title: A375 5 uM A-485, 24 h R1 [A2]


title: Dome H4K16ac rep 2

status: Public on Aug 26 2024

type: SRA

city: Pittsburgh

first: Miler

middle: T

last: Lee

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

country: USA

institute: University of Pittsburgh

library_source: genomic

data_processing:
Paired-end reads were mapped to the GRCz11 zebrafish genome assembly using bowtie2 v2.4.2 (Langmead and Salzberg, 2012) (--no-mixed --no-discordant). High-quality alignments (MAPQ ≥ 30) were retained, after additional filtering to also exclude reads mapping chrM, or to satellite DNA or rRNA as annotated by RepeatMasker.
For bigWigs, only mononucleosome sized fragments (140-250 bp) were retained. Each read pair was joined end-to-end then tag-centered to 73 bp. BigWigs normalized to total number of mononucleosome fragments per million were made using bedtools v2.30.0 genomecov and wigToBigWig. For triptolide and DMSO treatments, coverage was normalized to total yeast aligned reads per million
Assembly: Zebrafish GRCz11
Supplementary files format and content: bigWig files of mononucleosome coverage pooled across replicates. Fragment per million normalized; or yeast spike-in normalized (labeled with "spikein")
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Danio rerio

source_name: Whole embryos

extract_protocol:
The CUT&RUN procedure was adapted from Hainer et al (Hainer and Fazzio, 2019), which incorporates optimizations of the method of Skene and Henikoff (Skene and Henikoff, 2017). Embryos were subjected to either mechanical yolk separation or chemical yolk lysis. For chemical yolk lysis, embryos were transferred to 1.5 mL Eppendorf tubes removing excess liquid with a P200 pipettor, then yolk lysis buffer added (55 mM NaCl,1.8 mM KCl, 1.25 mM NaHCO3). Tubes were shaken at 1100 RPM for 5’ at room temperature (Eppendorf ThermoMixer C), centrifuged at 300xg for 30s to pellet, yolk lysis buffer drawn off, and 1 mL Yolk Lysis Wash Buffer was added (110 mM NaCl, 3.5 mM KCl, 2.7 mM CaCl2, 10 mM Tris pH 8.5). Tubes were shaken at 1100g for 2 minutes at room temperature, centrifuged at 300g to pellet, and supernatant was again removed and replaced with Nuclear Extraction Buffer (20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 500 µM spermidine, 0.1% Triton X-100, 20% glycerol). For manually de-yolking, yolks were pinched off using Dumont #5 forceps in Ca-free Ringer’s Solution (116 mM NaCl, 2.9 mM KCl, 5 mM HEPES, ph 7.2). Deyolked embryonic cells were transferred via Pasteur pipette into Nuclear Extraction Buffer taking care to transfer as little liquid as possible, mixed with gentle pipetting with a P200 pipettor, and then centrifuged at 600xg at 4ºC for 3 min. The free nuclei were then bound to 150 µL of activated concanavalin A beads (Polysciences #86057) at RT for 10mins. Nuclei were blocked for 5 min (5 mL Wash Buffer with 2 mM EDTA) at RT then incubated in 1:100 dilution of primary antibody for 2 hr at 4ºC, washed with Wash Buffer, incubated in a 1:200 dilution of pAG-MNase (gift from Sarah Hainer) for 1 hr at 4ºC, and washed again with Wash Buffer. The bound pAG-MNase was activated with 2 mM CaCl2 and allowed to digest for 30 mins at 0ºC, then stopped using 2x STOP buffer (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 µg/mL RNase A, 40 µg/mL glycogen). Yeast mononucleosomes were added to 2x STOP buffer at 10 pg/mL (untreated samples) or 20 pg/mL (triptolide/dmso samples) as a spike-in. Nuclei were incubated at 37ºC for 20 min followed by centrifuging for 5 min at 16,000xg, drawing off the DNA fragments with the supernatant. The extracted fragments were treated with SDS and proteinase K at 70ºC for 10 min followed by phenol chloroform extraction. Purified DNA was resuspended in 50 µL of water and verified by Qubit dsDNA high sensitivity and Fragment Analyzer.
CUT&RUN libraries were constructed using the NEB Ultra II DNA library prep kit (NEB #E7645) according to manufacturer’s protocol. DNA was end repaired and then ligated to sequencing adaptors diluted 1:100. Ligated DNA was purified with 0.9x AmpureXP beads and PCR amplified for 15 cycles, then purified again with 0.9x AmpureXP beads. Libraries were run on a 1.5% TBE agarose gel, and a band corresponding to 175 - 650 bp was cut out and gel purified using the NEB Monarch DNA gel extraction kit (#T1020). Concentration was verified by Qubit dsDNA high sensitivity and Fragment Analyzer.

treatment_protocol: For Triptolide experiments, embryos were bathed in blue water (0.06 g/L Instant Ocean + methylene blue 0.1% w/v) with 2uM final Triptolide made from 4mM stock in DMSO. Control DMSO embryos were bathed in 0.05% DMSO final.

tag: tissue

value: Whole embryos

tag: strain

value: TUAB

tag: genotype

value: WT

tag: developmental stage

value: dome

tag: antibody

value: Millipore #37707329


title: patient 1

city: Buffalo

first: Jianxin

last: Wang

state: NY

address: 665 Elm Street

department: Molecular and Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

description: archival colorectal cancer tissue

library_source: transcriptomic

data_processing:
Raws fastq files are processed with nf-core/rnaseq: 3.13.2 pipeline under Nexflow 23.10.1.
Assembly: GRCh38
Supplementary files format and content: comma separated text file

molecule: total RNA

organism: Homo sapiens

source_name: colorectal

extract_protocol:
SureSelect XT HS2 RNA Target Enrichment System (Agilent Inc)
200ng of RNA was fragmented and converted to cDNA followed by end repair, duplex UMI adaptor ligation, and 11 cycles of PCR to complete the dual- index adapters. Unique dual-indexed, molecular-barcoded libraries were purified with AMPureXP beads (Beckman Coulter) and validated for appropriate size (225-275bp) on a Tapestation 4200 DNA1000 screentape (Agilent Inc.). 200ng of purified library was then hybridized to the SureSelectXT Human All Exon V8+UTR Capture library (Agilent Inc.). The hybridized regions were then bound to streptavidin magnetic beads and washed to remove any non-specific bound products. Eluted library underwent a second 13 cycle PCR amplification to generate enough material for sequencing. Final libraries were purified, measured by Tapestation 4200 DNA1000 screentape (250-350bp), and quantitated using KAPA qPCR (KAPA Biosystems). Individual libraries were pooled in equimolar 2nM final concentration. Each pool is denatured and diluted to 200pM with 1% PhiX control library added. The resulting pool is then loaded into the appropriate NovaSeq Reagent cartridge, as determined by the number of sequencing cycles desired, and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).

value: colorectal


title: A375 DMSO R1 [A1]

city: Boston

first: Marianne

last: Collard

state: MA

address: 609 Albany Street, Department of Dermatology, 5th Floor, J508

department: Dermatology

institute: Boston University

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: Text files include raw counts for each sample

molecule: polyA RNA

source_name: tumor

growth_protocol: cell lines were cultured in Dulbecco’s Modified Eagle Medium (Gibco, ThermoFisher Scientific, Grand Island, NY, USA) supplemented with 10% bovine calf serum (Gibco, ThermoFisher Scientific, Grand Island, NY, USA), 1% penicillin/streptomycin (Gibco, ThermoFisher Scientific, Grand Island, NY, USA), and 2mM L-glutamine

extract_protocol:
RNA was then extracted using the RNeasy (Qiagen, Germantown, MD, USA) kit according to manufacturer instructions.
Library prepartion was done by Azenta Life Science LLC: RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: Cells were treated with 1:2000 DMSO or 5 uM A-485

value: tumor

tag: cell line

tag: cell type

value: melanoma

tag: treatment

value: DMSO control


title: WT, id 10, treated

city: Milano

first: Stefano

last: de Pretis

address: Via Olgettina, 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Institute

data_processing:
FASTQ sequencing reads were adaptor-trimmed and quality-filtered with Trimmomatic (Bolger et al., 2014)
Filtered reads were mapped to the mm10 mouse reference genome (https://www.gencodegenes.org/mouse/) with STAR (Dobin & Gingeras, 2016).
Gene counts were obtained using featureCounts (Liao et al., 2014).
Normalization and differential gene expression analysis (DEG) have been performed with DESeq2 (Love et al., 2014).
KO vs. WT DGE analysis was adjusted for cell culture and evaluated both in treated and untreated samples (“~cell_culture + genotype*treatment”). Treatment effect was evaluated independently for WT and KO samples and adjusted for the donor mouse (“mouse_id + treatment”).
Assembly: mm10
Supplementary files format and content: tab delimited text files including raw counts for each sample

organism: Mus musculus

source_name: Primary cortical neurons

growth_protocol: Primary cortical neurons were prepared from WT and Mecp2 KO male embryos at embryonic day 15.5 (E15.5). The pregnant dam was sacrificed, the embryos collected and sacrificed by decapitation. A tail biopsy was taken from each embryo to perform genotyping and sex determination. Brains were exposed, meninges removed and the cerebral cortex from both hemispheres was rapidly dissected and kept in ice-cold Hank's Buffered Salt Solution (HBSS; ThermoFisher, 14175095), a single embryo per tube. Tissues were washed in HBSS, incubated with 0.25% trypsin/EDTA (ThermoFisher, 25200056) for 10 min at 37°C, washed in HBSS and mechanically dissociated in Neurobasal Plus medium (ThermoFisher, A3582901) supplemented with 2% B-27TM Plus (ThermoFisher, A3582801), 2mM GlutaMAX-I (ThermoFisher, 35050038) and 1% Pen/Strep (Sigma-Aldrich, P0781). Neurons were plated in the same medium on plasticware coated with 0.01 mg/ml poly-D-lysine hydrobromide (Sigma-Aldrich, P7886), at a density of 300.000 cells/well in 6-well plates or 1.5 million cells/dish in 6-cm dishes. For immunofluorescence experiments, neurons were plated on 13-mm or 24-mm poly-D-lysine-coated (0.1 mg/ml) glass coverslips, at a density of 25.000 or 60.000 cells/coverslip.

extract_protocol:
After a rapid wash in PBS (Sigma D8537) to remove cellular debris, total RNA was extracted fromprimary cortical neurons using PureZOL (BioRad 7326890). In details, 0.3 mL of PureZOL (12wells plate) was added on cell culture and left 5 min at room temperature to allow the completedissociation of nucleoprotein complexes. 200L of chloroform was then added for 1 ml of PureZOLaccording to the manufacturer’s protocol. Following, samples were inverted for 15-20 seconds togently mix the phenol:chloroform mixture and incubated 3 min at RT. After centrifugation at12000g for 15 min at 4°C, the upper aqueous phase was transferred into RNAse free tube andprecipitated with 10 ug of RNA-grade glycogen and 100% isopropanol 1:2. Samples were storedo.n. at -20°C. The day after, the RNA was centrifuged at 12,000g for 10 min at 4°C and pellets werethen washed in 500ul of 70% ethanol (7,500 x g for 5 min at 4°C). To remove genomic DNA,sample pellets were treated with DNAse (Sigma-Aldrich, AMPD1) at 37°C for 15 min. A secondpurification with PureZOL was executed on RNAs and their pellets were finally resuspended in 10uL of RNAse-free H2O.
Total RNA was extracted from eight WT and eight KO cortical neurons (14 DIV) treated with trehalose and eight WT and eight KO untreated controls as described above for a total of 32 samples. Only high-quality RNA with an RNA Integrity Number (RIN) of 8 or higher was used. Library preparation and sequencing have been performed with TruSeq RNA Library Preparation Kit v2 (Illumina) by Genewiz. One WT untreated and corresponding treated sample and two KO untreated and related treated samples were found outliers and removed from the dataset.

treatment_protocol: Neurons were treated at 12 DIV with 25 mM trehalose (Sigma-Aldrich, T9531) in cell medium. After 48 hours of treatment, at 14 DIV, neurons were quickly washed in PBS and either lysed in hot SDS lysis buffer (50 mM Tris HCl pH 8, 10 mM EDTA, 1% SDS supplemented with 1:200 protease inhibitor cocktail [Sigma-Aldrich, P8340]) for western blotting, or scraped in -20°C-cold methanol for lipidomics, or fixed in the appropriate fixing solution for immunocytochemistry or electron microscopy experiments. Neurons were treated at 13 DIV neurons with 20 uM Leupeptin (Sigma- Aldrich, L2884) in cell medium. After 24 hours of treatment, at 14 DIV, neurons were lysed in hot SDS lysis buffer. Human fibroblasts at 70–80% confluency were treated with 25 mM trehalose for 48 hours, and cells were lysed in hot SDS lysis buffer. In vivo treatment was performed by intraperitoneal injection of 2g/kg of trehalose (Sigma-Aldrich, T9531) resuspended in sterile saline solution, every other day from postnatal day P18 to P40. Control mice were injected with the same volume of sterile saline solution. At the end of the treatment, mice were sacrificed. Cortices were collected, frozen in dry ice and stored at -80°C for subsequent lysis in SDS lysis buffer.

value: Primary cortical neurons

value: trehalose


title: WT, id 11_8, treated


title: Sample 21_d4_iMPC_S3 [scRNA-seq]

first: Yonglin

last: Zhu

address: 300 Longwood Ave

department: Cardiac Surgery

institute: Boston Children's Hospital

library_source: transcriptomic single cell

data_processing:
For bulk RNA-seq, raw reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file.
For scRNA-seq, the demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: tab-delimited text files include count values for all samples (bulk RNA-seq)
Supplementary files format and content: tab-delimited text files include count matrix for all samples (scRNA-seq)

source_name: Cell line

extract_protocol:
For bulk RNA-seq, total RNA was extracted from fresh frozen cell pellet samples using Qiasymphony RNA kit following manufacturer’s instructions (Qiagen, Hilden, Germany). For scRNA-seq, single-cell RNA samples were prepared using the Chromium Next 10X genomics kits (10xgenomics, PN-1000128, PN-1000127) following the manufacture's protocols.
For bulk RNA-seq, RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using the manufacturer’s instructions (NEB, Ipswich, MA, USA). For scRNA-seq, RNA sequencing libraries were prepared using the dual index kit (10xgenomics, PN-100021310x following the manufacturer's protocols.

value: Cell line

value: mixed cell population


title: 22Rv1, ZM11-kd2, rep2

city: shanghai

first: cheng

last: Lian

address: dongan road 131

country: China

institute: Fudan university

data_processing:
QC reports were generated from FastQC (version: 0.11.9)
Following quality assessment, Low-quality reads were trimmed and adapters were removed with AdapterRemoval (version: 2.3.2)
Cleaned data were then aligned to the reference genome (hg38) using STAR (version: 2.7.9a)
Reads for genes were counted from the sorted BAM file using htseq-count (version: 0.13.5)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: prostate

growth_protocol: 22Rv1 cells were maintained in RPMI1640 (Invitrogen)  with 10% fetal bovine serum (FBS, Giboc) and 1% penicillin-streptomycin (BI) to provide necessary nutrients and prevent bacterial contamination.Cells were kept at a constant temperature of 37°C in a 5% CO2 incubator.

extract_protocol:
The base medium was enriched with 10% fetal bovine serum (FBS, Giboc) and 1% penicillin-streptomycin (BI) to provide necessary nutrients and prevent bacterial contamination.
Total RNA from each sample was extracted using various kits such as TRIzol Reagent (Invitrogen), RNeasy Mini Kit (Qiagen)

treatment_protocol: No treatment

value: prostate

value: human prostate carcinoma cell

value: ZMYND11 knockdown

tag: group


title: WT, id 17


title: Dome H4K16ac rep 1


title: WT, id 10


title: Dome H3K64ac rep 1

value: Abcam #ab214808


title: Mecp2-KO, id 8, treated

value: Mecp2 knock-out


title: Dome H3K64ac rep 2

value: Whole embryos

value: TUAB


title: 22Rv1, ZM11-kd1, rep2


title: Sample 19_d11_iMCPosEC_S4 [scRNA-seq]


title: 22Rv1, ZM11-kd2, rep1


title: Sample 20_d2_meso_S2 [scRNA-seq]


title: Mecp2-KO, id 8


title: Dome H3K56ac

value: WT

value: dome

value: Invitrogen #PA5-40101


title: Sample 22_iPSPosECFC_S1 [scRNA-seq]


title: Sample 18_iSMC-rep3

value: smooth muscle cell


title: 22Rv1, ZM11-kd1, rep1


title: Dome H3K27ac rep 4

value: Abcam #ab4729


title: 22Rv1, control, rep2

value: control


title: Sample 17_iSMC-rep2


title: Dome H3K122ac

value: Abcam #ab33309


title: Sample 16_iSMC-rep1


title: Dome H3K27ac rep 3


title: 22Rv1, control, rep1


title: Mecp2-KO, id 3_8, treated

value: Primary cortical neurons

value: trehalose


title: Dome H3K27ac rep 2


title: Mecp2-KO, id 4


title: Sample 15_iMPC-NKX3-1rep3

value: Cell line

value: mural progenitor cell


title: Sample 14_iMPC-NKX3-1rep2


title: Mecp2-KO, id 3_8


title: Sample 13_iMPC-NKX3-1rep1


title: Dome H3K9ac rep 2

value: Cell Signaling #9649


title: Dome H3K27ac rep 1


title: A375-Parental-ITGB4pos-BottomR5-R1

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 309 Mossman Bldg. 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee

description: Arima-HiC+ Kit (Mammalian Cell Lines A160134v01)

data_processing:
Sequenced reads were mapped to the hg19 genome using bowtie2
Mapping, filtering, iterative correction, and binning were performed using the Hi-C pro pipeline available at: https://github.com/nservant/HiC-Pro
Assembly: hg19
Supplementary files format and content: Each .tar.gz file contains the iteratively corrected and raw matrix.gz files for 20 kb, 40 kb, 100 kb, 250 kb, 1 Mb, and 2.5 Mb in their respective directories. Bin size indicated as “C-40000” for example. All matrices are for individual chromosomes except for the 1 Mb and 2.5 Mb bin size

source_name: Melanoma (A375)

growth_protocol: A375 cells were obtained from ATCC (CRL‐1619). Cells were verified to be negative for mycoplasma and were grown using complete DMEM medium (Corning-10‐013‐CV; 10% FBS, 1% Pen‐Strep, 1% L‐Glutamine) at 37°C supplied with 5% CO2.

extract_protocol:
The first biological replicate of ITGB4 sorted cells was processed with the protocol described in (Golloshi et al., 2018). Briefly, 10 million cells were crosslinked with 1% formaldehyde for 10 min. Crosslinked cells were then suspended in lysis buffer to permeabilize the cell membrane and were dounce homogenized. Chromatin was then digested in-nucleus overnight using the DpnII restriction enzyme. Digested ends were filled in with biotin-dATP, and the blunt ends of interacting fragments were ligated together. DNA was then purified by phenol-chloroform extraction. For library preparation, the NEBNext Ultra II DNA Library prep kit (NEB) was used for libraries with size ranges from 200-400bp. End Prep, Adaptor Ligation, and PCR amplification reactions were carried out on bead-bound DNA libraries.  All other Hi-C experiments were performed using the Arima‐HiC+ Kit from Arima Genomics following the protocol for Mammalian Cell Lines (A160134 v01) and preparing the libraries using Arima recommendations for the NEBNext Ultra II DNA library prep kit (protocol version A16041v01).
Biotinylated DNA was pulled down using streptavidin coated magnetic beads and prepared for multiplex sequencing on an Illumina platform using the NEBNext Ultra II kit (NEB). All end preparation, adaptor ligation, and PCR amplification steps were carried out on bead bound DNA libraries.

treatment_protocol: Transwell filters with 5μm pore sizes (VWR‐10769‐236) were used. Briefly, the bottom of each filter was coated with 40μl of 10 μg/ml fibronectin for ~30 min. 24‐well plates were prepared for Transwell migration assay by adding 500 μl of 1× DMEM (Corning) with full supplements per well. A375 cells were detached from culture dishes at 80–90% confluency and aliquoted to 100,000 cells per 100μl of unsupplemented 1×DMEM. Each Transwell was placed into its corresponding well of the 24‐well plates, and 100μl of the cell suspension was added to the top of each filter. Cells were incubated at 37°C, 5% CO2 and allowed to migrate for 24hr. For sequential rounds of migration, the migrated cells were seeded into a new well of a 24‐well plate to expand. When cells reached 80–90% confluency, another Transwell migration was performed as previously described. Only the bottom cells were collected and continued to be used for sequential rounds of migration.  For FACS experiments, cells were sorted by either a FACS Aria cell sorter (Hi-C replicate 1 for ITGB4(+) and ITGB4(-) cells, and some initial 5um migration experiments) or a Sony MA900 cell sorter (All other experiments). Cells were harvested using trypsin (T25, 6-well, 24-well) and spun at 1000rpm for 5 minutes. Supernatant was removed and cells were resuspended in 400uL of PBS containing 10% FBS and 1.25ug of Abcam FITC Anti-ITGB4 (ab22486). Cells were incubated on ice for 30 minutes then diluted with 350uL of PBS containing 10% FBS and mixed by pipetting before being spun at 1000rpm for 5 minutes. Supernatant was removed and cells were washed 2 more times with 400uL of PBS containing 10% FBS to ensure excess antibody was washed away. To determine the cutoff for ITGB4 expression, an Unstained cell population was used as a negative control. These cells followed the same staining protocol described above but did not include 1.25ug of the ITGB4 antibody. For the FACS Aria, once the cells were gated for the live population and doublets were removed, anything that expressed ITGB4 (FIT-C) above the Unstained condition was sorted into a (+) tube, while everything else was sorted into a (-) tube. To get a more stringent cutoff for ITGB4(+) and ITGB4(-), we re-sorted using the Sony 6000 sorter and after gating for live cells and removing doublets we again used an Unstained population of cells to get a cutoff, but then set 2 thresholds, one above and one below the Unstained cutoff to create 3 populations. The highly ITGB4 expressing cells were sorted into the (+) tubes, the very little to no ITGB4 expressing cells were sorted into the (-) tube, and everything in between was not collected.

value: Melanoma (A375)

value: Parental population, High ITGB4 expression

value: 5 rounds of 5 micron pore migration


title: A375-Parental-ITGB4neg-BottomR5-R1

value: Parental population, No ITGB4 expression


title: A375-Clone3-ITGB4pos-R1

value: Clonal population, High ITGB4 expression


title: Mecp2-KO, id 2

value: Mecp2 knock-out


title: Mecp2-KO, id 4, treated


title: Sample 12_hpVSMC--rep3

value: human plumonary vascular smooth muscle cells


title: Dome H3K4me3 rep 2

value: Whole embryos

value: TUAB

value: WT

value: dome

value: Invitrogen #711958


title: A375-Parental-ITGB4pos-R2


title: A375-Clone3-ITGB4neg-R1

value: Clonal population, No ITGB4 expression


title: Mecp2-KO, id 10, treated

value: Primary cortical neurons

value: trehalose


title: Mecp2-KO, id 10


title: Dome H3K4me3 rep 1


title: Sample 10_hpVSMC--rep1

value: Cell line


title: WT, id 2


title: Sample 11_hpVSMC--rep2


title: Sample 9_hiPS-BJ273-rep3

value: human induced pluripotent stem cell


title: A375-Parental-ITGB4pos-R1

description: Hi-C protocol from Golloshi et al., 2018

value: Melanoma (A375)


title: Dome H3K4me2 rep 2

value: Invitrogen #710796


title: Mecp2-KO, id 2, treated


title: A375-Parental-ITGB4neg-R2


title: Dome H3K4me2 rep 3


title: Mecp2-KO, id 102


title: Dome H3K9ac rep 1

value: Cell Signaling #9649


title: Sample 8_hiPS-BJ273-rep2


title: Dome H3K4me2 rep 1


title: Sample 7_hiPS-BJ273-rep1


title: A375-Parental-ITGB4neg-R1

value: Parental population, No ITGB4 expression


title: NSCs, Ythdf2-WT, YTHDF2-RIP-seq YTHDF2 , rep3

city: Philadelphia

first: Feng

last: Zhang

address: 415 Curie Boulevard

department: Department of Neuroscience and Mahoney Institute for Neurosciences

institute: Perelman School for Medicine, University of Pennsylvania

description:
WT3_Input
Raw_count_table_YTHDF2-RIP-seq.txt
TPM_table_YTHDF2-RIP-seq.txt

data_processing:
Raw sequencing data were demultiplexed with bcl2fastq2 v2.17.1.14 (Illumina).
Adaptors were trimmed using Trimmomatic v0.32 software (parameter-NexteraPE-PE.fa:2:30:10; TRAILING:3; SLIDINGWINDOW:4:15; MINLEN:18).
Trimmed sequence reads were mapped to mouse reference genome GRCm38 using STAR v2.5.2a (parameters-quantMode GeneCounts --outSAMattributes All --outFilterMultimapNmax 20 --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1).
Only uniquely mapped reads were quantified at the gene level and summarized to gene counts using STAR-quantMode (GeneCounts), with multimapping and chimeric alignments discarded.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files including the raw count of all genes for all the samples of RNA-seq, m6A-IP-seq and  YTHDF2-RIP-seq, respectively
Supplementary files format and content: Tab-delimited text files including the TPM value of all genes for all the samples of RNA-seq, m6A-IP-seq and  YTHDF2-RIP-seq, respectively

source_name: Hippocampus

growth_protocol: WT or Ythdf2 cKO hippocampal NSCs  were maintained in plates pre-coated with 20 ng/mL poly-D-Lysine (pdL) and cultured in the DMEM/F12 medium containing 2% B27 supplement, 1% N2 supplement, bFGF (20 ng/mL), EGF (20 ng/mL), 1% Glutamax and 1% P/S, with the medium routinely changed every two days. Accutase was used to digest the NSC culture for passaging.

extract_protocol:
For RNA-seq, RNA was extracted using TRIZOL and the kit of Zymo RNA Clean & Concentrator™-5. 300ng of total RNA was used for the construction of sequencing libraries. For m6A-IP-seq, RNA from WT NSCs was pulled down with m6A antibody, and the pulldown RNA was purified with Zymo RNA Clean & Concentrator™-5 and used for library preparation. For YTHDF2-RIP-seq, cell lysates  from WT NSCs were pulled down with YTHDF2 antibody, and the pulldown RNA was purified with TRIZOL and Zymo RNA Clean & Concentrator™-5 and used for library preparation
RNA libraries for RNA-seq were prepared based on SMART-seq2 method. RNA libraries for m6A-IP-seq and  YTHDF2-RIP-seq were prepared based on modified SMART-seq3 method.

treatment_protocol: For RNA-seq, the NSCs were treatment with transcription inhibitor-Actinomycin D (5 μM) for 0, 2  and 4 hr

value: Hippocampus

value: Postnatal 0.5 day

value: Neural stem cells

value: Nestin-WT

value: No treatment


title: Top5-ITGB4pos-R3

data_processing:
The fastq reads were first processed with BBDuk tool (https://github.com/kbaseapps/BBTools), performing adapter trimming. Adapter trimmed reads were processed for quality trimming using the BBDuk tool to discard reads with quality score lower than 28.
The reads were aligned to the reference genome hg19 using STAR aligner (https://github.com/alexdobin/STAR). Finally, the mapped reads were sorted based on genomic coordinates and feature count was performed with HTSeq-Counts (https://github.com/simon-anders/htseq).
Differential gene expression was determined using DESeq through Galaxy.
Assembly: hg19
Supplementary files format and content: Each genecounts.tsv file contains the raw RNA counts per gene produced by HTSeq

extract_protocol:
RNA was extracted using the Qiagen RNAeasy plus mini kit. In short, cells were lysed and homogenized, spun down in gDNA eliminator columns to remove any genomic DNA. All samples were washed with ethanol, and the total RNA was eluted. The quality and quantity of the RNA were quantified using a nanodrop.
Total RNA was then sent for library preparation and sequencing at GeneWiz (polyA mRNA approach).

treatment_protocol: Transwell filters with 5μm pore sizes (VWR‐10769‐236) were used. Briefly, the bottom of each filter was coated with 40μl of 10 μg/ml fibronectin for ~30 min. 24‐well plates were prepared for Transwell migration assay by adding 500 μl of 1× DMEM (Corning) with full supplements per well. A375 cells were detached from culture dishes at 80–90% confluency and aliquoted to 100,000 cells per 100μl of unsupplemented 1×DMEM. Each Transwell was placed into its corresponding well of the 24‐well plates, and 100μl of the cell suspension was added to the top of each filter. Cells were incubated at 37°C, 5% CO2 and allowed to migrate for 24hr. For sequential rounds of migration, the migrated cells were seeded into a new well of a 24‐well plate to expand. When cells reached 80–90% confluency, another Transwell migration was performed as previously described. Top (unmigrated) or bottom (migrated) cells were collected and continued to be used for sequential rounds of migration.  For FACS experiments, cells were sorted by a FACS Aria cell sorter or a Sony MA900 cell sorter. Cells were harvested using trypsin (T25, 6-well, 24-well) and spun at 1000rpm for 5 minutes. Supernatant was removed and cells were resuspended in 400uL of PBS containing 10% FBS and 1.25ug of Abcam FITC Anti-ITGB4 (ab22486). Cells were incubated on ice for 30 minutes then diluted with 350uL of PBS containing 10% FBS and mixed by pipetting before being spun at 1000rpm for 5 minutes. Supernatant was removed and cells were washed 2 more times with 400uL of PBS containing 10% FBS to ensure excess antibody was washed away. To determine the cutoff for ITGB4 expression, an Unstained cell population was used as a negative control. These cells followed the same staining protocol described above but did not include 1.25ug of the ITGB4 antibody. For the FACS Aria, once the cells were gated for the live population and doublets were removed, anything that expressed ITGB4 (FIT-C) above the Unstained condition was sorted into a (+) tube, while everything else was sorted into a (-) tube. To get a more stringent cutoff for ITGB4(+) and ITGB4(-), we re-sorted using the Sony 6000 sorter and after gating for live cells and removing doublets we again used an Unstained population of cells to get a cutoff, but then set 2 thresholds, one above and one below the Unstained cutoff to create 3 populations. The highly ITGB4 expressing cells were sorted into the (+) tubes, the very little to no ITGB4 expressing cells were sorted into the (-) tube, and everything in between was not collected.

tag: initial cell_population_characteristics

value: Failed to migrate, 5 rounds 5 micron pores

tag: itgb4 expression_status

value: Positive

tag: biological replicate


title: Sample 6_hbMSC-rep3

value: human bone marrow mesenchymal stem cells


title: Top5-ITGB4pos-R2


title: NSCs, Ythdf2-WT, YTHDF2-RIP-seq Input , rep3

description:
WT3_YTHDF2
Raw_count_table_YTHDF2-RIP-seq.txt
TPM_table_YTHDF2-RIP-seq.txt


title: Dome H3K4me1 rep 1

value: Whole embryos

value: TUAB

value: WT

value: dome

value: Invitrogen #710795


title: Mecp2-KO, id 102, treated

value: Primary cortical neurons

value: Mecp2 knock-out

value: trehalose


title: NSCs, Ythdf2-WT, YTHDF2-RIP-seq YTHDF2 , rep2

description:
WT2_Input
Raw_count_table_YTHDF2-RIP-seq.txt
TPM_table_YTHDF2-RIP-seq.txt


title: 1K-cell IgG rep 2

value: 1K cell

value: Invitrogen #10500C


title: Bottom5-ITGB4neg-R3

value: Melanoma (A375)

value: Sequential constriction, 5 rounds, 5 micron pores

value: Negative


title: Top5-ITGB4pos-R1


title: Dome H3K4me1 rep 2


title: Dome H3K4me1 rep 3


title: Sample 3_coECiMPC-rep3

value: Cell line

value: mural cell


title: NSCs, Ythdf2-WT, YTHDF2-RIP-seq IgG , rep2

description:
WT2_IgG
Raw_count_table_YTHDF2-RIP-seq.txt
TPM_table_YTHDF2-RIP-seq.txt

value: Hippocampus

value: Postnatal 0.5 day

value: Neural stem cells

value: Nestin-WT

value: No treatment


title: 1K-cell H4K16ac rep 2

value: Whole embryos

value: TUAB

value: WT

value: Millipore #37707329


title: 1K-cell IgG rep 1


title: Bottom5-ITGB4neg-R2


title: Sample 2_coECiMPC-rep2


title: NSCs, Ythdf2-WT, YTHDF2-RIP-seq Input , rep2

description:
WT2_YTHDF2
Raw_count_table_YTHDF2-RIP-seq.txt
TPM_table_YTHDF2-RIP-seq.txt


title: Sample 4_hbMSC-rep1

value: human bone marrow mesenchymal stem cells


title: Sample 1_coECiMPC-rep1


title: Bottom5-ITGB4neg-R1


title: Pectoral axillary lobe scRNA

city: Bethesda

first: James

last: Iben

state: MD

address: 10 CENTER DR

department: NICHD

institute: NIH

description: Cells from 2 male, 2 female; 10X genomics

data_processing:
cellranger count v7.0.0
Assembly: zv11
Supplementary files format and content: TSV value and matrix files

source_name: Pectoral axillary lobe

extract_protocol:
Cell suspension prepared from 4 pectoral axillary lobes (2 from males, 2 from females) removed from adult zebrafish comprising ~10k cells
10X 3.1 GEM kits following manufacturer recommendations

value: Pectoral axillary lobe


title: ITGB4(+)-BottomR5-R3

value: Parental, ITGB4 positive, migrated 5 rounds through 5 micron pores

value: Positive


title: NSCs, Ythdf2-WT, YTHDF2-RIP-seq Input , rep1

description:
WT1_YTHDF2
Raw_count_table_YTHDF2-RIP-seq.txt
TPM_table_YTHDF2-RIP-seq.txt


title: NSCs, Ythdf2-WT, YTHDF2-RIP-seq IgG , rep3

description:
WT3_IgG
Raw_count_table_YTHDF2-RIP-seq.txt
TPM_table_YTHDF2-RIP-seq.txt


title: eGFP_vaccine_m1Y_rep1_sup

city: Barcelona

first: Gregor

last: Diensthuber

state: Barcelona

address: C/ Dr. Aiguader, 88

department: Genome Biology

country: Spain

institute: Center for Genomic Regulation (CRG)

data_processing:
Processing of raw fast5 files was peformed using the MasterOfPores nextflow pipeline. Reads were basecalled using guppy (v6.0.6) with each of the three tested basecalling models (default, ivt and sup).
Alignments to both reference genome ( -uf -ax splice -k14)  and transcriptome (-ax map-ont -k14) were performed using minimap2 (v2.17). Highly modified synthetic constructs and the corresponding unmodified control were mapped using graphmap (v0.5.2) with sensitive settings (--rebuild-index -v 1 --double-index --mapq -1 -x sensitive -z 1 -K fastq --min-read-len 0 -A 7 -k 5)
To extract error signature on a per-nucleotide basis, EpinanoRMS (v1.1) was run. For in vivo m6A analyisis, pairwise-comparisons between wildtype and knockout samples were performed using eligos2(v2.1.0). Cross-species comparison of read accuacies was performed on reads uniquely mapped to the reference transcriptome (-F 3840) with a mapping quality > 15 (-q 15). To balance reads for strongly varying expression profiles at most the 10 longest reads for each transcript were extracted (bam2select.py). Read identis were extracted using identity_density.py
Assembly: Reference files include curlcake_constructs_EcoRV_BamHI_digestion.fasta, riboswitches.fa and 2021-8_eGFP_mRNA.v2.fa for curlcakes, riboswitches and the syntehtic eGFP vaccine, respectively. We used the following genomic reference for H. sapiens : Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa. And transcriptomic references Homo_sapiens.GRCh38.cdna.all.fa, Mus_musculus.GRCm39.cdna.all.fa, xlaevisMRNA.fasta, Saccharomyces_cerevisiae.R64-1-1.cdna.all.fa and Arabidopsis_thaliana.TAIR10.cdna.all.fa for H. sapiens, M. musculus, X. laevis, S. cervisiae and A. thaliana, respecitvely.
Supplementary files format and content: Files ending in <model>_per_position.csv, contain EpinanoRMS results on a per position basis. Files ending in <model>_per_5mer.tsv contain EpinanoRMS results on a 5-mer basis generated by converting per position results using epinano_to_kmer.R.
Supplementary files format and content: Files ending in _eligos2.txt contain results generated by eligos2 for pairwise comparisons which were already filtered to remove  non-A-positions and homopolymer sequences.
Supplementary files format and content: Files starting with <species>.tsv contain read accuracies per aligned read (rows) for all three models (column 1).

organism: synthetic construct

source_name: synthetic construct

extract_protocol:
In vitro constructs were artifically poly-A-tailed using PAP (NEB, M0276S), and cleaned up using the RNEasy MinElute kit (Quiagen,  74204) for curlcake constructs and Zymo Clean and Concentrator kit (Zymo Resarch, R1013). Concentrations were determined using a Qubit 2.0 Fluorometer. For libraries that were not generated as part of this work please refer to the respective publications
Direct RNA-seqeuncing libraries were generated using the SQK-RNA002 according to the manufacturer's protocol (version : DRS_9080_v2_revR_14Aug2019-minion). For curlcakes a final library of 800ng war generated (200ng per curlcake construct) while 750ng for the UNM-S libraries was used (250ng per riboswitch). The reverse transcription step was peformed using SuperScript III R(Thermo Fisher Scientific, 18080044) in the case of ac4C, m5U-containing curlcake constructs and UNM-S, and Superscript IV (Thermo Fisher Scientific, 18090010) in the case of m1Ψ. For libraries that were not generated as part of this work please refer to the respective publications.

value: synthetic construct


title: NSCs, Ythdf2-WT, YTHDF2-RIP-seq IgG , rep1

description:
WT1_IgG
Raw_count_table_YTHDF2-RIP-seq.txt
TPM_table_YTHDF2-RIP-seq.txt


title: 1K-cell H4K16ac rep 1

value: 1K cell


title: 1K-cell H3K122ac

value: Abcam #ab33309


title: Sample 5_hbMSC-rep2

value: Cell line


title: ITGB4(+)-BottomR5-R2

value: Melanoma (A375)


title: 1K-cell H3K64ac rep 2

value: Abcam #ab214808


title: NSCs, Ythdf2-WT, m6A-IP-seq m6A , rep3

description:
WT3_m6A
Raw_count_table_m6A-IP-seq.txt
TPM_table_m6A-IP-seq.txt

data_processing:
Raw sequencing data were demultiplexed with bcl2fastq2 v2.17.1.14 (Illumina).
Adaptors were trimmed using Trimmomatic v0.32 software (parameter-NexteraPE-PE.fa:2:30:10; TRAILING:3; SLIDINGWINDOW:4:15; MINLEN:18).
Trimmed sequence reads were mapped to mouse reference genome GRCm38 using STAR v2.5.2a (parameters-quantMode GeneCounts --outSAMattributes All --outFilterMultimapNmax 20 --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1).
Only uniquely mapped reads were quantified at the gene level and summarized to gene counts using STAR-quantMode (GeneCounts), with multimapping and chimeric alignments discarded.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files including the raw count of all genes for all the samples of RNA-seq, m6A-IP-seq and  YTHDF2-RIP-seq, respectively
Supplementary files format and content: Tab-delimited text files including the TPM value of all genes for all the samples of RNA-seq, m6A-IP-seq and  YTHDF2-RIP-seq, respectively
Library strategy: m6A-IP-seq

value: Hippocampus

value: Postnatal 0.5 day

value: Neural stem cells


title: eGFP_vaccine_m1Y_rep1_default


title: ITGB4(+)-BottomR5-R1


title: ITGB4(-)-BottomR4-R3

value: Parental, ITGB4 negative, migrated 4 rounds through 5 micron pores

value: Negative


title: NSCs, Ythdf2-WT, YTHDF2-RIP-seq YTHDF2 , rep1

description:
WT1_Input
Raw_count_table_YTHDF2-RIP-seq.txt
TPM_table_YTHDF2-RIP-seq.txt

value: Nestin-WT

value: No treatment


title: eGFP_vaccine_U_rep1_sup


title: 1K-cell H3K64ac rep 1

value: Whole embryos

value: TUAB

value: WT


title: NSCs, Ythdf2-WT, m6A-IP-seq Input , rep3

description:
WT3_Input
Raw_count_table_m6A-IP-seq.txt
TPM_table_m6A-IP-seq.txt


title: NSCs, Ythdf2-WT, m6A-IP-seq m6A , rep2

description:
WT2_m6A
Raw_count_table_m6A-IP-seq.txt
TPM_table_m6A-IP-seq.txt


title: 1K-cell H3K56ac

value: Invitrogen #PA5-40101


title: eGFP_vaccine_U_rep1_default

value: synthetic construct


title: 1K-cell H3K27ac rep 2

value: 1K cell

value: Abcam #ab4729


title: ITGB4(-)-BottomR4-R1


title: NSCs, Ythdf2-WT, m6A-IP-seq Input , rep2

description:
WT2_Input
Raw_count_table_m6A-IP-seq.txt
TPM_table_m6A-IP-seq.txt


title: 1K-cell H3K27ac rep 1


title: Bottom10-ITGB4pos-R3

value: Sequential constriction, 10 rounds, 5 micron pores

value: Positive


title: NSCs, Ythdf2-WT, m6A-IP-seq Input , rep1

description:
WT1_Input
Raw_count_table_m6A-IP-seq.txt
TPM_table_m6A-IP-seq.txt


title: 1K-cell H3K9ac rep 2

value: Cell Signaling #9649


title: UNM-S_rep3_ivt


title: 1K-cell H3K9ac rep 1


title: UNM-S_rep3_default


title: Bottom10-ITGB4pos-R1

value: Melanoma (A375)


title: UNM-S_rep2_sup


title: Bottom10-ITGB4neg-R3


title: 1K-cell H3K4me3

value: Invitrogen #711958


title: NSCs, Ythdf2-WT, 4 hour post Actinomydin D, RNA-seq, rep3

description:
Decay4h_WT3
Raw_count_table_RNA-seq.txt
TPM_table_RNA-seq.txt

value: Hippocampus

value: Postnatal 0.5 day

value: Neural stem cells

value: 5 microM Actinomydin D

tag: time point


title: NSCs, Ythdf2-WT, 4 hour post Actinomydin D, RNA-seq, rep2

description:
Decay4h_WT2
Raw_count_table_RNA-seq.txt
TPM_table_RNA-seq.txt

value: Nestin-WT


title: Bottom10-ITGB4neg-R2

value: Negative


title: ITGB4(-)-BottomR4-R2

value: Parental, ITGB4 negative, migrated 4 rounds through 5 micron pores


title: NSCs, Ythdf2-WT, 4 hour post Actinomydin D, RNA-seq, rep1

description:
Decay4h_WT1
Raw_count_table_RNA-seq.txt
TPM_table_RNA-seq.txt


title: 1K-cell H3K4me2

value: Whole embryos

value: TUAB

value: WT

value: Invitrogen #710796


title: UNM-S_rep2_ivt

value: synthetic construct


title: UNM-S_rep2_default


title: UNM-S_rep1_sup


title: UNM-S_rep3_sup


title: NSCs, Ythdf2-WT, m6A-IP-seq m6A , rep1

description:
WT1_m6A
Raw_count_table_m6A-IP-seq.txt
TPM_table_m6A-IP-seq.txt

value: No treatment


title: Top10-ITGB4pos-R3

value: Failed to migrate, 10 rounds 5 micron pores

value: Positive


title: Bottom10-ITGB4neg-R1

value: Melanoma (A375)

value: Sequential constriction, 10 rounds, 5 micron pores


title: 1K-cell H3K4me1 rep 4

value: 1K cell

value: Invitrogen #710795


title: 1K-cell H3K4me1 rep 3


title: NSCs, Ythdf2-WT, 2 hour post Actinomydin D, RNA-seq, rep2

description:
Decay2h_WT2
Raw_count_table_RNA-seq.txt
TPM_table_RNA-seq.txt

value: Hippocampus

value: Postnatal 0.5 day

value: Neural stem cells


title: UNM-S_rep1_ivt


title: Top10-ITGB4pos-R2


title: Bottom10-ITGB4pos-R2


title: 1K-cell H3K4me1 rep 2 (ActiveMotif)

value: ActiveMotif #39297


title: UNM-S_rep1_default


title: Top10-ITGB4pos-R1


title: 1K-cell H3K4me1 rep 1 (ActiveMotif)


title: a.thaliana_rep1_sup

organism: Arabidopsis thaliana

source_name: leaves

value: leaves


title: Curlcake_m6A_stoich_rep1_ivt


title: Curlcake_m6A_stoich_rep1_sup


title: Top10-ITGB4neg-R1

value: Negative


title: ITGB4(+)-R3

value: Parental


title: NSCs, Ythdf2-WT, 2 hour post Actinomydin D, RNA-seq, rep3

description:
Decay2h_WT3
Raw_count_table_RNA-seq.txt
TPM_table_RNA-seq.txt

value: Nestin-WT

value: 5 microM Actinomydin D


title: Top10-ITGB4neg-R2


title: NSCs, Ythdf2-WT, 0 hour post Actinomydin D, RNA-seq, rep1

description:
Decay0h_WT1
Raw_count_table_RNA-seq.txt
TPM_table_RNA-seq.txt


title: NSCs, Ythdf2-WT, 0 hour post Actinomydin D, RNA-seq, rep3

description:
Decay0h_WT3
Raw_count_table_RNA-seq.txt
TPM_table_RNA-seq.txt


title: NSCs, Ythdf2-WT, 2 hour post Actinomydin D, RNA-seq, rep1

description:
Decay2h_WT1
Raw_count_table_RNA-seq.txt
TPM_table_RNA-seq.txt


title: Curlcake_m6A_stoich_rep1_default

value: synthetic construct


title: NSCs, Ythdf2-cKO, 4 hour post Actinomydin D, RNA-seq, rep3

description:
Decay4h_cKO3
Raw_count_table_RNA-seq.txt
TPM_table_RNA-seq.txt

value: Nestin-cKO


title: Curlcake_m1Y_rep1_sup


title: NSCs, Ythdf2-cKO, 4 hour post Actinomydin D, RNA-seq, rep2

description:
Decay4h_cKO2
Raw_count_table_RNA-seq.txt
TPM_table_RNA-seq.txt


title: Curlcake_m1Y_rep1_default


title: ITGB4(+)-R2


title: ITGB4(+)-R1


title: a.thaliana_rep1_default


title: NSCs, Ythdf2-cKO, 4 hour post Actinomydin D, RNA-seq, rep1

description:
Decay4h_cKO1
Raw_count_table_RNA-seq.txt
TPM_table_RNA-seq.txt


title: NSCs, Ythdf2-WT, 0 hour post Actinomydin D, RNA-seq, rep2

description:
Decay0h_WT2
Raw_count_table_RNA-seq.txt
TPM_table_RNA-seq.txt


title: NSCs, Ythdf2-cKO, 2 hour post Actinomydin D, RNA-seq, rep3

description:
Decay2h_cKO3
Raw_count_table_RNA-seq.txt
TPM_table_RNA-seq.txt


title: ITGB4(-)-R3


title: a.thaliana_rep1_ivt

value: WT


title: Zip13KO, biological rep2

type: RNA

city: Chuncheon

first: Sehyun

last: Chae

address: 1 Kangwondaehakgil

department: Division of Chemical Engineering and Bioengineering

country: South Korea

institute: Kangwon National University

description: Gene expression data from Zip13KO mice

hyb_protocol: Labelling cDNA were hybridized on Affymetrix GeneChip (MoGene-2.0-st) according to the manufacturer's instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

label: biotin

source_name: Fibroblasts from Zip13KO mice, biological rep2

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from fragmentation cDNA

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Fibroblasts


title: NSCs, Ythdf2-cKO, 2 hour post Actinomydin D, RNA-seq, rep2

description:
Decay2h_cKO2
Raw_count_table_RNA-seq.txt
TPM_table_RNA-seq.txt


title: ITGB4(-)-R2

value: Melanoma (A375)


title: Curlcake_ac4C_rep1_ivt


title: Pancreatic progenitor, WIKI4, rep3

city: Toronto

first: Maria

middle: Cristina

last: Nostro

address: 101 College Street

country: Canada

institute: McEwen Stem Cell Institute

data_processing:
Raw sequencing reads were first aligned to the Hg38 human genome 75 using HISAT2 (v2.0.5) 76 and uniquely mapping reads were quantified at the gene level using the featureCounts program from the Subread package (v1.6.2)
Assembly: Hg38
Supplementary files format and content: Excel text file includes raw counts for each sample

source_name: Dissociated cells

growth_protocol: hPSCs were expanded on mouse embryonic fibroblasts and differentiated to day 8 PDX1+ endoderm according to our published protocol (Nostro et al, Stem Cell Reports 2015)

extract_protocol:
Approximately 1,000,000 cells from 3 separate replicates generated from NA- and WIKI4-derived stage 4 populations at day 13 were harvested and RNA extraction was performed using PureLink RNA mini kit (Ambion).
Libraries were produced using Illumina TruSeq Stranded Total RNA Sample Preparation kit with RiboZero Gold.

treatment_protocol: Day 8 PDX1+ endoderm was treated with EGF, Noggin and either Nicotinamide or WIKI4 until day 13

value: Dissociated cells

value: Human pluripotent stem cell-derived pancreatic progenitors (day 13)


title: Curlcake_m1Y_rep1_ivt


title: NSCs, Ythdf2-cKO, 2 hour post Actinomydin D, RNA-seq, rep1

description:
Decay2h_cKO1
Raw_count_table_RNA-seq.txt
TPM_table_RNA-seq.txt


title: Zip13KO, biological rep1

description: Gene expression data from Zip13KO mice

source_name: Fibroblasts from Zip13KO mice, biological rep1


title: ITGB4(-)-R1


title: Curlcake_ac4C_rep1_default


title: Pancreatic progenitor, WIKI4, rep2


title: Curlcake_m5U_rep1_sup


title: Pancreatic progenitor, WIKI4, rep1


title: NSCs, Ythdf2-cKO, 0 hour post Actinomydin D, RNA-seq, rep3

description:
Decay0h_cKO3
Raw_count_table_RNA-seq.txt
TPM_table_RNA-seq.txt


title: BALF, X923241, replicate 2, scRNAseq

city: Yangpu District, Shanghai

first: Mu

state: Shanghai

address: 800 Xiangyin Road, Shanghai 200433, China

department: Institute of Immunology

institute: National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Second Milltary Medical University

description: Singleron GEXSCOPE®

data_processing:
Raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17  to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted.
STAR v2.6.1a to map reads to the reference genome GRCh38 (ensembl version 92 annotation).
UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 software, and used to generate expression matrix files for subsequent analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Subsegmental bronchus

extract_protocol:
Bronchoalveolar lavage was operated by virtue of wedging the bronchoscope into a subsegmental bronchus. Lavage was aspirated with 20 mL saline solution. One of the two equal aliquot each sample were resuspended in cooled RPMI 1640 and passed through a 70-μm nylon strainer to remove clumps, debris and phlegm three times. After the lysis of red blood cells, the aliquot was centrifuged to precipitate cells, resuspended and then counted using the Countstar viable cell counter. Dead cells were removed with low-speed centrifugation before single-cell capturing.
Single-cell suspensions (2×105 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) . Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: Subsegmental bronchus

value: Bronchoalveolar lavage fluid  total cell


title: WT, biological rep2

description: Gene expression data from WT mice

source_name: Fibroblasts from WT mice, biological rep2


title: Pancreatic progenitor, Nicotinamide, rep3

value: Nicotinamide


title: Curlcake_m5U_rep1_default


title: NSCs, Ythdf2-cKO, 0 hour post Actinomydin D, RNA-seq, rep1

description:
Decay0h_cKO1
Raw_count_table_RNA-seq.txt
TPM_table_RNA-seq.txt

value: Hippocampus

value: Postnatal 0.5 day

value: Neural stem cells


title: BALF, X811911, replicate 1, scRNAseq

description: Singleron GEXSCOPE®


title: Pancreatic progenitor, Nicotinamide, rep2


title: Curlcake_ac4C_rep1_sup


title: WT, biological rep1

description: Gene expression data from WT mice

source_name: Fibroblasts from WT mice, biological rep1


title: BALF, X771100, replicate 1, scRNAseq

description: Singleron GEXSCOPE®


title: Pancreatic progenitor, Nicotinamide, rep1


title: Brain from mouse with silibinin (STAT3 inhibitor) #9

city: Derio

first: Paloma

last: Velasco-Beltrán

state: Bizkaia

address: Bizkaia Science & Technology Park

institute: CIC bioGUNE

description: Rhapsody

data_processing: Library demultiplexing and targeted gene-expression library were aligned using Seven Bridges Genomics platform following the BD Biosciences RhapsodyTM Targeted Analysis pipeline (BD Biosciences).

source_name: Brain

extract_protocol:
Mouse brains were transferred to RPMI-1640 medium, dissociated gently, and then, the protocol described by Korin et al. was followed. Target population (DAPI-CD45+CX3CR1-) was sorted into Lowbind Eppendorf tubes or cells were separated by magnetic beads using Mouse CX3CR1 positive selection to remove unwanted cells, and the negative fraction was collected in Lowbind Eppendorf tubes.
Library was performed according to the manufacter’s instructions
scRNA-seq BD RhapsodyTM Immune response targeted panel

treatment_protocol: Silibinin in the formula of Legasil® was administered by oral gavage daily (200 mg/kg) three days after cancer cells inoculation and treatment continued until mice reached the endpoint of the experiment.

value: Brain microenvironment enriched in lymphocytes

value: Brain

tag: age

value: 10 weeks old


title: Curlcake_5hmC_rep1_sup


title: Curlcake_5hmC_rep1_ivt


title: Brain from mouse with vehicle #8

description: Rhapsody


title: BALF, X708237, replicate 1, scRNAseq

description: Singleron GEXSCOPE®


title: BALF, X771100, replicate 2, scRNAseq

description: Singleron GEXSCOPE®


title: Curlcake_5hmC_rep1_default


title: Size-matched input for FTO CLIP upon control non-targeting knockdown

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

institute: University of Toronto

description:
Processed data file: metagene_profile_of_FTO_in_siZBTB48_ratioOverInput.pdf
This PDF shows the results of an analysis done directly from BAM files where no intermediate files were produced.

data_processing:
Raw reads that consisted of 3 random positions, a 4-nt multiplexing barcode, and another 2 random positions, followed by the cDNA sequence, were initially trimmed to 49 nt from the 3'-end, and duplicates were discarded. Reads were de-multiplexed, and the random positions, barcodes, and any 3'-bases matching Illumina adaptors were removed. Remaining reads longer than 25 nt were mapped to the mouse genome/transcriptome (Ensembl annotation of NCBIm37) using TopHat with default settings. To prevent false assignment of reads from repetitive regions, any reads with a mapping quality < 3 were removed from further analysis. Note that this record contains demultiplexed but un-trimmed reads.
CLIP Tool Kit (CTK) was used to identify RNA-binding sites at single-nucleotide resolution.We  called CITS peaks on individual iCLIP replicates as well as SMI samples. CITS with FDR ≤ 0.01 were considered as significant. The identified iCLIP CITS were further normalized using SMI CITS by utilizing underlying reads from each dataset and performing a differential analysis (iCLIP/SMI). Remaining peaks from individual replicates were merged for downstream analysis.   miCLIP-seq data were processed similarly to the iCLIP-seq data (except for the SMI step), and putative anti-m6A mediated CITS were identified (FDR ≤ 0.01).
To generate meta-gene plots, the entire length of each gene (divided into 3 parts: 5’UTR, CDS, 3’UTR) plus 1kb upstream and downstream was allocated into 100 bins on the x-axis, the number of bins in each part is proportional to the median length of that part in all protein-coding genes. The Y-axis denotes coverage enrichment ratio over input/bin/gene, the shaded bands around each line represent 1xSE. All calculations and visualizations were performed with the R package 'GenomicPlot' (URL: https://github.com/shuye2009/GenomicPlot), the smoothing was done using R function "smooth.spline" in the stats package with the parameter df=20.
Assembly: hg19
Supplementary files format and content: BED files containing merged crosslink-induced termination site (CITS) locations from multiple replicates.
Supplementary files format and content: PDF files contains a meta-gene plot showing the mean normalized FTO iCLIP read density in different parts of the gene upon either ZBTB48 knockdown or control non-targeting knockdown. Figure was generated directly from aligned reads.

growth_protocol: Cell cultures were maintained in Dulbecco's modified Eagle's medium (DMEM) (Wisent Bioproducts catalogue number 319-005-CL) supplemented with 10% FBS (Wisent Bioproducts catalogue number 080-705), sodium pyruvate, non-essential amino acids, and penicillin/streptomycin.

extract_protocol:
Lysates were treated with Turbo DNase (Thermo Fisher Scientiﬁc) and RNase I (Thermo Fisher Scientiﬁc) diluted 1/250 in PBS for 5 minutes at 37°C to digest genomic DNA and partially digest RNA to short fragments of an optimal size range. RNA-protein complexes were puriﬁed using 100 mL of protein G Dynabeads (Thermo Fisher Scientiﬁc) and 10ug antibody, with 2% (20ul) of the total lysate retained for use as a size-matched input (SMI) control. SMI samples were processed as previously described (Van Nostrand et al., 2016). Following stringent high salt washes, the immunoprecipitated RNA was 3′ end dephosphorylated and ligated to a pre-adenylated adaptor at the 3′ end, as described previously. After extensive additional washes and buffer exchange, the immunoprecipitated RNA was 5′ end-labeled using ATP [γ-32P]. The puriﬁed protein-RNA complexes and SMI control samples were separated with SDS-PAGE and transferred to nitrocellulose membrane. Protein was digested using proteinase K, the RNA was puriﬁed using phenol/chloroform. miCLIP procedure was performed as decribed. Total RNA was extracted from HEK293 cells using TRIzol as per manufacturer's protocol. RNA was treated with DNase I to eliminate any contaminating genomic DNA. We used 12 μg of total RNA for miCLIP-seq. 2 μL of RNA Fragmentation Reagents was added to the RNA suspended in 20 μL of sterile water. The mixture was incubated in a heat block at 75°C for exactly 12 minutes. 2.2 μL of stop solution was added to stop the reaction. The fragmented RNA was incubated with 10 μg of m6A antibody for 2 hours at 4°C. RNA-antibody complexes were UV crosslinked twice with 0.15 J/cm2 at 254 nm in a Stratalinker 1800.  Protein G Dynabeads (100 μL) were added, and the samples were rotated for 2 hours at 4°C. Remaining steps, including dephosphorylation, adapter ligation, SDS-PAGE, and RNA-extraction are similar to the iCLIP procecure.
Purified RNA was reverse transcribed into cDNA. The cDNA was size selected by resolving samples on a 6% TBE-Urea gel, circularized to add the adaptor to the 5′ end, digested at the internal BamHI site, and then PCR ampliﬁed using AccuPrime SuperMix I (Thermo Fisher Scientiﬁc). The ﬁnal PCR libraries were puriﬁed by agarose gel electrophoresis using gel extraction columns (QIAGEN). The eluted DNA from the low, middle, and high fractions was pooled together and submitted for sequencing.

treatment_protocol: HEK293 cells were crosslinked (150mJ/cm2) at 254 nm with a Stratalinker 1800.

value: human embryonic kidney cells (HEK293)

value: FTO ORF under CMV promoter. Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/TO-FLAG containing FTO.

value: Control knockdowns were performed with non-targeting Silencer Select control siRNA (Thermo Fisher AM4611) for 72 hours in Flp-In T-Rex HEK293 cells, which had FLAG-FTO under the control of doxycycline. Expression was induced for 24 hours prior to crosslinking.

tag: protocol

value: iCLIP-seq

tag: clip antibody

value: none (input)

tag: barcoded reverse_transcription_primer


title: Size-matched input for FTO CLIP upon ZBTB48 knockdown

value: ZBTB48 knockdown was performed (s6568, Thermo Fisher Scientific Inc.) using siZBTB48 for 72 hours in Flp-In T-Rex HEK293 cells, which had FLAG-FTO  under the control of doxycycline. Expression was induced for 24 hours prior to crosslinking.


title: Brain from mouse with silibinin (STAT3 inhibitor) #8

description: Rhapsody

tag: tissue


title: BALF, X571559, replicate 2, scRNAseq

description: Singleron GEXSCOPE®


title: NSCs, Ythdf2-cKO, 0 hour post Actinomydin D, RNA-seq, rep2

description:
Decay0h_cKO2
Raw_count_table_RNA-seq.txt
TPM_table_RNA-seq.txt

value: Nestin-cKO

value: 5 microM Actinomydin D


title: Brain from mouse with silibinin (STAT3 inhibitor) #7

description: Rhapsody

tag: strain


title: BALF, X571559, replicate 1, scRNAseq

description: Singleron GEXSCOPE®

value: Subsegmental bronchus


title: Curlcake_m5U_rep1_ivt

value: synthetic construct


title: FTO iCLIP-seq upon control non-targeting knockdown, replicate 2

tag: genotype

value: anti-FLAG (Sigma F3165)


title: Curlcake_m5C_rep1_sup


title: Curlcake_m5C_rep1_ivt


title: Curlcake_m5C_rep1_default


title: Brain from mouse with silibinin (STAT3 inhibitor) #5

description: Rhapsody


title: BALF, X519402, replicate 1, scRNAseq

description: Singleron GEXSCOPE®

value: Bronchoalveolar lavage fluid  total cell


title: FTO iCLIP-seq upon ZBTB48 knockdown, replicate 2


title: Curlcake_pU_rep1_sup


title: BALF, X519402, replicate 2, scRNAseq

description: Singleron GEXSCOPE®


title: Brain from mouse with silibinin (STAT3 inhibitor) #4

description: Rhapsody


title: FTO iCLIP-seq upon ZBTB48 knockdown, replicate 1


title: Brain from mouse with silibinin (STAT3 inhibitor) #3

description: Rhapsody


title: Curlcake_pU_rep1_default


title: BALF, E08322, replicate 1, scRNAseq

description: Singleron GEXSCOPE®


title: BALF, E08262, replicate 1, scRNAseq

description: Singleron GEXSCOPE®


title: Brain from mouse with silibinin (STAT3 inhibitor) #6

description: Rhapsody


title: Curlcake_m6A_rep1_ivt


title: Brain from mouse with vehicle #7

description: Rhapsody


title: m6A iCLIP-seq upon GFP control overexpression, replicate 2

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus, under CMV promoter, were transfected with pDEST pcDNA5/FRT/TO-EGFP.

value: EGFP was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycycline, and expression was induced for 24 hours prior to crosslinking.

value: anti-m6A (MBL RN131P)


title: FTO iCLIP-seq upon control non-targeting knockdown, replicate 1


title: Curlcake_m6A_rep1_sup


title: Brain from mouse with silibinin (STAT3 inhibitor) #2

description: Rhapsody

value: Brain microenvironment enriched in lymphocytes

value: Brain


title: BALF, E08320, replicate 1, scRNAseq

description: Singleron GEXSCOPE®


title: BALF, E08320, replicate 2, scRNAseq

description: Singleron GEXSCOPE®


title: Brain from mouse with vehicle #6

description: Rhapsody

value: 10 weeks old


title: BALF, E08111, replicate 3, scRNAseq

description: Singleron GEXSCOPE®


title: Brain from mouse with silibinin (STAT3 inhibitor) #1

description: Rhapsody


title: m6A iCLIP-seq upon ZBTB48 overexpression, replicate 1

value: human embryonic kidney cells (HEK293)

value: ZBTB48 ORF under CMV promoter. Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/TO-FLAG containi ZBTB48.

value: EGFP-ZBTB48 was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycycline, and expression was induced for 24 hours prior to crosslinking.


title: BALF, E08111, replicate 2, scRNAseq

description: Singleron GEXSCOPE®


title: Curlcake_Unm_rep1_sup


title: Curlcake_m6A_rep1_default


title: m6A iCLIP-seq upon FTO overexpression, replicate 1

value: FTO ORF under CMV promoter. Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/TO-FLAG containing FTO.

value: FLAG-FTO was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycycline, and expression was induced for 24 hours prior to crosslinking.

value: iCLIP-seq


title: m6A iCLIP-seq upon FTO overexpression, replicate 2


title: Brain from mouse with vehicle #4

description: Rhapsody


title: BALF, E07928, replicate 3, scRNAseq

description: Singleron GEXSCOPE®


title: BALF, E08111, replicate 1, scRNAseq

description: Singleron GEXSCOPE®


title: Curlcake_Unm_rep1_ivt


title: Curlcake_pU_rep1_ivt


title: Brain from mouse with vehicle #5

description: Rhapsody


title: iCLIP-seq of FTO, replicate 4


title: m6A iCLIP-seq upon ZBTB48 overexpression, replicate 2


title: Brain from mouse with vehicle #3

description: Rhapsody


title: Curlcake_Unm_rep1_default


title: iCLIP-seq of FTO, replicate 3


title: Brain from mouse with vehicle #2

description: Rhapsody


title: BALF, E07928, replicate 2, scRNAseq

description: Singleron GEXSCOPE®


title: hy5 pif457, 8h W+FR, rep3

city: Valencia

first: jaume

middle: f

last: martinez-garcia

state: Valencia

address: CPI, Edifici 8E, Campus UPV, Carrer Enginyer Fausto Elio s/n

department: Development and Hormonal Action in Plants

institute: IBMCP, CSIC

data_processing:
Reads mapped with STAR v2.5.3a
Genes quantified with RSEM v1.3.0
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file with raw counts for each sample

source_name: whole seedlings

growth_protocol: Seeds were sterilized and sown in solid agar plates without sucrose (GM–; 0.215% (w/v) MS salts plus vitamins, 0.025% (w/v) MES pH 5.80). After 3-6 days of stratification, plates were incubated in growth chambers at 22°C under continuous white light (W) provided by 4 cool-white vertical fluorescence tubes for 2 days (PAR of 20–25 umol·m-2·s-1, R:FR of about 1.58). After that time, plates were maintained in W until the ahade treatment was provieded.

extract_protocol:
RNA was extracted using a commercial kit (Maxwell® RSC Plant RNA kits; www.promega.com) following the manufacturers protocol. RNA was quantified using NanoDropTM 8000 spectrophotometer (ThermoFischer ScientificTM).
RNA-Seq libraries were prepared using the KAPA Stranded mRNA-Seq Illumina Platforms Kit (Roche), following the manufacturer's recommendations.

treatment_protocol: At day 7, W-grown seedlings were transferred to simulated shade (W+FR). Simulated shade was generated by enriching W with supplementary FR provided by 4 horizontal LED lamps (PAR of 20–25 umol·m-2·s-1, R:FR of about 0.02). Seedlings were harvested immediately before (0h) and after 1 (1h) or 8 h (8h) of W+FR exposure.

value: whole seedlings

tag: developmental stage

value: 7-day-old seedlings

tag: growth conditions

value: Continuous W at 22°C

value: hy5 pif457

value: harvested after 8h of W+FR


title: iCLIP-seq of FTO, replicate 2

tag: cell line

value: anti-FLAG (Sigma F3165)


title: hy5 pif457, 8h W+FR, rep2


title: BALF, E07928, replicate 1, scRNAseq

description: Singleron GEXSCOPE®

value: Subsegmental bronchus

tag: cell type

value: Bronchoalveolar lavage fluid  total cell


title: BALF, E07866, replicate 1, scRNAseq

description: Singleron GEXSCOPE®


title: iCLIP-seq of FTO, replicate 1

tag: treatment


title: Size-matched input for ZBTB48 iCLIP

value: WT

value: none (input)


title: hy5 pif457, 8h W+FR, rep1


title: As4.1 cells treated with DMSO

city: Charlottesville

first: Jason

middle: Paul

last: Smith

state: VA

address: 409 Lane Rd

department: Pediatrics

institute: University of Virginia

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.10
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: kidney

extract_protocol:
600,000 cultured As4.1 cells were plated in duplicate in T25 flasks.  The cells were treated with 10 μM H89 or equivalent volume DMSO at 0, 24, and 48 hours. After 48 hours, cells were trypsinized and 4000 cells per condition were targeted for sequencing. The cells were centrifuged in a Sorvall RT7 refrigerated 4∘C centrifuge (Sorvall, Newtown, CT) at 500 x g for 10 minutes, washed 3X with 5mL of dPBS, then 1 mL of trypsin was added, and cells incubated at 37∘C for 2 minutes before adding 4 mL of fresh media.  The cells were gently pipetted up and down 20 times to dissociate and centrifuged at 800 x g for 3 minutes at room temperature.  The supernatant was removed, and pellets resuspended in 1.5mL dPBS supplemented with 0.04% BSA (UltraPureTM Bovine Serum Albumin, Invitrogen, Lithuania) by pipetting up and down 20 times.  Resuspended cells were passed through a 40 μm filter and repelleted by centrifugation for 3 minutes at room temperature at 150 x g.  The supernatant was carefully removed, and cells washed 3X in 1.5mL dPBS with 0.04% BSA as outlined above.  Cells were resuspended a final time in 1.5mL dPBS with 0.04% BSA and the volume adjusted to yield 1000 cells/μL.
Isolated single cells were loaded and captured using the Chromium System (10X Genomics, Pleasanton, CA) following the manufacturer's recommendation for the Chromium Next GEM Chip G with reagents of Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10X Genomics).

value: kidney

value: DMSO


title: hy5 pif457, 1h W+FR, rep3

value: harvested after 1h of W+FR


title: BALF, E07768, replicate 1, scRNAseq

description: Singleron GEXSCOPE®


title: Input of ChIP, replicate 2

data_processing:
ChIP-seq analysis was performed essentially as described previously (Schmitages F. et al. 2016. Genome Research). Illumina adaptor sequences were removed from the 3′ ends of 51-nt reads, and the reads were mapped to the human genome hg19 using Bowtie 2 with default settings.
Duplicate reads were discarded, and peaks were called jointly on the immunoprecipitated and input samples with MACS2 (version 2.1.2).
Assembly: hg19
Supplementary files format and content: ZBTB48_ChIPseq_peaks.narrowPeak is an output file from MACS2 in BED6+4 format, and contains peak location, p-value, and q-value.
Supplementary files format and content: ZBTB48_ChIPseq_summits.bed is an output file from MACS2 in BED format, and contains peak summit locations.

extract_protocol:
ChIP (Chromatin Immunoprecipitation) was performed as previously described (Najafabadi et al., Nat. Biotechnol. (2015)). Briefly, ~20 million HEK293 cells were crosslinked in 1% formaldehyde. Lysates were sonicated to a DNA fragment length range of 200-300 bp using a Bioruptor (Diagenode). SP1 was immunoprecipitated from the lysate with 10ug of Sp1 antibody (Santa Cruz) and Dynabeads Protein G (Invitrogen). Subsequently, crosslinks were reversed at 65°C over night and bound DNA fragments were purified (EZ-10 Spin Column PCR Product Purification kit, Bio Basic).
Sequencing libraries were constructed using the TruSeq ChIP-seq library kits (Illumina) according the manufacturer's instructions followed by PCR amplification and agarose gel size selection.

treatment_protocol: HEK293 cells were cross-linked for 10 min in 1% formaldehyde.

value: human embryonic kidney cells (HEK293)

value: ZBTB48 ORF under CMV promoter. Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/TO-eGFP containing FTO.

value: EGFP-ZBTB48 was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycyclin, and expression was induced for 24 hours prior to crosslinking.

tag: chip antibody


title: BALF, E07554, replicate 1, scRNAseq

description: Singleron GEXSCOPE®


title: As4.1 cells treated with 10 μM H89

description: 10x Genomics


title: Input of ChIP, replicate 1


title: As4.1 cells, IgG

data_processing:
Raw sequencing files were processed using the `nf-core/cutandrun` pipeline [v3.1-g42502fb] with alignment to the GRCm38/mm10 mouse genome.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig, merged replicate file signal tracks

growth_protocol: The renin-expressing As4.1 cell line (ATCC, CRL-2193) was maintained in high glucose DMEM (supplemented with 10% fetal bovine serum (both from Thermo Fisher Scientific) at 37°C in a humidified incubator containing 5% CO2.

extract_protocol:
Cells were washed in dPBS and trypsinized at 37°C until cells detached. Detached cells were then suspended in dPBS with a protease inhibitor added.
For each primary antibody, 100k cells were isolated and resuspended in Concanavalin A-coated beads. Primary antibodies to each histone modification were then added, with the guinea pig anti-Rabbit IgG used as the secondary antibody.  Tagmentation was performed using the pAG-Tn5 transposase.  Processed libraries were sent to Novogene (Durham, NC) for sequencing.


title: As4.1 cells, H3K27ac, rep2


title: BALF, D98585, replicate 1, scRNAseq

description: Singleron GEXSCOPE®


title: hy5 pif457, 1h W+FR, rep1


title: Brain from mouse with vehicle #1

description: Rhapsody

value: Brain microenvironment enriched in lymphocytes

value: Brain

value: 10 weeks old


title: ChIP-seq of ZBTB48 in HEK293 cells, replicate 2

value: anti-GFP (Abcam ab290)


title: BALF, D18348, replicate 2, scRNAseq

description: Singleron GEXSCOPE®


title: BALF, D18348, replicate 1, scRNAseq

description: Singleron GEXSCOPE®


title: As4.1 cells, H4K5ac, rep2


title: Top10-ITGB4neg-R3

value: Melanoma (A375)

tag: initial cell_population_characteristics

value: Failed to migrate, 10 rounds 5 micron pores

value: Negative


title: m6A iCLIP-seq upon GFP control overexpression, replicate 1

value: Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus, under CMV promoter, were transfected with pDEST pcDNA5/FRT/TO-EGFP.

value: EGFP was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycycline, and expression was induced for 24 hours prior to crosslinking.

value: iCLIP-seq

value: anti-m6A (MBL RN131P)


title: As4.1 cells, H3K27ac, rep1

value: kidney


title: hy5 pif457, 0h W+FR, rep2

value: whole seedlings

value: 7-day-old seedlings

value: Continuous W at 22°C

value: hy5 pif457

value: harvested immediately before W+FR


title: ChIP-seq of ZBTB48 in HEK293 cells, replicate 1

value: human embryonic kidney cells (HEK293)

value: ZBTB48 ORF under CMV promoter. Flp-In T-Rex HEK293 cells  which  contain a single stably integrated FRT site at a transcriptionally active genomic locus were transfected with pDEST pcDNA5/FRT/TO-eGFP containing FTO.

value: EGFP-ZBTB48 was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycyclin, and expression was induced for 24 hours prior to crosslinking.


title: pif457, 8h W+FR, rep3

value: harvested after 8h of W+FR


title: BALF, C94598, replicate 1, scRNAseq

description: Singleron GEXSCOPE®

value: Subsegmental bronchus

value: Bronchoalveolar lavage fluid  total cell


title: HC, replicate 1, scRNAseq

city: Nanjing

first: Hongmei

state: (None)

address: Ding jia qiao 87, gulou region

institute: Southeast University

description: 10x Genomics

data_processing:
The Cell Ranger Software Suite (v.6.0.1) was used to perform sample de-multiplexing, barcode processing and single-cell 5' unique molecular identifier (UMI) counting.
Cell barcodes were then determined based on the distribution of UMI counts automatically.
The following criteria were then applied to each cell of each subject: gene number between 200 and 7,000, mitochondrial gene percentage < 0.1, and hemoglobin gene percentage < 0.03.
In parameter settings, the first 50 dimensions of principal-component analysis (PCA) were used. We employed Harmony for actual batch effect correction. Harmony was run to remove batch effects in the PCA space when clustering of major cell lineages.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format

source_name: lung tissue

extract_protocol:
Freshly obtained resected tissues were rinsed with Hanks’ Balanced Salt Solution (HBSS) after the operation, subsequently shredded on ice to smaller pieces with collagenase I/IV in HBSS, and incubated for 30 min at 37 °C with manual shaking every 10 min. The digested tissues were then passed through a 70-μm nylon mesh filter, and the cell suspension were centrifuged at 400 g for 5 min at 4 °C. After removing the supernatant, the pelted cells were suspended in red blood lysis buffer, and next resuspended in PBS after being washed with HBSS. The cDNA library was constructed within 24 h.
We mixed a single-cell suspension with 0.4% trypan blue dye at a ratio of 9:1. Cells were counted using a Countstar Rigel S2. The proportion of living cells was calculated and should exceed 90% for quality control. Libraries were prepared according to the manufacturer’s protocol (10x Genomics, CG000086_RevM). After quality checks, single-cell RNA-seq libraries were pooled and sequenced on a NovaSeq 6000 instrument.

value: lung tissue

value: single-cell suspensions of lung tissue

tag: disease

value: healthy


title: hy5 pif457, 1h W+FR, rep2

value: harvested after 1h of W+FR


title: 21_CD40

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

data_processing:
RNA sequencing reads were processed by Single Cell Discoveries Utrecht. Reads were mapped to hg38 using  BWA MEM 0.7.15.
Assembly: hg38
Supplementary files format and content: read counts per transcript

source_name: monocytes from healthy donor

growth_protocol: PBMCs were isolated by Ficoll-Paque density gradient centrifugation (Lymphoprep, StemCell Technologies, Inc.). PBMCs were washed twice with PBS and were resuspended in RPMI 1640 culture medium supplemented with 1 mM pyruvate, 2 mM glutamax, and penicillin/streptomycin (Thermo Fisher Scientific). Monocytes were isolated from PBMCs by negative MACS isolation using human Pan Monocyte Isolation Kit (Miltenyi Biotec)

extract_protocol:
RNA was isolated from 1*10^6 monocytes using RNeasy Mini kit (Qiagen) including DNAse I digestion according to manufacturer’s instructions.
RNA isolated from monocytes was used for the preparation of the RNA sequencing libraries, which was performed according to the CEL-seq2 protocol. RNA bulk sequencing was performed by Single Cell Discoveries (Utrecht, The Netherlands) with a sequencing depth of 20 million reads/sample.

treatment_protocol: Human PBMCs were trained as described previously. Briefly, PBMCs and monocytes were seeded into 96-well flat bottom plates in a density of 5*106 cells/mL. Cells were allowed to adhere for 1 h at 37 ºC, 5 % CO2 (v/v). Cells were washed twice with PBS and where indicated, cells were treated with CD40-TRAF6 signaling inhibitor (10 µM, Sigma) for 1 hr. Subsequently, cells were stimulated with the primary stimulus HKCA (10^5 cells/ml, Invivogen) or culture medium for 24 h at 37 ºC, 5 % CO2 (v/v), in presence or absence of CD40-TRAF6 signaling inhibitor. After 24 h, supernatant was collected, cells were washed three times with PBS and incubated in culture medium containing 10% FBS for 5 days at 37 ºC, 5 % CO2 (v/v).

value: HKCA + CD40-TRAF6i

value: monocytes

tag: disease state

value: healthy donor


title: MOLM13, shNAT10-2, ac4C, IP, rep2

city: Guangzhou

first: Huilin

last: Huang

address: #651 East Dong-feng Road

institute: Sun Yat-Sen University Cancer Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by by cutadapt v. 4.1 with parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q 20,20 --max-n 0.25 --trim-n.
The clean reads were then mapped to the human genome (hg38) with HISAT2 v.2.1.1 with “--rna-strandness RF” parameters, and supplying the GENCODE Release 39 gene annotation. A post-alignment filter was preformed to remove alignments to ribosomal RNA (rRNA), secondary alignment and non-concordant mate pairs.
Ac4C peaks on each transcripts of gene were called using homemade Perl scripts according to the strand, separated by “-f 83 (and 163)” or “-f 99 (and 147) with SAMtools v. 1.16.1.
Peaks were identified as regions concentrated with significantly more normalized reads (fold change > 1.5 and adjusted P-value < 0.05) in IP than their corresponding input samples.
Assembly: hg38
Supplementary files format and content: bigwig files were generated by deepTools v3.5.2. BedWig files can be uploaded to UCSC Genome Browser for visualization.
Library strategy: acRIP-seq

growth_protocol: MOLM13 cells were maintained in regular RPMI-1640 medium containing 10% FBS and 1% penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37 ℃.

extract_protocol:
MOLM13 total RNA was isolated using the TRIzol reagent. IVT control RNA was generated by constructing cDNA templates with T7 promoters using MOLM13 mRNA and performing in  vitro transcription with nucleoside triphosphate free of modifications.
After acRIP, input samples and IP products were used to construct NGS libraries using the SMARTer® Stranded Total RNA-Seq Kit v2 following manufacturer’s protocol.

treatment_protocol: MOLM13 cells were transfected with NAT10-sh1, NAT10-sh2 or shNS lentiviruses to silence NAT10 expression.

value: Human acute myeloid leukemia (AML) cells

value: IP


title: As4.1 cells, H4K5ac, rep1

value: kidney


title: As4.1 cells, H2BK5ac, rep2


title: MOLM13, shNAT10-2, ac4C, IP, rep1


title: 19_CD40


title: 19_HKCA

value: HKCA


title: As4.1 cells, H4K16ac, rep2


title: As4.1 cells, H2BK5ac, rep1


title: hy5 pif457, 0h W+FR, rep3

value: whole seedlings

value: 7-day-old seedlings

value: Continuous W at 22°C

value: hy5 pif457

value: harvested immediately before W+FR


title: OP, replicate 1, scRNAseq

last: Wang

description: 10x Genomics

value: OP patient


title: 21_HKCA


title: pif457, 8h W+FR, rep2

value: harvested after 8h of W+FR


title: As4.1 cells, H4K16ac, rep1


title: 18_HKCA


title: MOLM13, shNAT10-1, ac4C, IP, rep2


title: As4.1 cells, H3K4me3, rep2


title: pif457, 8h W+FR, rep1


title: pif457, 1h W+FR, rep2


title: 21_RPMI

value: untreated


title: pif457, 1h W+FR, rep1


title: pif457, 1h W+FR, rep3


title: 19_RPMI


title: MOLM13, shNS, ac4C, IP, rep2

value: shNS


title: 18_RPMI


title: MOLM13, shNS, ac4C, IP, rep1


title: hy5 pif457, 0h W+FR, rep1


title: pif457, 0h W+FR, rep1


title: pif457, 0h W+FR, rep2


title: 18_CD40


title: As4.1 cells, H3K4me1, rep2


title: As4.1 cells, H3K4me3, rep1


title: As4.1 cells treated with 1 μM JQ1, replicate 2

data_processing:
For initial processing of sequenced reads, the 150 bp paired-end reads were aligned to the mouse genome  (GRCm38/mm10) using the PEPATAC (v0.10.4) pipeline. Enzymatic bias of aligned reads was corrected using `seqOutBias`.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig files represent the processed, bias-corrected ATAC-seq signals.

extract_protocol:
After 48 hours, 50,000 cells were collected, washed 3X with 5 mL dPBS (Dulbecco's Phosphate Buffered Saline, Gibco, UK), treated with Lysis Buffer, and resuspended.
Tagmentation was performed using a Nextera DNA library Prep Kit (Illumina) according to the manufacturer's directions.

treatment_protocol: At 0-, 24-, and 48-hours, cells were treated with either 10μM H89, 10μM A-485, 1μM JQ1, or equivalent volume DMSO.


title: pif457, 0h W+FR, rep3


title: MOLM13, shNAT10-1, ac4C, IP, rep1


title: hy5, 8h W+FR, rep3


title: MOLM13, shNAT10-1, ac4C, input, rep2

value: input


title: As4.1 cells treated with 1 μM JQ1, replicate 1


title: As4.1 cells, H3K4me1, rep1


title: As4.1 cells treated with DMSO, replicate 3

value: DMSO


title: MOLM13, shNAT10-2, ac4C, input, rep1


title: BC2121 HKCA + CD40i H3K27Ac

description: H3K27ac ChIP-seq

data_processing:
ChIP-sequencing data were aligned to human genome hg38 with BWA. Samtools was used to filter reads with a quality score lower than 20. PCR duplicates were removed with Picard. Peaks were identified with MACS 2.2.6 in paired-end mode and ‘call-summits’ enabled at a false discovery rate of 0.01. A union of all identified peaks was generated with BEDTools, which was used to count reads per peak in all samples. DESeq2 package in R was used to identify significant changes in detected peaks among treatments. Samples derived from one donor were paired. Significant dynamics in peaks was defined by FC < 0.5 or FC > 2 and an FDR > 0.10.
Assembly: hg38
Supplementary files format and content: bigwig files

extract_protocol:
Monocytes were resuspended in RPMI culture medium containing 1% formaldehyde (Sigma Aldrich) and incubated for 10 min at RT. Formaldehyde was quenched using 125 mM glycine, which was incubated for 5 min at RT. Monocytes were washed twice in cold PBS supplemented with protease inhibitor cocktail (Roche). Cell pellets were snap frozen in liquid nitrogen and stored at -70°C until further use. Cells and nuclei were lysed using Magna ChIP™ Cell Lysis buffer and Nuclear Lysis buffer (Merck Millipore) according to manufacturer’s instructions. Lysates were sonicated using a Bioruptor pico sonicator (Diagenode; 10 cycles, 30 s on, 30 s off, at 4°C) in a density of 15*106 cells/mL and spun down. Sheared chromatin was collected and fragment sizes were determined by DNA purification using MinElute Reaction Cleanup Kit (Qiagen) followed by gel electrophoresis. Immunoprecipitation was performed using the Magna ChIP™ A Chromatin Immunoprecipitation Kit (Merck Millipore) according to manufacturer’s instructions. In short, sonicated lysates derived from 5*105 cells were incubated overnight with 1 μg H3K4me3 antibody or H3K27ac (Diagenode) and protein A magnetic beads at 4 °C on a rotating platform. Protein A beads-antibody/chromatin complexes were washed with buffers provided by the Magna ChIP kit for 5 min at 4 °C on a rotating platform. Chromatin was eluted by incubation in Elution buffer supplemented with proteinase K (Magna ChIP kit, Merck Millipore) for 2 h at 62 °C, shaking, followed by 10 min at 95 °C. DNA was purified and eluted in 25 uL milliQ.
ChIP-seq libraries were prepared using the Kapa Hyper Prep Kit according to manufacturer’s instructions, with the following modifications. For adaptor ligation of each sample, 2.5 mL of the NEXTflex adaptor stock (600 nM, Bioo Scientific) was used. Libraries were amplified with 12-15 PCR cycles followed by a double post-amplification clean-up to ensure proper adapter removal. Samples were analyzed for purity using a High Sensitivity DNA Chip on a Bioanalyzer 2100 system (Agilent). Libraries were paired-end sequenced to a read length of 42 bp on an Illumina NextSeq500.

value: HKCA + CD40-TRAF6i

value: monocytes


title: As4.1 cells treated with DMSO, replicate 4


title: BC2119 HKCA + CD40i H3K27Ac

description: H3K27ac ChIP-seq

value: healthy donor


title: BC2121 HKCA H3K27Ac

description: H3K27ac ChIP-seq


title: MOLM13, shNAT10-2, ac4C, input, rep2

value: Human acute myeloid leukemia (AML) cells


title: MOLM13, shNAT10-1, ac4C, input, rep1


title: MOLM13, shNS, ac4C, input, rep2


title: BC2121 RPMI H3K27Ac

description: H3K27ac ChIP-seq


title: hy5, 1h W+FR, rep3

value: harvested after 1h of W+FR


title: BC2119 RPMI H3K27Ac

description: H3K27ac ChIP-seq


title: BC2119 HKCA H3K27Ac

description: H3K27ac ChIP-seq

value: HKCA


title: hy5, 8h W+FR, rep1

value: whole seedlings


title: MOLM13, shNS, ac4C, input, rep1


title: As4.1 cells treated with DMSO, replicate 2

value: kidney


title: hy5, 1h W+FR, rep2

value: 7-day-old seedlings

value: Continuous W at 22°C


title: hy5, 8h W+FR, rep2


title: As4.1 cells treated with DMSO, replicate 1


title: As4.1 cells treated with 10 μM H89, replicate 2


title: MOLM13, IVT, ac4C, IP, rep2

value: WT-IVT

value: IP


title: BC2118 HKCA+CD40i H3K27Ac

description: H3K27ac ChIP-seq


title: As4.1 cells treated with 10 μM H89, replicate 1


title: hy5, 1h W+FR, rep1


title: MOLM13, IVT, ac4C, input, rep2


title: hy5, 0h W+FR, rep3

value: harvested immediately before W+FR


title: BC2118 HKCA H3K27Ac

description: H3K27ac ChIP-seq


title: BC2118 RPMI H3K27Ac

description: H3K27ac ChIP-seq

value: untreated


title: hy5, 0h W+FR, rep2


title: hy5, 0h W+FR, rep1


title: BC2121 HKCA H3K4me3

description: H3K4me3 ChIP-seq


title: B6N-OFL-3

data_processing:
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling.
Illumina adapter sequences were removed using the cutadapt software (version 2.7), and the remaining reads sequences were aligned to the mouse genome (GRCm38) using Tophat2 software (version 2.1.1) with the default parameters.
After the alignment, the numbers of reads mapped to the gene features (GTF file of GRCm38.91) were counted using HTseq sofrware. The read counts for the samples in each condition were then normalized using the TMM (trimmed mean of M-values) normalization of the edgeR package.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include TMM-normalized read counts for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: anterior cingulate cortex (ACC) tissue

extract_protocol:
Total RNAs were obtained from anterior cingulate cortex (ACC) tissues using Trizol reagent (Invitrogen Life Technologies, Grand Island, NY). TruSeq RNA Sample Prep Kit v2 for Illumina kit was used for the construction of sequencing libraries, according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: anterior cingulate cortex

value: C57BL/6NJ mice

tag: condition

value: OFL


title: MOLM13, WT, ac4C, IP, rep2

value: WT


title: WT, 8h W+FR, rep3

value: wild-type (Col-0)

value: harvested after 8h of W+FR


title: As4.1 cells treated with 10 μM A-485, replicate 1


title: BC2121 RPMI H3K4me3

description: H3K4me3 ChIP-seq

value: monocytes

value: healthy donor


title: MOLM13, IVT, ac4C, IP, rep1

value: Human acute myeloid leukemia (AML) cells


title: BC2121 HKCA + CD40i H3K4me3

description: H3K4me3 ChIP-seq

value: HKCA + CD40-TRAF6i


title: MOLM13, WT, ac4C, IP, rep1


title: B6N-OFL-2


title: MOLM13, WT, ac4C, input, rep1

value: input


title: BC2119 HKCA + CD40i H3K4me3

description: H3K4me3 ChIP-seq


title: WT, 8h W+FR, rep2

value: whole seedlings

value: 7-day-old seedlings


title: MOLM13, shNAT10-2, mRNA, rep2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by by cutadapt v. 4.1 with parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q 20,20 --max-n 0.25 --trim-n.
The clean reads were then mapped to the human genome (hg38) with HISAT2 v.2.1.1 with “--rna-strandness RF” parameters, and supplying the GENCODE Release 39 gene annotation. A post-alignment filter was preformed to remove alignments to ribosomal RNA (rRNA), secondary alignment and non-concordant mate pairs.
Read counts on genes were calculated by HTSeq v.2.0.2 against the GENCODE Release 39 gene annotation. Differentially expressed genes were calculated by DESeq2 with fold change > 1.5 and adjusted P-value < 0.05.
Assembly: hg38
Supplementary files format and content: Raw read count of genes and processed results from DESeq2.

extract_protocol:
MOLM13 total RNA was isolated using the TRIzol reagent. mRNA was then purified from total RNA using VAHTS® mRNA Capture Beads.
Libraries for RNA-seq were constructed using VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina following manufacturer’s protocol.

treatment_protocol: MOLM13 cells were transfected with NAT10-sh1, NAT10-sh2 or shNS lentiviruses to induse knockdown of NAT10.


title: MOLM13, WT, ac4C, input, rep2


title: BC2119 RPMI H3K4me3

description: H3K4me3 ChIP-seq


title: AKR-OFL-3

value: AKR/J mice


title: AKR-OFL-2


title: B6N-OFL-1


title: As4.1 cells treated with 10 μM A-485, replicate 2

value: kidney


title: AKR-OFL-1


title: MOLM13, IVT, ac4C, input, rep1

value: WT-IVT


title: WT, 1h W+FR, rep3

value: Continuous W at 22°C

value: harvested after 1h of W+FR


title: BC2119 HKCA H3K4me3

description: H3K4me3 ChIP-seq

value: HKCA


title: BC2118 HKCA+CD40i H3K4me3

description: H3K4me3 ChIP-seq


title: WT, 1h W+FR, rep2


title: MOLM13, shNAT10-2, mRNA, rep1


title: B6N-naive-3

value: anterior cingulate cortex

value: C57BL/6NJ mice

value: naïve


title: WT, 0h W+FR, rep3

value: wild-type (Col-0)

value: harvested immediately before W+FR


title: WT, 1h W+FR, rep1


title: MOLM13, shNAT10-1, mRNA, rep2


title: MOLM13, shNS, mRNA, rep2

value: shNS


title: MOLM13, shNAT10-1, mRNA, rep1

value: Human acute myeloid leukemia (AML) cells


title: B6N-naive-4


title: BC2118 HKCA H3K4me3

description: H3K4me3 ChIP-seq

value: monocytes

value: healthy donor


title: WT, 8h W+FR, rep1

value: whole seedlings

value: harvested after 8h of W+FR


title: MOLM13, shNS, mRNA, rep1


title: B6N-naive-1


title: WT, 0h W+FR, rep1

value: 7-day-old seedlings


title: s3L1

city: Madison

first: Barak

last: Blum

state: Wisconsin

address: 4551 WIMR II, 1111 Highland Ave.

institute: University of Wisconsin-Madison

data_processing:
Base-calling: bcl2fastq v2.20.0.422
Trimming: skewer 0.1.123
Alignment: STAR 2.5.3a
Expression: RSEM 1.3.0
DE: edgeR v.3.16.5
Assembly: ENSEMBL_GRCm38.89_p5
Supplementary files format and content: comma-delimited text file include TPM values for each sample

source_name: Pancreas

extract_protocol:
Mouse neonate islets were digested from pancreata and purified by Histopaque centrifugation. The isolated islets were trypsinized and sorted through flow cytometer for mCherry+ cells (β cell). The RNA extraction was performed on sorted cells via TRIzol phenol-chloroform.
DNA libraries were generated using Takara’s SMART-Seq v4 Low Input RNA Kit for Sequencing (Takara, Mountain View, CA) for cDNA synthesis and the Illumina NexteraXT DNA Library Preparation (Illumina, San Diego, CA) kit for cDNA dual indexing. Full-length cDNA fragments were generated from 1 to 10 ng total RNA by SMART (Switching Mechanism at 5′ End of RNA Template) technology. cDNA fragments were fragmented and dual indexed in a single step using the Nextera kit’s simultaneous transposon and tagmentation step. Quality and quantity of completed libraries were assessed using Agilent DNA series chip assay (Agilent Technologies, Santa Clara, CA) and Invitrogen Qubit ds DNA HS Kit (Invitrogen, Carlsbad, CA), respectively. Each library was standardized to 2 nM.

value: Pancreas

value: Pancreatic Beta cell

value: Rosa26-lsl-H2B-mCherry/+; Ucn3-Cre/+; Robo1delta/delta; Robo2flx/flx

tag: age

value: neonate day 13


title: s5L1


title: B6N-naive-2


title: s2L1

value: Rosa26-lsl-H2B-mCherry/+; Ucn3-Cre/+; Robo1+/+; Robo2+/+


title: 8W_SW,rep1

city: Chongqing

first: Yuhan

address: Xinqiao Central Street, Shapingba District

institute: Army Medical University (Third Military Medical University)

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome)
Assembly: Rnor_6.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: brain

extract_protocol:
Fresh brain tissue was anatomized into gray and white matters under the dissecting microscope and then cut into small tissue masses and transferred into gentleMACSTM C tubes (Miltenyi Biotec, Germany) containing papain and deoxyribonuclease. The C tubes were installed to the gentleMACS Octo Dissociator with the gentleMACS Program 37C_ABDK_01 running for 30 minutes. The effect of enzymolysis was terminated using horse serum, and after brief centrifugation and discarding the supernatant the pellet was collected and resuspended. The cell strainer with a diameter 70 μm was applied to filter the resuspended pellet and obtain cell suspension. The myelin debris remaining in the cell suspension was removed using Percoll solution by mean of density gradient centrifugation, and the red blood cell was eliminated from the cell suspension via red blood cell lysis buffer. Single-cell pellet was resuspended in 80μL PB buffer and incubated with 20μL CD11b/c (Microglia) MicroBeads for 30 minutes in the refrigerator. MS column was chosen for cell sorting and rinsed with 500 μL PB buffer inadvance. The single‑cell suspension was applied onto the column in the magnetic field of the MiniMACS™ separator and the column was washed with 500 μL PB buffer threetimes. Finally, 1mL PB buffer was pipetted onto the column, and the magnetically labeled cells, principally consisted of microglia, were flush out immediately by firmly pushing the plunger into the column.
R1 (read 1 primer sequence) are added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) are added during library construction via End Repair, Atailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: brain

tag: tissue region

value: white matter

value: Microglia

value: Sprague-Dawley

tag: Sex

value: male

value: sham

tag: time


title: WT, 0h W+FR, rep2

tag: tissue

value: Continuous W at 22°C

value: wild-type (Col-0)

value: harvested immediately before W+FR


title: AKR-naive-4

value: anterior cingulate cortex

tag: strain

value: AKR/J mice

value: naïve


title: 8W_SG,rep1

value: gray matter