_protocol: Samples were either incubated with 200 μL distilled water or 200 μL SAPYR (0.5 μM) in the dark for 5 min and then either illuminated for 10 min or kept in the dark for 10 min.

value: control

tag: irradiation

value: not irradiated

value: UC L-


title: SCRmus_Sox2-SCR_dCTCF_Sox2_rep1


title: WT1

value: experiment 1


title: Arabidopsis,ATX4, rep2

value: Express 3x FLAG-tagged ATX4 under native promoter in the atx4 mutant background


title: N2.4


title: KO2

value: TCRb-/-


title: SCRmus_Sox2-SCR_dCTCF_SCR_rep2

value: F1 with insertion of ANCH1 into SCR-proximal region of musculus allele, and ANCH3 into Sox2 promoter-proximal region of musculus allele; homozygous deletion of CTCF motif at SCR


title: Arabidopsis,ATX3, rep2

value: 15 dai seedling

value: Express 3x FLAG-tagged ATX3 under native promoter in the atx3 mutant background


title: N2.2


title: N2.3


title: KO1


title: SCRmus_Sox2-SCR_dCTCF_SCR_rep1

value: Embryonic stem cells


title: FD146.5

source_name: Strain FD146

value: Strain FD146


title: Arabidopsis,WT, H3, rep1

source_name: 14 dai seedling

value: 14 dai seedling

value: WT


title: Arabidopsis,nontransgenic control, rep2

value: WT (non transgenic)


title: SCRmus_Sox2-SCR_WT_d3

value: F1 with insertion of ANCH1 into SCR-proximal region of musculus allele, and ANCH3 into Sox2 promoter-proximal region of musculus allele


title: SCRmus_Sox2-SCR_WT_d2


title: Arabidopsis,ATXR3, rep1

value: Express 3x FLAG-tagged ATXR3 under native promoter in the atxr3 mutant background


title: Input_3

city: Vienna

first: Giulio

last: Superti-Furga

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

library_source: other

data_processing:
read trimming (transporter-focused KO libraries): tracrRNA sequences flanking the 3’ end of the sgRNA regions were trimmed from the reads using Cutadapt (Galaxy Version 4.8+galaxy1)
read trimming (transporter-focused OE libraries): 5’ flanking primer sequences (ACCCAGCTTTCTTGTACAAAG) were removed from the reads using cutadapt (Galaxy Version 4.8+galaxy1) and the remaining sequence was trimmed after the first 10 bp to receive the cDNA barcodes.
read trimming (genome-wide KO libraries): 5' flanking primer sequences and 3' flanking tracrRNA sequences were trimmed from the reads using Cutadapt (Galaxy Version 4.8+galaxy1) to receive the sgRNA sequences.
read/barcode mapping: MAGeCK count (Galaxy Version 0.5.9.2.4).
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited raw gRNA count tables
Library strategy: Amplicon-Seq

molecule: other

organism: Homo sapiens

source_name: HAP1 (RRID:CVCL_Y019)

growth_protocol: HAP1 (RRID:CVCL_Y019) cells were cultivated in DMEM (D5796 Sigma) supplemented with 10% Fetal Bovine Serum (10270-106, Lot 42F8381K, Gibco) and Penicillin-Streptomycin (15140-122, Gibco).

extract_protocol:
Genomic DNA was purified using QIAamp DNA Mini columns (Qiagen)
For transporter-focused KO screen samples, gDNA was digested overnight with 20U PacI (NEB) and double size-selected to enrich the sgRNA containing fragments (620 bp). Briefly, 0.6 x vol AmpliClean magnetic beads (Nimagen) were added to the sample to bind large gDNA fragments; the cleared supernatant was added to fresh beads (0.6 x volume of the original gDNA sample) to bind the smaller fragments. After size selection, sgRNA sequences were amplified in  with Q5 Polymerase (NEB) using the program recommended by the manufacturer (28 cycles, 72°C annealing temperature). PCR products were further double size-selected to remove residual large gDNA fragments as described above. For transporter-focused overexpression (OE) screen samples, barcode sequences were amplified from 10-20 µg gDNA per sample using pooled staggered primer containing partial Illumina adapter sequences with Q5 Polymerase (NEB) using the program recommended by the manufacturer (30 cycles, 63°C annealing temperature, 30 seconds extension). PCR products were double size selected using 0.65 x (to bind and remove gDNA) and 0.55 x volumes (to bind PCR products) AmpliClean magnetic beads (Nimagen). 2 µl of the purified PCR products were used in a second PCR with indexing primer with Q5 polymerase (10 cycles, 72°C annealing, 30 seconds extension) to generate Illumina libraries. For genome-wide KO screen samples, libraries were prepared as described previously (doi: 10.1038/nprot.2017.016).

treatment_protocol: Cells were transduced with lentiviral particles containing KO or OE libraries and selected with antibiotics to remove non-transduced cells. After 7-10 days of selection, each replicate was seeded to separate culture dishes and drug treatment was started the next day.

value: HAP1 (RRID:CVCL_Y019)

value: Myeloid haploid karyotype cell line

tag: screening library

value: Toronto KnockOut CRISPR Library TKOv3 (Addgene #90294)


title: Input_1


title: FD146.4

value: Mixed-stage embryos


title: Input_2


title: Arabidopsis,ATX5, rep1

value: Express 3x FLAG-tagged ATX5 under native promoter in the atx5 mutant background


title: Arabidopsis,ATXR7, rep1

value: Express 3x FLAG-tagged ATXR7 under native promoter in the atxr7 mutant background


title: SCRmus_Sox2-SCR_WT_OR_rep2

value: Transfection of 2 µg each of OR1-EGFP and OR3-IRFP, two days prior to collection


title: SCRmus_Sox2-SCR_WT_d1


title: FD146.3


title: D_3


title: D_2


title: FD135.5

source_name: Strain FD135

value: Strain FD135


title: Arabidopsis,ATX4, rep1

value: 15 dai seedling

value: Express 3x FLAG-tagged ATX4 under native promoter in the atx4 mutant background


title: SCRmus_Sox2-SCR_WT_OR_rep1

value: Embryonic stem cells


title: FD135.4


title: Arabidopsis,ATX3, rep1

value: Express 3x FLAG-tagged ATX3 under native promoter in the atx3 mutant background


title: D_1


title: SCRmus_Sox2-SCR_WT_d0_rep1


title: Arabidopsis,ATX2, rep1

value: Express 3x FLAG-tagged ATX2 under native promoter in the atx2 mutant background


title: B_2

value: 250 nM d9A-2 for 2 days


title: FD135.3


title: Arabidopsis,ATX1, rep1

value: Express 3x FLAG-tagged ATX1 under native promoter in the atx1 mutant background


title: SCRmus_F1_rep2

value: F1 wild-type


title: B_3


title: SCRmus_F1_rep1


title: SCRmus_Sox2-SCR_WT_d0_rep2

value: F1 with insertion of ANCH1 into SCR-proximal region of musculus allele, and ANCH3 into Sox2 promoter-proximal region of musculus allele


title: B_1

value: HAP1 (RRID:CVCL_Y019)


title: MA1-M2-3rd

status: Public on Sep 22 2024

city: Heidelberg

first: Yiman

last: Wang

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

data_processing:
remove adaptor sequences, contamination and low-quality reads by SOAPnuke software developed by BGI with filter parameters: " -n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim"
The Galaxy platform version 23.1
Sequence reads were mapped to hg38 using HISAT2 tools.
Read count extraction were performed using featureCounts tool.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: All parental melanoma cell lines were cultivated in DMEM (Gibco, Life Technologies) supplemented with 10% FCS (Biochrom), 1% penicillin (100 units/mL, Sigma-Aldrich) and streptomycin (100 μg/mL, Sigma-Aldrich) (pen/strep), 1% (v/v) of non-essential amino acid solution (NEAA,10 mM, Sigma-Aldrich) and 0.1% (v/v) β-mercaptoethanol (Gibco, Life Technologies). All melanoma cell lines were cultured in a humidified incubator with 5% CO2 at 37°C. Experiments were conducted when cells reached approximately 80% confluency. Subsequently, the cells were rinsed with PBS from Sigma-Aldrich to eliminate dead cells and debris. The process was followed by detachment using 21mM trypsin-EDTA (Sigma-Aldrich). The detached cells were then treated with trypan blue solution (Sigma-Aldrich), and viable cells were enumerated using a hemocytometer counting chamber. These viable cells were then seeded at specific densities as per the experimental requirements. For extended preservation, cells were cryopreserved using a freezing medium (FCS + 20% DMSO) and stored either at -80°C or in liquid nitrogen.

extract_protocol:
To extract RNA, cells were gathered and washed once with PBS. The RNeasy Mini Kit (QIAGEN) was employed following the manufacturer's instructions to isolate total RNA. To prevent genomic DNA contamination, an on-column DNase digest was carried out using RNase-Free DNase (QIAGEN) for 15 minutes at room temperature (RT). The concentration and quality of the RNA were assessed using a NanoDrop ND1000 spectrophotometer (PEQLAB Biotechnologie GmbH, Erlangen, Germany).
The strandedlibrarywas constructed using theDNBSEQ Eukaryotic Strand-specific mRNA librarykit (BGI Genomics, Shenzhen, China)

treatment_protocol: The melanoma cells that were successfully selected for all four factors were used for the transdifferentiation experiments. The cells were grown in MEF Medium, which contained DMEM supplemented with 10% FCS, 1% pen/strep, 1% (v/v) NEAA, 0.1% (v/v) β-mercaptoethanol and doxycycline (1 µg/ml). Doxycycline induced the expression of the transdifferentiation factors Ascl1, Brn2, Myt1L and NeuroD1. The medium was changed every 2-3 days. After a minimum of 4 days, cells were used for functional studies or molecular analyses.

value: Melanoma cells

value: BRAF V602E mutated

value: Doxycycline 7 days


title: MA1-4F-7d-2nd

value: BRAF V604E mutated


title: MA1-4F-7d-3rd

value: BRAF V605E mutated


title: MA1-4F-7d-1st

value: BRAF V603E mutated


title: Arabidopsis,nontransgenic control, rep1

value: WT (non transgenic)


title: MA1-M2-1st

value: BRAF V600E mutated


title: FD146.2

value: Strain FD146

value: Mixed-stage embryos


title: MA1-M2-2nd

value: BRAF V601E mutated


title: SKMel103-4F-7d-1st

value: NRAS mutated


title: SKMel103-M2-3rd


title: FD135.2

value: Strain FD135


title: A375-4F-7d-3rd


title: SKMel103-M2-1st


title: A375-4F-7d-2nd


title: A375-4F-7d-1st


title: SKMel103-4F-7d-2nd


title: A375-4F-4d-1st

value: Doxycycline 4 days


title: LIS-002408, CD

city: Lausanne

first: Yasmine

middle: J

last: Liu

address: Station 19 CH-1015 Lausanne

department: Laboratory of intergrative systems physiology

country: Switzerland

institute: EPFL

data_processing:
After sequencing on the BGIseq-500 platform, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality (phred quality < 20) reads from raw reads.
Sequenced reads were mapped to the GRCm38   mm10   primary   assembly  of the mouse genome using ensembl release 95 gene annotation with STAR aligner version 2.7.3a
Reads were counted using STAR aligner
Assembly: Mus_musculus.GRCm38.95
Supplementary files format and content: xlsx file with normalized counts per gene per sample

source_name: Liver

extract_protocol:
RNA was extracted in Trizol and purified using NucleoSpin RNA purification kit (MACHEREY-NAGEL). mRNA concentration was measured for all samples. All samples passed a quality check of purity (NanoDrop) and fragmentation (FragmentAnalyzer).
BGISEQ-500 library construction was performed by BGI

treatment_protocol: The C57BL/6J male mice were imported from Charles River, acclimatized at the École Polytechnique Fédérale de Lausanne (EPFL) animal facility for 2 weeks before initiation of the experiment. After the acclimatization period, animals were randomized based on their body weight and separated into three groups: one group fed WD (Research Diets D12079B; 40% kCal from fat, 17 % kCal from protein, and 43 % kCal from carbohydrates), the second fed WD admixed with 25 mg/kg body weight /day ACMSD inhibitor TLC-065 and the third fed on a matched CD (Research Diets D16042904B; 10 % kCal from fat, 17 % kCal from protein, and 73 % kCal from carbohydrates). All mice were housed at 30°C (TN) from 7 wks of age and TLC-065 treatment was started from 16 wks of age.

value: Liver

value: CD


title: LIS-002406, CD


title: A375-3rd


title: LIS-002324, WD+TLC-065


title: A375-2nd


title: A375-1st


title: A375-M2-3rd


title: A375-M2-2nd


title: A375-M2-1st


title: A375-4F-7d-select-1st

value: Doxycycline from day 0 to 7, Palbociclib from day 5 to 7


title: A375-4F-7d-select-3rd

value: Melanoma cells


title: RB1311.4

source_name: Strain RB1311

value: Strain RB1311


title: LIS-002229, CD


title: LIS-002216, WD

value: WD


title: A375-4F-4d-3rd


title: LIS-002214, WD


title: RB1311.3


title: LIS-002212, WD


title: PANC1-BRG oe_Igg

city: South San Francisco

first: Marc

last: Hafner

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

description: IGG control

data_processing:
The sequencing reads were mapped to the human genome using Bowtie2 (v2.4.1)
ENCODE blacklisted regions were removed from the alignment files using the data downloaded from Dr. Kundaje’s lab.
The files were then sorted using Samtools (v1.9) and PCR duplicates were removed using Picard Tools (v2.23.9).
Peak calling was done using MACS2 (v2.2.7.1) with p<1e-3 as cutoff.
Assembly: GRCh38
Supplementary files format and content: narrowPeak
Library strategy: Cut and Run

source_name: pancreatic

extract_protocol:
Cut & Run was performed using the CUTANA ChIC/Cut&Run Kit (Epicypher, Cat. No. 14-1048) exactly as per manufacturer’s recommendations with 0.5X106 cells per condition. Additional modifications made were mild crosslinking of cells as recommended for the BRM antibody (Epichypher Cat No. 13-2006).
Libraries were constructed using NEB Ultra II DNA Library Prep Kit (NEB, Cat. No. E7465) with PCR parameters for index PCR and library amplification based on recommendations from the Epicycpher Cut&Run kit. Quality of libraries was assessed with a Tapestation high sensitivity DNA kit (Agilent Technologies) before submitting for sequencing.

value: pancreatic

value: pancreatic cells

value: stable cell line expressing BRG1


title: LIS-002409, CD


title: SKMel103-4F-7d-3rd

value: Doxycycline 7 days


title: SKMel103-M2-2nd


title: LIS-002402, WD+TLC-065


title: LIS-002407, CD


title: PANC1-BRG oe_K4ME3_Rep2


title: PANC1-BRG oe_K27AC_Rep1


title: LIS-002400, WD+TLC-065


title: LIS-002326, WD+TLC-065


title: LIS-002314, WD


title: LIS-002316, WD


title: L31 TCDD 72h RNA

city: Chicago

first: Calvin

last: Law

state: IL

address: 303 E Superior St Lurie 5-220

department: Dermatology

institute: Northwestern University

description:
L31_TCDD_72h
Time_coure_RNAseq_normcounts.csv

data_processing:
Sequence quality was assessed with FastQC (v.0.11.5). FASTQ files were trimmed using BBduk from BBMap (v.38.90) according to the Lexogen QuantSeq manufacturer parameters, and mappged to hg38 using STAR (v.2.6.0).
HTSeq was used to count uniquely mapped reads and significantly differentially expressed genes (DEGs) at each time point were determined using DESeq2.
Time-course analyses were performed using maSigPro using default settings.
Volcano plots and PCA plots were generated using R (v.4.1.1).
Assembly: hg38
Supplementary files format and content: csv, DEseq2 normalized counts.

source_name: blood

growth_protocol: Human memory CD4+ T cells was isolated from cells (200,000 cells) stimulated with anti-CD3/CD28 Dynabeads and cultured in TGFβ1 with either AHR antagonist or agonist for 12, 24, 48 and 72 h.

extract_protocol:
RNA was isolated with Rneasy Plus Micro Kit (Qiagen no. 74034) following the manufacturer protocol.
RNA libraries were prepared using the QuantSeq FWD Kit for Illumina Sequencing (Lexogen) for 3′ RNA-seq. Sequencing was performed on the Illumina NextSeq platform.
RNA-seq, 3 biological replicates of each sample were sequenced.

value: blood

value: primary CD4+ memory T cells

value: TGF-β + AHR agonist (TCDD) for 72 hours


title: PANC1-BRG oe_SMARCC1_Rep1


title: LIS-002230, CD


title: PANC1-BRG oe_SMARCC1_Rep2


title: PANC1-BRG oe_NRF2_Rep2


title: A375-4F-4d-2nd

value: BRAF V600E mutated


title: LIS-002213, WD


title: PANC1-BRG oe_BRG1_Rep2


title: L29 AHRinh 72h RNA

description:
L29_AHRinh_72h
Time_coure_RNAseq_normcounts.csv

treatment_protocol: Human memory CD4+ T cells was isolated from cells (200,000 cells) stimulated with anti-CD3/CD28 Dynabeads and cultured in TGFβ1 with either AHR antagonist or agonist for 12, 24, 48 and 72 h.

value: TGF-β + AHR inhibitor (CH-223191) for 72 hours


title: PANC1-BRG oe_K27AC_Rep2


title: L30 TCDD 48h RNA

description:
L30_TCDD_48h
Time_coure_RNAseq_normcounts.csv

value: TGF-β + AHR agonist (TCDD) for 48 hours


title: iBRM_NRF2_Rep1

value: stable cell line expressing dox-inducible BRM


title: iBRM_SMARCC1_Rep2


title: iBRM_SMARCC1_Rep1


title: L29 TCDD 48h RNA

description:
L29_TCDD_48h
Time_coure_RNAseq_normcounts.csv


title: L29 AHRinh 48h RNA

description:
L29_AHRinh_48h
Time_coure_RNAseq_normcounts.csv

value: TGF-β + AHR inhibitor (CH-223191) for 48 hours


title: L30 AHRinh 48h RNA

description:
L30_AHRinh_48h
Time_coure_RNAseq_normcounts.csv


title: PANC1-BRG oe_K4ME3_Rep1


title: PANC1-BRG oe_K4ME1_Rep2


title: L31 AHRinh 72h RNA

description:
L31_AHRinh_72h
Time_coure_RNAseq_normcounts.csv


title: L30 TCDD 72h RNA

description:
L30_TCDD_72h
Time_coure_RNAseq_normcounts.csv


title: L30 AHRinh 72h RNA

description:
L30_AHRinh_72h
Time_coure_RNAseq_normcounts.csv


title: L30 AHRinh 24h RNA

description:
L30_AHRinh_24h
Time_coure_RNAseq_normcounts.csv

value: TGF-β + AHR inhibitor (CH-223191) for 24 hours


title: BRGoe_SMARCC1_Rep1


title: L29 TCDD 72h RNA

description:
L29_TCDD_72h
Time_coure_RNAseq_normcounts.csv


title: BRGoe_NRF2_Rep2


title: PANC1-BRG oe_NRF2_Rep1


title: L30 TCDD 12h RNA

description:
L30_TCDD_12h
Time_coure_RNAseq_normcounts.csv

value: TGF-β + AHR agonist (TCDD) for 12 hours


title: BRGoe_K4ME1_Rep2


title: L31 TCDD 48h RNA

description:
L31_TCDD_48h
Time_coure_RNAseq_normcounts.csv


title: PANC1-BRG oe_BRG1_Rep1


title: L31 AHRinh 48h RNA

description:
L31_AHRinh_48h
Time_coure_RNAseq_normcounts.csv


title: PANC1-BRG oe_K4ME1_Rep1


title: L30 AHRinh 12h RNA

description:
L30_AHRinh_12h
Time_coure_RNAseq_normcounts.csv

value: TGF-β + AHR inhibitor (CH-223191) for 12 hours


title: iBRM_NRF2_Rep2


title: BRGoe_K27AC_Rep2


title: iBRM_K4ME1_Rep2


title: L31 TCDD 24h RNA

description:
L31_TCDD_24h
Time_coure_RNAseq_normcounts.csv

value: TGF-β + AHR agonist (TCDD) for 24 hours


title: L31 AHRinh 24h RNA

description:
L31_AHRinh_24h
Time_coure_RNAseq_normcounts.csv


title: iBRM_K4ME1_Rep1


title: iBRM_K27AC_Rep2


title: BRGoe_BRG1_Rep2


title: L30 TCDD 24h RNA

description:
L30_TCDD_24h
Time_coure_RNAseq_normcounts.csv


title: iBRM_K27AC_Rep1


title: GSC3565 cells, shControl_3

city: Bloomington

first: QIQI

last: XIE

state: IN

address: 3209 E 10th St Apt E6

department: Biology

institute: Indiana University Bloomington

data_processing:
Total RNA was isolated from GSC3565 cells with control or SUV39H1 knockdown and subjected to RNA-seq analysis at Novogene Corporation.
Quality control of the raw RNA-seq reads was performed using FastQC (https://github.com/s-andrews/FastQC) and fastp (https://github.com/OpenGene/fastp), with adapter sequences removed using TrimGalore (https://github.com/FelixKrueger/TrimGalore). The trimmed reads were then aligned to the human reference genome (hg38) using the STAR aligner (https://github.com/alexdobin/STAR). Transcript abundance quantification was carried out using Salmon in quasi-mapping mode.
The resulting quantification files were imported into R for differential expression analysis using the DESeq2 package (https://github.com/thelovelab/DESeq2). Differentially expressed genes (DEGs) were identified using a threshold of log2 fold change > 1 or < -1 and an adjusted P value < 0.05. To visualize the DEGs, we generated volcano plots using the ggplot2 package in R.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: GBM

growth_protocol: enti-X-293T cells (Takara Bio, cat# 632180) were cultured in DMEM media (Gibco, cat# 11995065) supplemented with 10% FBS (Corning, cat# 35015CV).

extract_protocol:
Lenti-X-293T cells cultured in DMEM media were transfected with lentivirus packaging plasmids (pMD2.g and psPAX2), along with either control or SUV39H1 shRNA vectors (Sigma-Aldrich Mission shRNA, #1 TRCN0000285355 and #2 TRCN0000275322), or pHAGE PGK-GFP-IRES-LUC-W (Addgene, cat# 46793) using the jetPRIME transfection reagent (Polyplus, cat# 101000001). After 24 hrs, the DMEM media was replaced with GSC culture media, and the cells were incubated for an additional 48 hrs at 37°C to produce lentivirus. The supernatant containing the lentivirus was harvested and saved in -80°C. For lentivirus infection, GSCs (4 x 105 cells per well in a 6-well plate) were exposed to the lentivirus for 18 hrs, followed by a media change to GSC culture media and a further 48 hrs incubation.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: GBM

value: GSC3565 cells

value: GSC

value: WT


title: L29 TCDD 24h RNA

description:
L29_TCDD_24h
Time_coure_RNAseq_normcounts.csv


title: L31 TCDD 12h RNA

description:
L31_TCDD_12h
Time_coure_RNAseq_normcounts.csv


title: BRGoe_NRF2_Rep1

value: pancreatic

value: pancreatic cells

value: stable cell line expressing BRG1


title: L31 AHRinh 12h RNA

description:
L31_AHRinh_12h
Time_coure_RNAseq_normcounts.csv

value: blood

value: primary CD4+ memory T cells


title: SO4(Crimson) DAF105 rep1

city: Wuhan

first: Wenying

last: Zhong

address: Shizi Street No.1

institute: Huazhong Agricultural University

data_processing:
Illumina PE150/SE50  software used for basecalling.
Compare the clean reads to the reference sequence useing Hisat2 software
Use Stringtie software to splice the reads into transcripts and quantify them
Quantitative expression levels of all detected and predicted samples

organism: Vitis vinifera

source_name: fruit

extract_protocol:
Total RNA was extracted from DCs using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), accordance with the instructions of the kits used.
mRNA libraries were prepared for sequencing using standard Illumina protocols

tag: graph condition

value: SO4(Crimson) DAF105

value: peel of fruit


title: SO4(Crimson) DAF75 rep3

value: SO4(Crimson) DAF75


title: SO4(Crimson) DAF75 rep2


title: L29 TCDD 12h RNA

description:
L29_TCDD_12h
Time_coure_RNAseq_normcounts.csv


title: BRGoe_K4ME1_Rep1


title: BRGoe_K27AC_Rep1


title: BRGoe_SMARCC1_Rep2


title: L29 AHRinh 24h RNA

description:
L29_AHRinh_24h
Time_coure_RNAseq_normcounts.csv


title: SO4(Crimson) DAF75 rep1


title: SO4(Crimson) DAF45 rep3

value: SO4(Crimson) DAF45


title: L29 AHRinh 12h RNA

description:
L29_AHRinh_12h
Time_coure_RNAseq_normcounts.csv


title: SO4(Crimson) DAF45 rep2


title: BRGoe_Igg_Rep1

description: IGG control


title: SO4(Crimson) DAF45 rep1


title: db4

city: Shanghai City

first: Yanying

last: Yang

state: Shanghai City

address: Shanghai

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (UCSC MM10) by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps.
These peaks identified by both softwares overlapping with exons of mRNA were figured out and choosed by home-made scripts.
Assembly: MM10
Supplementary files format and content: Acetylated_RNA_sites.mRNA.xlsx: acetylation sites and enrichment information of all samples.

source_name: liver

growth_protocol: All mice were raised under Specific Pathogen Free conditions with a 12-hour dark/light cycle, 20–22 °C and 45–65% humidity with water and food provided ad libitum.

extract_protocol:
Total RNAs were obtained from db/db mice and lean control mice using TRIzol reagent (catalog T9108, Takara) according to the manufacturer's protocol.
The ac4C-IP-Seq service was provided by CloudSeq Inc. (Shanghai, China). Total RNA was rRNA depleted with Ribo-zero (Illumina) and then subjected to immunoprecipitation with the GenSeqTM ac4C-IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the ac4C antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. The RNA/antibody complexes are then digested with Proteinase K and the eluted RNA is purified by phenol:chloroform extraction. RNA libraries for IP and input samples were then constructed with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a HiSeq platform (Illumina)
acRIP-ac4C-mRNA-seq

value: liver

tag: Sex

value: male

value: db/db


title: db4 Input


title: db3


title: GSC3565 cells, shSUV39H1_4

value: SUV39H1 knockdown


title: 110R(Crimson) DAF105 rep3

value: 110R(Crimson) DAF105


title: db2 Input


title: GSC3565 cells, shSUV39H1_3

value: GBM

value: GSC3565 cells


title: GSC3565 cells, shControl_4

value: GSC

value: WT


title: AAV-GFP IP

data_processing:
The RNA immunoprecipitation assay was carried out with GenSeq RIP kit (GenSeq Inc.) according to the manufacturer’s instructions. Briefly, cell lysate was immuno-precipitated by using antibody to protein of interest or IgG along with protein A/G magnetic beads.
After proteinase K digestion, the RNA co-immunoprecipitated with proteins was purified by phenol/chloroform extraction and precipitated in ethanol.
RNA was re-suspended in RNase-free water and subjected to GenSeq rRNA Removal Kit (GenSeq, Inc.) to remove rRNA. RNA libraries were constructed by using rRNA-depleted RNAs with GenSeq Low Input RNA Library Prep Kit (GenSeq, Inc.), according to the manufacturer’s instructions.
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc.). Library sequencing was sequenced with 150bp paired end reads.
Assembly: MM10
Supplementary files format and content: RIP_RNA_sites.mRNA.xlsx:  Differentially comparision  sites and enrichment information of all samples.

extract_protocol:
Total RNAs were obtained from db/db mice and lean control mice using TRIzol reagent (catalog T9108, Takara) according to the manufacturer's protocol.
RIP-Seq service was provided by Cloud-Seq Biotech (Shanghai, China). The RNA immunoprecipitation assay was carried out with GenSeq RIP kit (GenSeq Inc.) according to the manufacturer’s instructions. Briefly, cell lysate was immuno-precipitated by using antibody to protein of interest or IgG along with protein A/G magnetic beads. After proteinase K digestion, the RNA co-immunoprecipitated with proteins was purified by phenol/chloroform extraction and precipitated in ethanol. Then, RNA was re-suspended in RNase-free water and subjected to GenSeq rRNA Removal Kit (GenSeq, Inc.) to remove rRNA. RNA libraries were constructed by using rRNA-depleted RNAs with GenSeq Low Input RNA Library Prep Kit (GenSeq, Inc.), according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc.). Library sequencing was sequenced with 150bp paired end reads.
acRIP-ac4C-mRNA-seq


title: SO4(Crimson) DAF105 rep3


title: BRGoe_BRG1_Rep1

value: pancreatic

value: pancreatic cells


title: SO4(Crimson) DAF105 rep2


title: db2


title: AAV-NAT10 Input


title: AAV-NAT10 IP


title: db1


title: 110R(Crimson) DAF75 rep2

value: 110R(Crimson) DAF75


title: lean4 Input


title: AAV-GFP Input


title: lean2 Input


title: GSC3565, H3K9me3_shSUV39H1, ChIP

data_processing:
ChIP-seq reads were aligned to the Homo sapiens genome (hg38) using Bowtie 2  with default parameters, which allows multiple alignment.
Peaks were called using MACS2 software with default parameters. The midpoint of each estimated fragment by MACS2 and its location on the genome was calculated.
The genome was divided into non-overlapping windows of the default 100 bp. An aligned read was considered to be located in a window if the midpoint of its estimated fragment was within the window.
The number of midpoints in each window was counted and an empirical distribution of window counts was created. A zero-truncated negative binomial model was fit to the distribution, and a peak was determined based on the FDR (0.001, default) calculated from the model.
Overlapping enriched windows were merged into regions and reported. For analysis of REs, a list of H3K9me3 peaks associated with REs was created by intersecting H3K9me3 binding peaks with RE loci obtained from RepeatMasker (https://github.com/rmhubley/RepeatMasker), which was used in the downstream analysis. Reads were mapped and assigned to the H3K9me3-associated REs using EDTA with the recommended parameters (https://github.com/oushujun/EDTA).
Assembly: hg38
Supplementary files format and content: bw

growth_protocol: Following centrifugation, the supernatant was diluted and subjected to H3K9me3 ChIP using the ChIPAb+ Trimethyl-Histone H3 (Lys9) kit (Millipore, cat# 17-10242).

extract_protocol:
Bound material was recovered after incubation with 15 μL of protein G beads (Millipore, cat # 16-266) at 4°C, washed sequentially, and eluted.
DNA was extracted using the Gel Extraction Kit (Qiagen cat# 28704) and submitted to Novogene for standard sequencing.

value: GBM stem cell

tag: antibody

value: Millipore, cat# 17-10242


title: db3 Input


title: GSC3565, H3K9me3, ChIP


title: 110R(Crimson) DAF45 rep1

value: 110R(Crimson) DAF45

value: peel of fruit


title: GSC3565, Input_H3K9me3_shSUV39H1, ChIP


title: 110R(Crimson) DAF105 rep2


title: 110R(Crimson) DAF105 rep1


title: GSC3565, Input_H3K9me3, ChIP


title: 110R(Crimson) DAF75 rep3


title: db1 Input


title: lean4


title: lean2


title: 110R(Crimson) DAF75 rep1


title: 101-14MG(Crimson) DAF105 rep1

value: 101-14MG(Crimson) DAF105


title: lean3 Input

value: liver


title: 101-14MG(Crimson) DAF75 rep3

value: 101-14MG(Crimson) DAF75


title: 110R(Crimson) DAF45 rep3


title: Skin, PN2 replicate 4

city: Baltimore

first: Margaret

middle: M

last: McCarthy

state: Maryland

address: 670 W Baltimore St

institute: University of Maryland, Baltimore

data_processing:
Sequencing reads were pseudo-aligned to rat transcript models (Rnor 6.0, Ensembl V96) and tables of read counts per gene were generated using kallisto
Assembly: Rnor 6.0
Supplementary files format and content: tab-delimited text file including the processed counts for all samples

organism: Rattus norvegicus

source_name: Skin

extract_protocol:
Single-cell suspensions were prepared from PN2 hippocampus, hypothalamus, bone marrow, and skin and PN7 hippocampus and hypothalamus as described above using a 37% Percoll gradient to purify immune cells. Three to five independent biological replicates were prepared from each condition, with each replicate containing pooled cells from 6 separate animals. We sorted mast cells using a BD Aria II cytometer (courtesy of UMB Flow Cytometry Core), gated on SSC/FSC, singlets, live cells, CD45hi, CD11b-, and FcERI+ in each tissue
1,000-10,000 cells per sample were collected into 350 μL RLT lysis buffer (Qiagen) containing 2-mercaptoethanol per manufacturer’s instructions and stored at -80 °C until further processing. RNA was extracted using the Qiagen RNeasy Micro kit. RNA-seq library preparation and sequencing were performed by the Maryland Genomics core facility within the Institute for Genome Sciences. Ultra-low input strand specific RNA-Seq libraries were produced with the SMART-Seq v4 UltraLow Input RNA Kit for Sequencing (Takara, Japan). cDNA was made according to the manufacturer protocol with no modifications. Adapters for sequencing were added using the Illumina Nextera XT library preparation kit (Illumina, San Diego, CA). Input amount was 9 nanograms. Libraries were sequenced using an Illumina NovaSeq 6000 run, targeting 60-70 million read pairs per sample.

treatment_protocol: Pups ranging in age from PN2 to PN7 were anesthetized and perfused with PBS.

value: Skin

tag: age


title: 101-14MG(Crimson) DAF105 rep2


title: lean3

value: male


title: 110R(Crimson) DAF45 rep2


title: 101-14MG(Crimson) DAF75 rep2


title: lean1 Input


title: 101-14MG(Crimson) DAF105 rep3


title: Skin, PN2 replicate 2


title: Skin, PN2 replicate 3


title: Hypothalamus, PN7 replicate 1

source_name: Hypothalamus

value: Hypothalamus


title: lean1


title: Skin, PN2 replicate 5


title: 101-14MG(Crimson) DAF75 rep1


title: GCAKO_ALDO

type: RNA

city: Kyoto

first: Takuya

last: Ishimura

state: Kyoto

address: Sakyo-ku Syogoinkawaharatyo 54

department: Nephrology

country: Japan

institute: Kyoto University

description: ALDO treatment = uninephrectomy and continuous subcutaneous injection of aldosterone with 6% high salt diet

hyb_protocol: Each sample was hybridized to an Affymetrix mouse genome 430 2.0 array at TAKARA Bio (Shiga, Japan).Hybridization control was GeneChip Eukaryotic Hybridization Control Kit and hybridization was perfomed for 2 hours at 45C in 60rpm by GeneChip Hybridization Oven 640

scan_protocol: The genechips were scanned by a Affymetrix GeneChip Command Console.

data_processing: Data normalization, log transformation, statistical analysis, and pattern study were performed with the Affymetrix GeneChip Expression Console.

label: biotin

source_name: GC-A KO mouse with ALDO treatment

label_protocol: Complementary RNA probes were generated using the GeneChip 3’ IVT Express Kit (Applied Biosystems, Foster city, CA)

extract_protocol: Total RNA from the glomeruli was extracted by RNeasy Mini Kit (Qiagen) in these mice.

tag: gender

value: glomeruli


title: Paddy rice ileum

city: Nagoya

first: Atsushi

last: Murai

address: Furo-cho, Chikusa-ku

department: Department of Animal Sciences

institute: Nagoya University

description: Gene expression data of ileum of chickens given paddy rice-based diet

hyb_protocol: Following fragmentation, biotinylated cRNA were hybridized for 17 hr at 45C on GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Expression Analysis Data Analysis Fundamentals using GeneChip Operating Software ver 1.4 with MAS5 algorithm.

organism: Gallus gallus

source_name: Ileum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Affymetrix Gene Chip 3' IVT PLUS Reagent Kit, Affymetrix).

growth_protocol: One-wk-old chickens were allocated into two groups (9 birds each) on the basis of BW to give a similar mean BW (60-75 g at 1 wk of age) across all groups, and each bird was caged individually. The birds were allowed free access to experimental diets containing 650 g/kg corn or paddy rice for 2 wk

extract_protocol: Total RNA was extracted from ileum using TRI reagent (Molecular Research Center, Cincinnati, OH). The total RNA from 3 birds per treatment was pooled for each chip, and then the mixed RNA at 100 µg was cleaned up and purified by RNeasy® Mini Kit.

treatment_protocol: At 3 wk of age, the birds were euthanized by decapitation. The small intestine was excised, and then the luminal contents were removed by flushing with PBS. Segments (50 to 70 mg) of ileum were further excised for DNA microarray analysis.

tag: diet

value: Paddy rice


title: Skin, PN2 replicate 1


title: WT_ALDO

source_name: wild-type mouse with ALDO treatment


title: GCAKO_control

description: control treatment = uninephrectomy and continuous subcutaneous injection of 2% EtOH with normal diet

source_name: GC-A KO mouse with control treatment


title: Corn ileum

description: Gene expression data of ileum of chickens given corn-based diet

value: Control


title: 101-14MG(Crimson) DAF45 rep3

value: 101-14MG(Crimson) DAF45


title: 101-14MG(Crimson) DAF45 rep2


title: WT_control

source_name: wild-type mouse with control treatment


title: Crimson Seedless DAF105 rep3

value: Crimson Seedless DAF105


title: Hypothalamus, PN2 replicate 2

value: WT


title: 101-14MG(Crimson) DAF45 rep1


title: FLEP_seq_fpa

city: Guangzhou

first: Weipeng

last: Mo

state: Guangdong

address: 58 Zhongshaner Rd

department: The First Affiliated Hospital

institute: Sun Yat-sen University

description: nuclear RNA

data_processing:
Guppy basecaller (Oxford Nanopore Technologies, v4.0.11) was used to convert Nanopore raw signal to sequence, with parameters --c dna_r9.4.1_450bps_hac.cfg, --qscore_filtering. The basecalled reads were mapped to Arabidopsis TAIR10 genome using Minimap2 v2.10-r761 with parameters: -ax splice, –secondary=no, -G 12000. The unmapped reads, not primary alignment reads, and supplementary alignment reads were removed using SAMtools view with parameter -F 2308. The 5’ or 3’ unmapped sequences (soft-clip sequences) plus the flanking 20 nt mapped sequences were used to search the template-switching oligo sequence (5’-AAGCAGTGGTATCAACGCAGAGTACATGGG-3’) and the 3’ adapter sequence (5’-ATTGATGGTGCCTACAG-3’) using BLAST v.2.9.0+ with the parameter: -word_size 6. The template-switching oligo and the 3’ adapter can be used to characterize the integrity of 5’ and 3’ end of reads and to provide the strand information. Therefore, only reads containing both sequences were used for subsequent analysis. PolyAcaller (https://github.com/ZhaiLab-SUSTech/FLEPSeq) was used to estimate poly(A) tail lengths of Nanopore reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include read_infor for each Read

source_name: fpa single mutant_seedlings

growth_protocol: Seeds were grown on 1/2 MS medium at 22 °C (16 h light–8 h dark) for 12 d before collection.

extract_protocol:
Two grams of seedlings were ground with liquid nitrogen into fine powder and transferred to an ice-cold 50 ml tube with 10 ml Honda buffer (0.44 M Sucrose, 1.25% (wt/vol) Ficoll, 2.5% (wt/vol) Dxtran T40, 20 mM HEPES-KOH pH 7.4, 10 mM MgCl2, 0.5% (wt/vol) Triton X-100, 1 mM DTT, 1× protease inhibitor (Roche), 100 ng/μl tRNA). After homogenization by vortexing, the homogenate was filtered through one layer of miracloth. Another 10 ml Honda buffer was added to the filter to wash the remaining plant material. After centrifugation at 4 ℃ and 3,500 g for 5 min, the supernatant was collected as the cytoplasmic fraction and the pellet was resuspended and washed once with another 20 ml Honda buffer. Then the pellet was resuspended in 1 ml Honda buffer (0.44 M Sucrose, 1.25% (wt/vol) Ficoll, 2.5% (wt/vol) Dxtran T40, 20 mM HEPES-KOH pH 7.4, 10 mM MgCl2, 0.5% Triton X-100, 1 mM DTT, 500 ng/μl tRNA, 2× proteinase inhibitor (Roche), 10 μl RNase inhibitor (RNase out, Thermo)) and centrifuged at 4 ℃, 8000 g for 1 min. The supernatant was completely removed and the nuclei pellet was retained as the nuclear RNA fraction.
After rRNA removal by using RiboMinus Plant Kit for RNA-Seq (Invitrogen, A10838-08), the nuclear RNA was mixed with 50 pmol 3’ adapter (5’-rAppCTGTAGGCACCATCAAT–NH2 -3’, NEB 1315) at 65 ℃ for 5min, and then placed on ice for more than 1 min. 2 μl 10× T4 RNA ligase reaction buffer (NEB, M0242), 10 μl 50% PEG 8000 (NEB, M0242), 1 μl 40 U μl-1 RNaseOUT (Invitrogen, 10777019) and 1 μl T4 RNA ligase 2, truncated K227Q (NEB, M0242) were added to the RNA. The ligation reaction was performed at 16 ℃ for 10 h. The ZYMO RNA Clean & Concentrator kit (ZYMO, R1013) was used for RNA purification. Reverse transcription and template-switching were performed using the SMARTer PCR cDNA Synthesis Kit (Takara, 634926) with minor modification. The SMART CDS Primer II A was replaced by the custom primer (5’-AAGCAGTGGTATCAACGCAGAGTACATTGATGGTGCCTACAG-3’) which is complementary to the 3’ adapter sequence. To minimize the PCR bias resulting from over-amplification, PCR cycle optimization was performed to determine the best cycle number for cDNA amplification. VAHTS DNA Clean Beads (Vazyme, N411) was used to purify PCR products. 200 fmol cDNA was used to construct the Nanopore library (using Ligation Sequencing Kit, SQK-LSK109, Oxford Nanopore Technologies). Libraries were loaded onto R9.4 flow cell (Oxford Nanopore Technologies) and sequenced on MinION device for ~48 hr.
FLEP-seq

tag: ecotype

tag: genotype/variation

value: fpa single mutant

value: 12d old

value: seedlings


title: FLEP_seq_met1

description: nuclear RNA

source_name: met1 single mutant_seedlings

value: met1 single mutant


title: Hippocampus, PN7 replicate 3

source_name: Hippocampus

value: Hippocampus


title: Hypothalamus, PN2 replicate 1


title: Crimson Seedless DAF105 rep1

value: peel of fruit


title: Hippocampus, PN7 replicate 1


title: Hippocampus, PN2 replicate 4


title: FLEP_seq_WT

data_processing:
library strategy: FLEP-seq
Guppy basecaller (Oxford Nanopore Technologies, v4.0.11) was used to convert Nanopore raw signal to sequence, with parameters --c dna_r9.4.1_450bps_hac.cfg, --qscore_filtering. The basecalled reads were mapped to Arabidopsis TAIR10 genome using Minimap2 v2.10-r761 with parameters: -ax splice, –secondary=no, -G 12000. The unmapped reads, not primary alignment reads, and supplementary alignment reads were removed using SAMtools view with parameter -F 2308. The 5’ or 3’ unmapped sequences (soft-clip sequences) plus the flanking 20 nt mapped sequences were used to search the template-switching oligo sequence (5’-AAGCAGTGGTATCAACGCAGAGTACATGGG-3’) and the 3’ adapter sequence (5’-ATTGATGGTGCCTACAG-3’) using BLAST v.2.9.0+ with the parameter: -word_size 6. The template-switching oligo and the 3’ adapter can be used to characterize the integrity of 5’ and 3’ end of reads and to provide the strand information. Therefore, only reads containing both sequences were used for subsequent analysis. PolyAcaller (https://github.com/ZhaiLab-SUSTech/FLEPSeq) was used to estimate poly(A) tail lengths of Nanopore reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include read_infor for each Read

extract_protocol:
Two grams of seedlings were ground with liquid nitrogen into fine powder and transferred to an ice-cold 50 ml tube with 10 ml Honda buffer (0.44 M Sucrose, 1.25% (wt/vol) Ficoll, 2.5% (wt/vol) Dxtran T40, 20 mM HEPES-KOH pH 7.4, 10 mM MgCl2, 0.5% (wt/vol) Triton X-100, 1 mM DTT, 1× protease inhibitor (Roche), 100 ng/μl tRNA). After homogenization by vortexing, the homogenate was filtered through one layer of miracloth. Another 10 ml Honda buffer was added to the filter to wash the remaining plant material. After centrifugation at 4 ℃ and 3,500 g for 5 min, the supernatant was collected as the cytoplasmic fraction and the pellet was resuspended and washed once with another 20 ml Honda buffer. Then the pellet was resuspended in 1 ml Honda buffer (0.44 M Sucrose, 1.25% (wt/vol) Ficoll, 2.5% (wt/vol) Dxtran T40, 20 mM HEPES-KOH pH 7.4, 10 mM MgCl2, 0.5% Triton X-100, 1 mM DTT, 500 ng/μl tRNA, 2× proteinase inhibitor (Roche), 10 μl RNase inhibitor (RNase out, Thermo)) and centrifuged at 4 ℃, 8000 g for 1 min. The supernatant was completely removed and the nuclei pellet was retained as the nuclear RNA fraction.
After rRNA removal by using RiboMinus Plant Kit for RNA-Seq (Invitrogen, A10838-08), the nuclear RNA was mixed with 50 pmol 3’ adapter (5’-rAppCTGTAGGCACCATCAAT–NH2 -3’, NEB 1315) at 65 ℃ for 5min, and then placed on ice for more than 1 min. 2 μl 10× T4 RNA ligase reaction buffer (NEB, M0242), 10 μl 50% PEG 8000 (NEB, M0242), 1 μl 40 U μl-1 RNaseOUT (Invitrogen, 10777019) and 1 μl T4 RNA ligase 2, truncated K227Q (NEB, M0242) were added to the RNA. The ligation reaction was performed at 16 ℃ for 10 h. The ZYMO RNA Clean & Concentrator kit (ZYMO, R1013) was used for RNA purification. Reverse transcription and template-switching were performed using the SMARTer PCR cDNA Synthesis Kit (Takara, 634926) with minor modification. The SMART CDS Primer II A was replaced by the custom primer (5’-AAGCAGTGGTATCAACGCAGAGTACATTGATGGTGCCTACAG-3’) which is complementary to the 3’ adapter sequence. To minimize the PCR bias resulting from over-amplification, PCR cycle optimization was performed to determine the best cycle number for cDNA amplification. VAHTS DNA Clean Beads (Vazyme, N411) was used to purify PCR products. 200 fmol cDNA was used to construct the Nanopore library (using Ligation Sequencing Kit, SQK-LSK109, Oxford Nanopore Technologies). Libraries were loaded onto R9.4 flow cell (Oxford Nanopore Technologies) and sequenced on MinION device for ~48 hr.

value: wild-type

tag: molecule type

value: nuclear RNA


title: Hippocampus, PN7 replicate 2

tag: tissue


title: KPC Pancreas Tum AZD6244 Rep5

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

country: United Kingdom

institute: Cancer Research UK Scotland Institute

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: matrix of raw counts

source_name: Pancreas

extract_protocol:
RNA was isolated using the Rneasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Libraries for cluster generation and DNA sequencing were prepared using an Illumina TruSeq RNA sample kit, then run on an Illumina NextSeq 500 (2x36 cycles, paired end, single index).

treatment_protocol: Where noted, MEK inhibitor AZD6244 was administered twice daily at 25 mg/kg via oral gavage in a vehicle of 0.5% HPMC and 01% Tween-80.

value: Pancreas

tag: sample type

value: Tumour

tag: sample run

tag: genotype

value: Pdx1Cre KrasG12D/+ P53R172H/+


title: Crimson Seedless DAF75 rep2

value: Crimson Seedless DAF75


title: MA1_M2_2

type: genomic

description: Treated with doxycycline for 7 days

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

scan_protocol: standard recommended Illumina scanner setting

data_processing: ChaMP package (version 2.18.3) in R environment (version 4.0.1)

label: Cy5 and Cy3

source_name: MA1 melanoma cells

label_protocol: Standard Illumina Protocol

extract_protocol: QIAGEN DNeasy Blood & Tissue Kit (250) (Cat. No. 69506)


title: Hippocampus, PN2 replicate 3


title: Crimson Seedless DAF105 rep2


title: MA1_4F_3

description: Treated with doxycycline for 7 days


title: KPC Pancreas Tum AZD6244 Rep3

tag: treatment


title: Crimson Seedless DAF75 rep1


title: KPC Pancreas Tum AZD6244 Rep4


title: MA1_4F_2

description: Treated with doxycycline for 7 days


title: KPC Pancreas Tum AZD6244 Rep2


title: Crimson Seedless DAF45 rep3

value: Crimson Seedless DAF45


title: MA1_M2_3

description: Treated with doxycycline for 7 days


title: Hippocampus, PN2 replicate 1


title: KPC Pancreas Tum AZD6244 Rep1


title: leaves, SFZ_Mock3

first: Liu

last: Hailun

address: Tianhe District

institute: Guangdong Academy of Agricultural Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence by STAR. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome.
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample.
HTSeq(v 0.5.4) was used to count the reads numbers mapped to each gene.
Assembly: The reference genome sequencing and assembly can be found in the NCBI database under accession number PRJNA747875.
Supplementary files format and content: tab-delimited text files include readcount values for each Sample.
Supplementary files format and content: tab-delimited text files include fpkm values for each Sample.

organism: Litchi chinensis

source_name: leaves

growth_protocol: Lychee trees were planted in national lychee germplasm nursery located in institute of fruit tree research Guangdong Academy of Agricultural Aciences.

extract_protocol:
RNA was extracted using the TRIzol method (Invitrogen, CA, USA) and treated with RNase-free DNase I (Takara, Kusatsu, Japan). A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Lychee leaves were inoculated with P.litchii (1 × 104 spores·mL-1) or mock-inoculation (sterile water).

value: leaves

value: SFZ

value: Mock treatment


title: Crimson Seedless DAF45 rep2


title: SKMel103_4F_1

description: Treated with doxycycline for 7 days

source_name: SKMel103 melanoma cells


title: Crimson Seedless DAF45 rep1


title: Crimson Seedless DAF75 rep3


title: Bone Marrow, PN2 replicate 4

source_name: Bone Marrow

value: Bone Marrow

value: WT


title: SKMel103_4F_2

description: Treated with doxycycline for 7 days


title: leaves, SFZ_P1

value: P.litchii treatment


title: KPC Pancreas Tum Veh Rep5

value: Vehicle


title: A375-4F-7d-select-2nd

data_processing:
remove adaptor sequences, contamination and low-quality reads by SOAPnuke software developed by BGI with filter parameters: " -n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim"
The Galaxy platform version 23.1
Sequence reads were mapped to hg38 using HISAT2 tools.
Read count extraction were performed using featureCounts tool.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
To extract RNA, cells were gathered and washed once with PBS. The RNeasy Mini Kit (QIAGEN) was employed following the manufacturer's instructions to isolate total RNA. To prevent genomic DNA contamination, an on-column DNase digest was carried out using RNase-Free DNase (QIAGEN) for 15 minutes at room temperature (RT). The concentration and quality of the RNA were assessed using a NanoDrop ND1000 spectrophotometer (PEQLAB Biotechnologie GmbH, Erlangen, Germany).
The strandedlibrarywas constructed using theDNBSEQ Eukaryotic Strand-specific mRNA librarykit (BGI Genomics, Shenzhen, China)

tag: cell line

tag: cell type

value: Melanoma cells

value: BRAF V600E mutated

value: Doxycycline from day 0 to 7, Palbociclib from day 5 to 7


title: Hippocampus, PN2 replicate 2

value: Hippocampus


title: MA1_4F_1

description: Treated with doxycycline for 7 days


title: leaves, SFZ_P2


title: Crimson DAF105 rep3

source_name: fruit

value: Crimson DAF105

value: peel of fruit


title: KPC Pancreas Tum Veh Rep3

value: Pancreas

value: Tumour


title: FLEP_seq_xrn3

source_name: xrn3 single mutant_seedlings

value: xrn3 single mutant (xrn3-4)

value: 12d old

value: seedlings

value: nuclear RNA


title: Bone Marrow, PN2 replicate 1


title: Crimson DAF105 rep2


title: leaves, SFZ_Mock2

value: leaves

value: SFZ

value: Mock treatment


title: KPC Pancreas Tum Veh Rep4

value: Pdx1Cre KrasG12D/+ P53R172H/+


title: SKMel103_M2_1

description: Treated with doxycycline for 7 days


title: KPC Pancreas Tum Veh Rep1

value: Vehicle


title: Bone Marrow, PN2 replicate 2

value: Bone Marrow

value: WT


title: leaves, SFZ_Mock1


title: SKMel103_4F_3

description: Treated with doxycycline for 7 days


title: leaves, GW_P3

value: GW

value: P.litchii treatment


title: Crimson DAF105 rep1

value: Crimson DAF105


title: A375_4F_2

description: Treated with doxycycline for 7 days

source_name: A375 melanoma cells


title: Crimson DAF75 rep3

value: Crimson DAF75

value: peel of fruit


title: KPC Pancreas Tum Veh Rep2

value: Pancreas

value: Tumour


title: leaves, GW_P2


title: IBRM_IGG_Rep1

description: IGG control

source_name: pancreatic

value: pancreatic

value: pancreatic cells

value: stable cell line expressing dox-inducible BRM


title: A375_4F_1

description: Treated with doxycycline for 7 days


title: KPCf Pancreas Rep6

value: Tissue

value: Pdx1Cre KrasG12D/fl P53R172H/+


title: SKMel103_M2_3

description: Treated with doxycycline for 7 days


title: IBRM_H3K4ME3_Rep1


title: KPCf Pancreas Rep5


title: Crimson DAF75 rep1


title: leaves, SFZ_P3

value: leaves

value: SFZ


title: IBRM_H3K4ME3_Rep2


title: A375_M2_3

description: Treated with doxycycline for 7 days


title: leaves, GW_P1


title: leaves, GW_Mock3

value: Mock treatment


title: Crimson DAF45 rep3

value: Crimson DAF45


title: leaves, GW_Mock2


title: Crimson DAF75 rep2


title: leaves, GW_Mock1


title: Crimson DAF45 rep2


title: IBRM_BRM_Rep2


title: BRGOE_H3K4ME3_Rep2

value: stable cell line expressing BRG1


title: KPCf Pancreas Rep3


title: KPCf Pancreas Rep4


title: IBRM_BRM_Rep1


title: SKMel103_M2_2

description: Treated with doxycycline for 7 days


title: SAM24402082_scRNA-seq_BRM_dox

library_source: transcriptomic single cell

data_processing:
CellRanger v6.1.1 was used for demultiplexing, filtering, barcode counting, and UMI counting. Data produced by Cell Ranger v6.1.1 were imported into Scanpy 1.9.1, and data were filtered based on the following criteria: cells with a minimum of 200 genes expressed, genes detected in at least 3 cells, cells with minimum 1% and maximum 15% total counts from mitochondrial genes, and cells with a range of 1,500 to 9,000 genes with non-zero counts. Lineage barcodes detected using Kallisto bustools were mapped to cell barcodes of the AnnData object, and cells without a lineage barcode assignment were filtered out. Data was filtered for single cells using Scrublet, with an expected doublet rate of 0.06 and threshold of 0.4 (https://github.com/swolock/scrublet). Data was logarithmized and normalized (counts per 1x104). Principal component analysis was then run on the highly variable genes. Data across samples were harmonized using Harmonypy version 0.0.6 (https://github.com/slowkow/harmonypy) before using the top 40 principal components to compute a neighborhood graph. Scores for the S and G2M cell cycle phases were calculated with the score_genes_cell_cycle function from Scanpy using canonical markers and cell cycle phase scores were regressed out. Leiden clustering was performed using Scanpy’s implementation of Leiden community detection with a resolution of 0.5. Cells were scored for gene signatures using Scanpy’s tl.score_genes function.
TraCe-seq lineage barcode readout: Lineage barcodes were recovered from scRNA-seq FASTQ files using kallisto version 0.46.2 (bus command). The custom kallisto index was built from both the human transcriptome (GRCh38 genome, derived from Ensembl 90 annotations) and the list of lineage barcodes from the TraCe-seq plasmid library. The resultant BUS files were sorted with bustools (sort command) and barcodes at a Hamming distance 1 were corrected (bustools correct command). Gene count matrices were generated with bustools (count command). Cells with multiple lineage barcodes expressed were assigned a single barcode if expression of one barcode was threefold higher than other detected barcode(s). A SingleCellExperiment object was created for each sample library, enabling readout of cell barcodes coupled with their lineage barcode assignments. Lineage barcode assignments were imported to Scanpy and mapped to cell barcodes of the AnnData object. Log2 fold change of lineage barcodes were first calculated by adding a pseudocount of 1 to all barcode counts, averaging the counts per lineage barcode across replicates for each sample, then calculating the log2 fold change from baseline.
Assembly: GRCh38
Supplementary files format and content: The tsv and mtx files contains the cell barcode and gene counts.
Supplementary files format and content: The csv file contains lineage barcode information per cell.

molecule: polyA RNA

extract_protocol:
Cultured cells were trypsinized into single cell suspensions, counted using the Vi-CELL XR cell counter (Beckman Coulter) and were then processed using the Chromium Single Cell Gene Expression Reagent Kit v3.1 (10x Genomics, Cat. No. 1000121, Single Index kit) as per the manufacturer’s recommendations.
Library was constructed according to the manufacturer’s instructions (Single Cell Gene Expression Reagent Kit v3.1, 10x Genomics, Cat. No. 1000121, Single Index kit). Libraries were profiled using the Tapestation High Sensitivity DNA kit (Agilent Technologies) and quantified with the Kapa Library Quantification Kit (Kapa Biosystems).

value: 2ug/ml Doxycycline


title: KPCf Pancreas Rep2


title: A375_M2_2

description: Treated with doxycycline for 7 days


title: LTP-C9-shM1-rnc

first: Haining

address: Zhongshan road 2

institute: The first affiliated hospital of sun yat-sen university

data_processing:
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Reads per kilo base per million mapped reads (RPKM) using edegR.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015). The read counts of tRNA are normalized as reads per million (RPM) by the total number of small RNA reads that are matched to tRNAs in each sample.
Assembly: hg38
Supplementary files format and content: RNA-Seq RPKMs
Supplementary files format and content: TRAC-Seq RPMs

source_name: intrahepatic cholangiocarcinoma cell line

growth_protocol: Human ICC cell lines were  cultured in RMPI 1640 medium. LTP-C9 mouse ICC cell line was cultred in DMEM medium. Cells were grown in a 5% CO2 cell culture incubator at 37℃. Mouse ICC tissues was established by hydrodynamic transfection of myrAKT and YAPS127A

extract_protocol:
Total RNA samples were isolated with Trizol following the manufacturer’s instructions. small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit, TruSeq Ribo Profile (Mammalian) Library Prep Kit and the NEBNext® Small RNA Library Prep Set.

treatment_protocol: Mettl1 gene knockdown was mediated by short hairpin RNA. Mettl1 gene knockout was mediated by CRISPR-Cas9 system

value: Mettl1 knockdown

value: RNA-Seq

value: intrahepatic cholangiocarcinoma cell


title: KPCf Pancreas Rep1


title: A375_4F_3

description: Treated with doxycycline for 7 days


title: KPC Pancreas Rep5

value: Pdx1Cre KrasG12D/+ P53R172H/+


title: SAM24402081_scRNA-seq_BRM_nodox

value: untreated


title: SAM24401744_LACZ_Rep3

data_processing:
RNA-Seq reads were first aligned to ribosomal RNA sequences to remove ribosomal reads
remaining reads were aligned to the human reference genome (GRCh38) using GSNAP version 2013-11-1, allowing a maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 —pairmax-rna=200000—clip-overlap)
To quantify gene expression levels, the number of reads mapped to the exons of each RefSeq gene was calculated.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file that include gene counts for each sample

extract_protocol:
cells were trypsinized, washed with 1× PBS, counted and RNA was extracted using Qiagen RNeasy Plus Mini kit (Cat. No. 74034),
For sequencing library generation, the Truseq Stranded mRNA kit (Illumina) was used with an input of 100-1000 nanograms of total RNA. Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 million single-end 50-base pair reads for each sample.

value: stable cell line expressing LACZ


title: Bone Marrow, PN2 replicate 3

value: Bone Marrow

value: WT


title: Crimson DAF45 rep1

value: peel of fruit


title: BRGOE_H3K4ME3_Rep1

data_processing:
The sequencing reads were mapped to the human genome using Bowtie2 (v2.4.1)
ENCODE blacklisted regions were removed from the alignment files using the data downloaded from Dr. Kundaje’s lab.
The files were then sorted using Samtools (v1.9) and PCR duplicates were removed using Picard Tools (v2.23.9).
Peak calling was done using MACS2 (v2.2.7.1) with p<1e-3 as cutoff.
Assembly: GRCh38
Supplementary files format and content: narrowPeak
Library strategy: Cut and Run

extract_protocol:
Cut & Run was performed using the CUTANA ChIC/Cut&Run Kit (Epicypher, Cat. No. 14-1048) exactly as per manufacturer’s recommendations with 0.5X106 cells per condition. Additional modifications made were mild crosslinking of cells as recommended for the BRM antibody (Epichypher Cat No. 13-2006).
Libraries were constructed using NEB Ultra II DNA Library Prep Kit (NEB, Cat. No. E7465) with PCR parameters for index PCR and library amplification based on recommendations from the Epicycpher Cut&Run kit. Quality of libraries was assessed with a Tapestation high sensitivity DNA kit (Agilent Technologies) before submitting for sequencing.

value: pancreatic

value: pancreatic cells


title: LTP-C9-shM1-input


title: MA1_M2_1

description: Treated with doxycycline for 7 days


title: SAM24401743_LACZ_Rep2


title: SAM24403646 _TM_Rep1

data_processing:
ATAC-seq reads were analyzed using the ENCODE ATAC-seq pipeline v1.8
Reads were trimmed of adapters by cutadapt (version 1.9.1) and mapped to hg38 by Bowtie2 (version 2.2.6).
Bam files were converted to tagAlign format, which was then adjusted for Tn5 by shifting +4 bp for positive strand and by −5bp for negative strand.
TagAlign files were used to call peaks using MACS2 (version 2.1.0). Peaks with p<1e-6 were retained for differential analysis.
Assembly: GRCh38
Supplementary files format and content: narrowPeak

extract_protocol:
cells were trypsinized, washed with 1× PBS, counted and processed for library prep
About 100,000 cells were then lysed for 5 minutes on ice in 100 mL of Lysis buffer (10 mM Tris, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20 and 0.01% digitonin). 1 ml of wash buffer (10 mM Tris, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) was then added and the pellets were spun down at 500 g for 10 minutes at 4 °C. The supernatant was discarded, and the pellet was resuspended in 50 mL of tagmentation buffer (25 µL 2× TD buffer, 16.5 mL PBS, 0.5 mL 10% tween 20, 0.5 mL of 1% Digitonin, 2.5 µL Tn5 transposase and 5 mL H2O). The tubes were incubated at 37 °C for 30 minutes, followed by DNA isolation using the Qiagen MinElute Cleanup Kit (Cat. No. 28206). The DNA was then amplified using NEBNext 2× PCR Master mix (Cat. No. M0541L) and analyzed by Tapestation High Sensitivity DNA kit (Agilent Technologies) before submitting for sequencing.

value: stable cell line expressing TM BRG1


title: KPC Pancreas Rep4

value: Pancreas

value: Tissue


title: LTP-C9-shNC-rnc

value: wild type


title: SAM24403644 _KR_Rep2

value: stable cell line expressing KR BRG1


title: SAM24401742_LACZ_Rep1


title: KPC Pancreas Rep3


title: SAM24403647 _TM_Rep2


title: A375_M2_1

description: Treated with doxycycline for 7 days


title: KPC Pancreas Rep2


title: LTP-C9-shNC-input


title: SAM24403641 _KR_Rep1


title: SAM24403645_LACZ_Rep2


title: SAM24401741_KR_Rep3


title: SAM24401740_KR_Rep2


title: KPC Pancreas Rep1


title: KPCf Pancreas AZD6244 Rep5

value: Pdx1Cre KrasG12D/fl P53R172H/+


title: SAM24401739_KR_Rep1


title: SAM24403642_LACZ_Rep1


title: KPCf Pancreas AZD6244 Rep4


title: SAM24401738_TM_Rep3


title: 24h-KO-2

city: Shanghai

first: Hongyi

last: Tang

address: Chongqing Nan Road 280

department: Department of Biochemistry and Molecular Cell Biology

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Processed reads were aligned to the mouse reference genome (GRCm38.p6) using HISAT2, and raw counts were generated with HTSeq-count.
FPKM values for each sample were calculated using StringTie.
Assembly: GRCm38
Supplementary files format and content: text file of gene counts
Supplementary files format and content: excel file of gene TPM values

source_name: Liver

extract_protocol:
RNA was harvested using Trizol reagent and the Qiagen miRNeasy Mini kit. 500ng total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using Illumina’s NEBNext Ultra II RNA Library Prep Kit (following standard protocols, E7775S)

treatment_protocol: WT and Orm2 KO mice were injected with APAP or PBS, and liver tissues were collected 24 hours later for RNA extraction.

value: Liver

value: Mouse liver cells

value: Orm2 knockout

value: Acetaminophen injection


title: 24h-KO-1


title: KPCf Pancreas AZD6244 Rep3


title: SAM24401737_TM_Rep2


title: SAM24403643 _WT_Rep2

value: stable cell line expressing WT BRG1


title: SAM24403640_WT_Rep1


title: 0h-KO-2

value: PBS injection


title: 24h-WT-1


title: SAM24401736_TM_Rep1


title: SAM24410229_siBRM_Rep2

value: transfected with siBRM


title: 0h-KO-1


title: KPCf Pancreas AZD6244 Rep2


title: SAM24401735_WT_Rep3


title: KPCf Pancreas AZD6244 Rep1


title: SAM24410228_siBRM_Rep1


title: 0h-WT-2

value: WT


title: SAM24401734_WT_Rep2


title: SAM24410227_siNT_Rep2

value: transfected with siNT


title: 0h-WT-1


title: KPCf Pancreas Veh Rep4

value: Vehicle


title: KPCf Pancreas Veh Rep5


title: SAM24401733_WT_Rep1

value: pancreatic

value: pancreatic cells


title: SAM24410226_siNT_Rep1


title: Replicate 4, dDAVP alone

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

data_processing:
RNA-seq raw sequencing reads were aligned by STAR to the mouse Ensembl genome (release 106). Transcript per million (TPM) and expected counts were generated by RSEM. All samples are of high percentage of uniquely mapped reads (> 80%) and are included for downstream analysis. Unless otherwise specified, the computational analyses were performed on the National Institutes of Health Biowulf High-Performance Computing platform
Assembly: Ensemble release 106
Supplementary files format and content: excel file include counts and TPM values for each sample

source_name: Kidney

extract_protocol:
RNA was extracted using Direct-zol RNA MicroPrep kit
Trizol-extracted RNA was proceeded to cDNA generation using the SMARTer V4 Ultra Low RNA Kit (Takara Bio).cDNA was generated with 8 PCR cycles. 1 ng of the resulting cDNA was “tagmented” and barcoded by using the Nextera XT DNA Sample Preparation Kit (Illumina) to generate sequencing libraries for high throughput sequencing. Libraries were purified by AmPure XP magnetic beads (Beckman Coulter), and quantified using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). An equal amount of index libraries were pooled and sequenced (paired-end 50 bp) on an Illumina platform.

value: Kidney

value: mpkCCD

value: dDAVP alone


title: 24h-WT-2


title: RNC-RBE-KO1

value: Mettl1 knockout

value: RNA-Seq

value: RBE

value: intrahepatic cholangiocarcinoma cell


title: Replicate 3, dDAVP alone


title: RNC-RBE-NC1

value: wild type


title: KPCf Pancreas Veh Rep2

value: Pancreas

value: Tissue

value: Pdx1Cre KrasG12D/fl P53R172H/+


title: SAM24399622_BRM_NoDox_Rep2

data_processing:
The sequencing reads were mapped to the human genome using Bowtie2 (v2.4.1)
ENCODE blacklisted regions were removed from the alignment files using the data downloaded from Dr. Kundaje’s lab.
The files were then sorted using Samtools (v1.9) and PCR duplicates were removed using Picard Tools (v2.23.9).
Peak calling  was done using MACS2 (v2.2.7.1). The resulting peaks were filtered for blacklisted regions using bedtools (v2.29.2). The MACS2 peaks with p<1e-5 were used for further comparative analysis
Assembly: GRCh38
Supplementary files format and content: narrowPeak
Library strategy: CUT&RUN

value: stable cell line expressing dox-inducible BRM

value: untreated


title: SAM24399625_BRM_Dox_Rep2

value: 2ug/ml Doxycycline


title: SAM24399616_BRM_NoDox_Rep1


title: Replicate 2, dDAVP alone


title: KPCf Pancreas Veh Rep1

value: Vehicle


title: Replicate 1, dDAVP alone


title: SAM24399619_BRM_Dox_Rep1

value: pancreatic


title: Input-RBE-NC1


title: KPCf Pancreas Veh Rep3


title: Alkb and NaBH4-Treated-mouseICC-TRACseq

data_processing:
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Reads per kilo base per million mapped reads (RPKM) using edegR.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015). The read counts of tRNA are normalized as reads per million (RPM) by the total number of small RNA reads that are matched to tRNAs in each sample.
Assembly: hg38
Supplementary files format and content: RNA-Seq RPKMs
Supplementary files format and content: TRAC-Seq RPMs
Library strategy: TRAC-Seq

source_name: intrahepatic cholangiocarcinoma tissue

value: small RNA-TRAC-Seq

value: intrahepatic cholangiocarcinoma tissue


title: Replicate 4, Tolvaptan plus dDAVP

value: Kidney

value: mpkCCD

value: Tolvaptan plus dDAVP


title: RNC-CT1-KO

value: Mettl1 knockout

value: RNA-Seq


title: Input-RBE-KO1

value: RBE

value: intrahepatic cholangiocarcinoma cell


title: Replicate 3, Tolvaptan plus dDAVP


title: colon epithelial cells, 3CK, scRNA-seq

first: Kazuo

last: Takayama

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: refdata-gex-GRCh38-2020-A (July 7,2020)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colon organoids

growth_protocol: The iPS cell line, 1383D6 (provided by Dr. Masato Nakagawa, Kyoto University), was maintained on 0.5 μg/cm2 recombinant human laminin 511 E8 fragments (iMatrix-511, Cat# 892 012, Nippi) with StemFit AK02N medium (Cat# RCAK02N, Ajinomoto) containing 10 μM Y-27632 (Cat# 034-24024, FUJIFILM Wako Pure Chemical). To passage the cells, human iPS cell colonies were treated with TrypLE Select Enzyme (Cat# 12563029, Thermo Fisher Scientific) for 10 min at 37°C. After centrifugation, cells were seeded on Matrigel® Growth Factor Reduced Basement Membrane (Cat# 354230, Corning)-coated cell culture plates (2.0×105 cells/4 cm2) and cultured for 2 days. From day 0 to 3, human iPS cells were treated with 100 ng/mL Activin A (Cat# 338-AC-01M, R&D Systems) and 10 μM Y-27632 in 1:1 mixture of advanced DMEM/F12 (Cat# 12634-010, Gibco) and D-MEM(High Glucose) (Cat# 044-29765, FUJIFILM Wako Pure Chemical) supplemented with 2 % Corning® Fetal Bovine Serum (Cat# 35-010-CV, Corning), 2 % B-27 Supplement Minus Vitamin A (Cat# 12587001, Thermo Fisher Scientific), 1 % MEM Non-Essential Amino Acids Solution (Cat# 11140050, Gibco), 1 % N2 Supplement with Transferrin (Holo) (Cat# 141-08941, FUJIFILM Wako Pure Chemical), 1× GlutaMAX (Cat# 35050-079, Thermo Fisher Scientific), and 1× penicillin-streptomycin (Cat# 26239-42, Cat# 32204-92, Nacalai Tesque). From day 3 to 7, the cells were treated with 100 ng/mL FGF2 (Cat# 160-0010-3, Katayama Chemical Industries) in advanced DMEM/F12 supplemented with 2 % Corning® Fetal Bovine Serum, 1× GlutaMAX, and 1× penicillin-streptomycin. In order to generate organoids, the cells were embedded in Matrigel Growth Factor Reduced Basement Membrane (Cat# 354230, Corning). For colonic differentiation, the cells were treated with 20 ng/mL EGF (Cat# AF-100-15, PeproTech), 30 µM Forskolin (Cat# 063-02193, FUJIFILM Wako Pure Chemical), 20 µM PD98059 (Cat# S1177, Selleck Chemicals), 5 µM 5-Aza-2'-Deoxycytidine (Cat# 018-20941, FUJIFILM Wako Pure Chemical), and 0.5 μM A-83-01 (Cat# 035-24113, FUJIFILM Wako Pure Chemical) in advanced DMEM/F12 supplemented with 2 % Corning® Fetal Bovine Serum, 1× GlutaMAX, 1 % MEM Non-Essential Amino Acids Solution, 2 % B-27 Supplement Minus Vitamin A, 1 % N2 Supplement with Transferrin (Holo), and 1× penicillin-streptomycin for 6 days. Then, organoids were dissociated into clumps and plated on Matrigel Growth Factor Reduced Basement Membrane-coated multi-well plates. In order to promote colonic maturation, the cells were treated with Wnt3a-conditioned medium, 50 ng/mL Noggin (Cat# 120-10C, PeproTech), 100 ng/mL R-spondin 1 (Cat# 120-38, PeproTech), 10 ng/mL Gastrin (Cat# 3006/1, Tocris Bioscience), 20 ng/mL EGF, 20 ng/mL FGF2, 10 ng/mL IGF1 (Cat# 100-11, PeproTech), 1 µM A83-01, and 10 µM Y27632 in advanced DMEM/F12 supplemented with 2 % Corning® Fetal Bovine Serum, 1× GlutaMAX, and 1× penicillin-streptomycin for 8 days. Finally, the cells were treated with 20 ng/mL EGF, 20 ng/mL FGF2, 10 ng/mL FGF7 (Cat# AF-100-19, PeproTech), 1 µM A83-01, and 10 µM Y27632 in advanced DMEM/F12 supplemented with 2 % Corning® Fetal Bovine Serum, 1× GlutaMAX, and 1× penicillin-streptomycin for 4 days.

extract_protocol:
Human iPS cell-derived colon organoids treated with or without 3CK were dissociated and the cell concentration was adjusted to 1,000 cells/μL.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Breifly, each single-cell suspension containing approximately 8300 cells was loaded onto a 10xGenomics chromium chip G to generate GEMS. The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added (Dual Index Kit TT Set A).

treatment_protocol: HiPSC-COs were treated with TNF-α (Cat# 300-01A, PeproTech), IFN-γ (Cat# 300-02, PeproTech), and IL-1β (Cat# 200-01B, PeproTech) for 8 days.

value: Colon organoids

value: human iPS cell-derivatives


title: RNC-CT1-NC

value: wild type


title: Replicate 2, Tolvaptan plus dDAVP


title: Tg(elavl3:eGFP), Tg(nbt:DsRed)

city: New York

first: Caghan

last: Kizil

department: Neurology & TAUB Institute

institute: Columbia University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/metrics)
The fastq files were aligned to zebrafish genome (GRCz11) and (ensemble transcripts from Ensembl Release 105) by using STAR. The BAM files were as input for Cell Ranger (10X genomics) to generate processed data files that include gene names (row names) and cell names (column names) and counts. Further analysis done by using Seurat package in R.
Assembly: GRCz11
Supplementary files format and content: filtered_bc_matrix outputs from Cell Ranger

organism: Danio rerio

source_name: atrium

growth_protocol: Zebrafish were kept in the re-circulating system on a 14/10-h light/dark cycle, pH7.5, at 28°C (±1°C) in groups of 20 animals per 2.8L.

extract_protocol:
Cells from zebrafish heart were dissociated. In addition to GFP and DsRed in the genome of the fish, viability indicator dyes Sytox Blue (Invitrogen, Cat No. S34857) and Dycle Ruby (Invitrogen, Cat. No. V10309) were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol.
10X genomics

value: atrium

value: Tg(elavl3:eGFP), Tg(nbt:DsRed)


title: BS_seq_xrn3

data_processing:
For each library, adapters were trimmed by using fastp v0.20 and reads were mapped to Arabidopsis TAIR10 genome using BSMAP. The DMA methylation level in each 100 bp bin was calculated as the ratio of methylated cytosines to the total number of cytosines (#C/(#C+#T)).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include methylation ratios from BSMAPz mapping result.

extract_protocol:
Genomic DNA was extracted from 12-day-old seedlings of wildtype and xrn3 mutant using Hi-DNAsecure Plant Kit (TIANGEN, Cat. DP350-02).
Genomic DNA was fragmented by sonication. Then, DNA-end repair, 3’-dA overhang and ligation of methylated sequencing adaptors were performed. The bisulfite conversion was treated by using EZ DNA Methylation-Gold kit (Zymo Research).

value: xrn3 single mutant

value: 12d old

value: seedlings


title: colon epithelial cells, CNT, scRNA-seq

description: 10x Genomics

value: CNT


title: Tg(elavl3:eGFP)

description: 10x Genomics

source_name: whole heart

value: whole heart


title: Replicate 1, Tolvaptan plus dDAVP

value: Kidney


title: Input-CT1-NC


title: BS_seq_WT

value: wild-type