title: KD, KD60

description: Library name: KD60_S83


title: S153

status: Public on Jan 10 2025

type: genomic

city: LYON

first: Benjamin

last: Gibert

address: 28 promenade Léa et Napoléon Bullukian

country: France

institute: CRCL – UMR 1052 / CNRS 5286

hyb_protocol: Infinium MethylationEPIC BeadChip (850K) array were carried out following Infinium HD Methylation Assay Protocol by the Infinium MethylationEPIC Array Service (Diagenode Cat# G02090000)

data_processing: Data were analyzed using the methylkey R package (accessible at https://github.com/IARCbioinfo/methylkey).   Briefly, raw intensity data files were preprocessed and normalized using the minfi Bioconductor package.   Beta-values, which measure the proportion of methylated alleles at any given locus, were generated for each CpG site.   CpG sites for which detected signals were not significantly different from background levels (p > 0.02) and for which data were missing in >20% of the samples were excluded.   Cross-reactive probes, probes located on the X and Y chromosomes and at chromosome locations associated with known SNPs were also excluded, resulting in a final dataset of 792,079 CpG probes.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Mesenteric Lymph Node

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from frozen tissue using Qiagen All prep DNA/RNA Extraction kit according to standard instructions.

tag: tumor type

value: multifocal

tag: primary tumor site

value: ILEUM

tag: discovery cohort

value: NO


title: KD, KD56

type: SRA

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: Library name: KD56_S79

library_source: genomic

data_processing:
After demultiplexing the 16S sequence reads based on sample-specific indices, primer sequences were trimmed using Cutadapt v.1.15. The trimmed reads were then processed using the DADA2 R package v.1.18.0 to construct amplicon sequence variants (ASVs). This was achieved using the filterAndTrim function with the standard parameters (maxN = 0, truncQ = 2, and maxEE = 2). Possible chimeric reads were removed using the remote Bimera Denovo function of DADA2. Taxonomic assignment of each amplicon sequence variant (ASV) was performed by similarity searching against the Greengene v13.8 database with a threshold of 97% similarity. The rarefied feature table was then converted into the linear discriminant analysis effect size (LEfSe) format using tools available on Galaxy Hutlab (http://huttenhower.sph.harvard.edu/galaxy/) and MicrobiomeAnalyst (https://www.microbiomeanalyst.ca/MicrobiomeAnalyst/home.xhtml).
Supplementary files format and content: Excel, Phylum-, Genus- and Species-Level Taxonomy Tables
Library strategy: 16S rRNA-seq

organism: human feces metagenome

source_name: fecal matter (not tissue)

extract_protocol:
Stool DNA extraction was performed according to the manufacturer’s protocol using a QiAamp DNA Stool Mini Kit (Qiagen). The extracted DNA was stored in 1X ATE buffer (10 mM Tris-Cl pH 8.3, 0.1 mM EDTA, and 0.04% NaN3) at -20°C for subsequent 16S rRNA-targeted sequencing.
PCR was performed using the forward primer 5′- TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CCT ACG GGN GGC WGC AG-3′ and reverse primer 5′- GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGA CTA CHV GGG TAT CTA ATC C-3′ for the V3–V4 region of the 16S rRNA gene. Amplicons generated from each sample (~ 330 bp) were purified using AMPure XP magnetic beads (Beckman Coulter).

tag: tissue

value: fecal matter (not tissue)


title: S154

scan_protocol: Infinium MethylationEPIC BeadChip (850K) array were carried out following Infinium HD Methylation Assay Protocol by the Infinium MethylationEPIC Array Service (Diagenode Cat# G02090000)

source_name: Tumor


title: KD, KD53

description: Library name: KD53_S76


title: KD, KD55

description: Library name: KD55_S78


title: KD, KD54

description: Library name: KD54_S77


title: KD, KD57

description: Library name: KD57_S80


title: S152

value: YES


title: KD, KD51

description: Library name: KD51_S74


title: KD, KD52

description: Library name: KD52_S75


title: KD, KD50

description: Library name: KD50_S73


title: S150


title: S151

value: unifocal

value: JEJUNUM


title: KD, KD49

description: Library name: KD49_S72


title: S149


title: KD, KD4

description: Library name: KD4_S59


title: KD, KD3

description: Library name: KD3_S58


title: S146


title: S148


title: KD, KD41

description: Library name: KD41_S64


title: S145


title: KD, KD2

description: Library name: KD2_S57


title: RNAi DNMT3A HeLa replicate 2

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

hyb_protocol: Genomic DNA (300–800 ng) was converted with sodium bisulfite using the EZ DNA Methylation Kit (Zymo Research), and it was hybridized with the Illumina MouseMethylation BeadChip array according to the manufacturer’s protocol.

scan_protocol: Arrays were imaged using HiScan Reader using standard recommended Illumina scanner setting.

data_processing: Raw Infinium MouseMethylation data were preprocessed as followed: CpG probes of low quality (detection p-value threshold of 0.05) were removed from the analysis and Beta-values were computed using the following formula: Beta-value = M/[U+M] where M and U are the raw “methylated” and “unmethylated” signals, respectively. Beta-values were corrected for type I and type II bias using the peak-based correction.

source_name: RNAi control HeLa

growth_protocol: HeLa cells were cultured at 37°C under 5% CO2 in DMEM (Gibco) media supplemented with 10% FBS and 1% 100X Pen Strep (Gibco).

extract_protocol: Genomic DNA was extracted with the QIAamp DNA Mini Kit (from QIAGEN) following the manufacturer’s protocol.

treatment_protocol: In RNAi experiments, HeLa cells were transfected in 10 cm dishes with 20 nM short interfering RNAs (siRNAs, Horizon), using INTERFERin (Sartorius) according to the manufacturer's protocol. RNAi induction was performed in two rounds: an initial siRNA transfection followed by a second transfection 48 hours later. Cells were reseeded between transfection rounds and harvested after 96 hours (from the first transfection). The knockdown efficiency was checked by western blotting.

tag: RNAi

tag: replicate


title: KD, KD1

description: Library name: KD1_S56


title: KD, KD19

description: Library name: KD19_S74


title: KD, KD18

description: Library name: KD18_S73


title: KD, KD43

description: Library name: KD43_S66


title: S147


title: KD, KD42

description: Library name: KD42_S65


title: S144


title: KD, KD44

description: Library name: KD44_S67


title: KD, KD16

description: Library name: KD16_S71


title: RNAi DNMT3B HeLa replicate 3


title: KD, KD15

description: Library name: KD15_S70


title: S143


title: KD, KD14

description: Library name: KD14_S69


title: KD, KD12

description: Library name: KD12_S67


title: S142


title: S140


title: KD, KD11

description: Library name: KD11_S66


title: Experiment2_MULTIseq_barcodes4: scRNA-seq from the V-SVZ

city: San Francisco

first: Arantxa

last: Cebrian Silla

state: California

address: 35 Medical center Way

department: Neurological Surgery

country: USA

institute: UCSF

description: Library name: ACSAAB02_b4

library_source: transcriptomic single cell

data_processing:
Sequencing and read alignment. Libraries were sequenced in an Illumina NovaSeq 6000. Alignment was performed on STAR v2.7.11 and included both intronic and exonic mappings (--soloFeatures Gene GeneFull Velocyto). We used an optimized mouse reference genome Pool et al., 2023 edited to include GFP and Cre genes. We also included a WPRE sequence to serve as a proxy for TdTomato expression (as it is present in the 3' end of the TdTomato gene in Mizrak et al 2020).
Single cell RNAseq data normalization and dimensionality reduction. Cell barcodes were filtered to remove barcodes associated with multiple Multi-seq barcodes, high mitochondrial reads (> 10% reads in mitochondrial genes). We also filtered out barcodes in the bottom or top 2% of total number of reads in order to remove low-quality cells and doublets not detected by Multi-seq barcoding, respectively. Data from different technical replicates were integrated for batch correction (Stuart 2019) using CCA integration in Seurat v. 5. Counts were normalized using a negative binomial model (SCTransform v2), dimensionality was reduced to 100 principal components (PCs), which were used to project in two dimensions using uniform manifold approximation and projection (UMAP).
Integration with another dataset: Data from ACSAAB01 (Experiment_1) and ACSAAB02 (Experiment_2) were integrated with the P30 V-SVZ dataset from Cebrian-Silla et al., 2021 (GEO: GSE165555, sample: GSM5039270).
Assembly: Mus Musculus, source: Pool, A.-H., Poldsam, H., Chen, S., Thomson, M., and Oka, Y. (2023). Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references. Nat. Methods 20, 1506–1515.
Supplementary files format and content: Processed data files include barcodes, features .txt files and matrices .mtx files. We also include a .cvs file with Metadata. Processed data files include the integrated data from ACSAAB01(Experiment_1), ACSAAB02 (Experiment_2) and Cebrian-Silla et al 2021 datasets. To identify each one of the datasets in our metadata: Cebrian-Silla et al., (batch_1), ACSAAB01 (batch_2) and ACSAAB02 (batch_3). Region anotations are: LV (Lateral Ventricle, refering to dissections from the V-SVZ with no subdivisions), LW (Lateral Wall, refering to microdissections from the V-SVZ that only include periventricular regions) and Wedge (microdissections of the dorsolateral extension of the V-SVZ or wedge). bcell_subtype identifies B cells by region and activation states. b_type identifies B1 and B2 cells.

molecule: polyA RNA

organism: Mus musculus

source_name: Brain, Ventricular-Subventricular zone

extract_protocol:
Samples from mice injected with Ad:Cre:GFP were prepared as following:  15-24 hours after Ad:Cre:GFP intraventricular injections, mice (Experiment 1: n=14, P27-30, Experiment 2: n=12, P27-p30) received intraperitoneal administration of 2.5% Avertin followed by decapitation. Brains were extracted and 0.5 mm slices were obtained with a mouse brain slicer (Steel Brain Matrix - Coronal 0.5mm, Alto). The V-SVZ lateral wall and dorsal wedge were microdissected and considered separate samples. To analyze the transcriptomic profile of aged mice we also microdissected the V-SVZ of two non-infected hGFAP:GFP 1 year old mice. The wedge region was not included. All V-SVZ micro-dissections were performed in L-15 medium on ice and the tissue was transferred to Papain-EBSS (LK003150, Worthington). Tissue was digested for 30 min at 37ºC in a thermomixer at 900 RPM. Mechanical dissociation with a P1000 pipette tip (20 seconds), then with a  fire-polished pasteur pipette for 3 min.  Cells were centrifuged for 5 min, 300 RCF at room temp, and the pellet was resuspended with DNAase/ovomucoid inhibitor according to the manufacturer's protocol (Worthington). Cells were incubated in red blood cell lysis buffer (420301, Biolegend) 3-4 min at 4ºC. For MULTI-seq barcoding, cells were suspended with Anchor:Barcode solution for 5 minutes at 4ºC. A Co-Anchor solution was added and incubated for 5 min87. Samples were combined and filtered with a FlowMi 40µm filter (BAH136800040-50EA, Sigma). To remove myelin, the cell suspension was incubated with Myelin Removal Beads (130-096-733, Miltenyi Biotec) (6μl/brain) for 15 min at 2-8°C. Cells were washed with 0.5% BSA-PBS and transferred to MACS columns. The effluent was collected, and the cell density was counted.
Cells were loaded into a 10x Genomics Chromium Single Cell Controller. We used the 10x Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 to generate cDNA libraries for sequencing according to the manufacturer's protocols. MULTI-Seq barcode libraries were prepared according to MULTI-Seq (McGinnis et al. 2019)  protocols.

value: Brain, Ventricular-Subventricular zone

tag: age

value: Postnatal day 30

tag: Sex

value: pooled males and females

tag: genotype

value: Ai14 mice

tag: treatment

value: Intraventricular injection AdCreGFP


title: NC, SC62

description: Library name: SC62_S48


title: S139


title: KD, KD10

description: Library name: KD10_S65


title: KD, KD20

description: Library name: KD20_S75


title: KD, KD59

description: Library name: KD59_S82


title: NC, SC63

description: Library name: SC63_S49


title: Experiment2_MULTIseq_barcodes3: scRNA-seq from the V-SVZ

description: Library name: ACSAAB02_b3


title: NC, SC60

description: Library name: SC60_S46


title: S138


title: Experiment2_MULTIseq_barcodes1: scRNA-seq from the V-SVZ

description: Library name: ACSAAB02_b1


title: S136


title: NC, SC58

description: Library name: SC58_S44


title: S137

source_name: Normal


title: S135


title: NC, SC55

description: Library name: SC55_S41


title: RNAi DNMT3A HeLa replicate 3


title: NC, SC59

description: Library name: SC59_S45


title: Experiment2_MULTIseq_barcodes2: scRNA-seq from the V-SVZ

description: Library name: ACSAAB02_b2


title: NC, SC54

description: Library name: SC54_S40


title: NC, SC57

description: Library name: SC57_S43


title: Experiment2_Gene_expression4: scRNA-seq from the V-SVZ

description: Library name: ACSAAB02_g4


title: KD, KD17

description: Library name: KD17_S72


title: NC, SC56

description: Library name: SC56_S42


title: KD, KD13

description: Library name: KD13_S68


title: S141


title: Experiment2_Gene_expression3: scRNA-seq from the V-SVZ

description: Library name: ACSAAB02_g3


title: NC, SC53

description: Library name: SC53_S39


title: NC, SC52

description: Library name: SC52_S38


title: S134


title: NC, SC51

description: Library name: SC51_S37


title: Experiment2_Gene_expression2: scRNA-seq from the V-SVZ

description: Library name: ACSAAB02_g2


title: NC, SC50

description: Library name: SC50_S36


title: S133


title: S132


title: Experiment1_MULTIseq_barcodes2: scRNA-seq from the V-SVZ

description: Library name: ACSAAB01_b2

value: Postnatal day 30 and 365

value: Ai14 mice (P30) and hGFAP:GFP (P365)


title: NC, SC45

description: Library name: SC45_S32


title: NC, SC49

description: Library name: SC49_S35


title: S131


title: NC, SC46

description: Library name: SC46_S33


title: Experiment2_Gene_expression1: scRNA-seq from the V-SVZ

description: Library name: ACSAAB02_g1


title: Experiment1_MULTIseq_barcodes1: scRNA-seq from the V-SVZ

description: Library name: ACSAAB01_b1


title: NC, SC39

description: Library name: SC39_S27


title: RNAi SETD2 HeLa replicate 2


title: NC, SC43

description: Library name: SC43_S31


title: S130


title: RNAi control HeLa replicate 4

value: Control


title: NC, SC35

description: Library name: SC35_S25


title: Experiment1_Gene_expression2: scRNA-seq from the V-SVZ

description: Library name: ACSAAB01_g2


title: RNAi DNMT1 HeLa replicate 2


title: NC, SC31

description: Library name: SC31_S30


title: Experiment1_Gene_expression1: scRNA-seq from the V-SVZ

description: Library name: ACSAAB01_g1


title: NC, SC29

description: Library name: SC29_S21


title: RNAi SETD2 HeLa replicate 3


title: RNAi DNMT1 HeLa replicate 1


title: S128


title: RNAi control HeLa replicate 1


title: NC, SC61

description: Library name: SC61_S47


title: RNAi control HeLa replicate 3


title: E16.5 primary cortical cells, 12 hr, replicate C

city: Durham

first: Lucas

last: Serdar

state: NC

address: 213 Research Dr

institute: Duke University

library_source: transcriptomic

data_processing:
For samples that were sequenced twice, reads were combined for downstream steps. Sequenced reads were processed with the SlamDunk tool v0.4.3, using the mm10 genome and exons extracted from the GENCODE vM24 gene annotation. The number of covered (T)s and converted (T)s for each exon was extracted from the SlamDunk results. Covered (T) counts for all exons within a gene were summed together, and the same was done for converted (T)s. A conversion rate was calculated for each gene as the percentage of converted (T)s to covered (T)s. These conversion rates were calculated for each time point, and a half-life value was calculated for each gene based on the decay in these conversion rates over time. The decay curve was estimated in R with the “nlsLM” function from "minpack.lm" package, using the model “y ~ exp(-(k*x))”, where “x” are the time points and “y” are the conversion rates scaled such that the initial conversion rate (at time point 0) is 1. The “k” value was extracted from the fit curve, and the half-life was calculated as “ln(0.5) / -k”.
Assembly: mm10
Supplementary files format and content: Text files containing read counts in CPM, T-to-C conversion rates, and calculated half-lives.
Library strategy: SLAM-seq

molecule: total RNA

source_name: primary cortical cells

growth_protocol: Embryos were dissected in cold PBS and cortical tissue was microdissected from three biological replicates. Each biological replicate consisted of pooled cortical tissue from 7 embryos (E11.5), or 2 embryos (E14.5 and E16.5). Cortices were dissociated by incubation with 0.25% Trypsin (Thermo Fisher) at 37 °C for 5 min (E11.5), 10 min (E14.5) or 20 min (E16.5). Trypsinization was halted by addition of trypsin inhibitor (Sigma T6522) diluted in neural progenitor media [DMEM (Thermo Fisher 11995-065) supplemented with N-acetyl-L-cysteine (Sigma A9165, 1 mM), N2 (Thermo Fisher 17502048, 1X), B27 without vitamin A (Thermo Fisher 12587-010, 1X), and mouse bFGF (R&D Systems 3139-FB025, 10 ng/mL)]. Following trituration with a P1000 pipette, cells were pelleted at 200 g for 5 min to remove debris then resuspended in fresh neural progenitor media. Cells from each biological replicate were divided into five wells of a 24-well plate coated with poly-D-lysine (Sigma P7280) and placed at 37 °C in a humidified incubator with 5% CO2. Cells were allowed to attach to the plate for 2 hr.

extract_protocol:
Cells from a single well per replicate were lysed 0, 2, 4, 8, and 12 hr after addition of uridine by addition of RLT buffer (Qiagen RNeasy Plus Micro Kit, cat. 74034) supplemented with 1 mM DTT. Lysates were stored at -80 °C before further processing. RNA was extracted from lysates using the Qiagen RNeasy Plus Micro Kit according to manufacturer’s instructions, except all buffers were supplemented with 1 mM DTT. Alkylation of 4sU RNA was performed as previously described (Herzog et al., Nat. Methods 2017) using ~1.5 µg of RNA per replicate. After alkylation, RNA was re-purified using the RNA Clean and Concentrator Kit (Zymo 11-325).
Sequencing libraries were generated using 400 ng of alkylated input RNA per sample and the Illumina Stranded mRNA Prep Kit (cat. 20040532) according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with 100 uM 4sU for 20 hr. The time of 4sU addition was designated as the t = -20 hr time point. Media was replaced with fresh 4sU containing media at t = -12, -8, -4, and -1 hr. At t = 0 hr, a 50X molar excess (i.e. 5 mM) of uridine was added to the media.

tag: cell type

value: primary cortical cells

value: WT

value: 100 uM 4sU


title: NC, S8

description: Library name: S8_S20


title: NC, S7-1

description: Library name: S7_S51


title: S127

value: multifocal

value: ILEUM


title: NC, S9

description: Library name: S9_S21

value: fecal matter (not tissue)


title: NC, SC34

description: Library name: SC34_S24


title: S129

value: NO


title: S126


title: NC, S7

description: Library name: S7_S19


title: E16.5 primary cortical cells, 8 hr, replicate C


title: RNAi DNMT3B HeLa replicate 2


title: NC, S6

description: Library name: S6_S16


title: NC, SC48

description: Library name: SC48_S34


title: RNAi DNMT3A HeLa replicate 1


title: RNAi DNMT1 HeLa replicate 3


title: E16.5 primary cortical cells, 4 hr, replicate C


title: RNAi DNMT3B HeLa replicate 1


title: E16.5 primary cortical cells, 2 hr, replicate C


title: NC, S5

description: Library name: S5_S50


title: NC, S4

description: Library name: S4_S18


title: S124


title: S125


title: NC, S1

description: Library name: S1_S8


title: NC, S3

description: Library name: S3_S9


title: E16.5 primary cortical cells, 0 hr, replicate C


title: S123

value: unifocal

value: YES


title: NC, S50

description: Library name: S50_S55


title: NC, S14

description: Library name: S14_S17


title: RNAi control HeLa replicate 2


title: E16.5 primary cortical cells, 8 hr, replicate B


title: S120


title: NC, C7

description: Library name: C7_S81


title: S122


title: NC, C5

description: Library name: C5_S79


title: NC, C32

description: Library name: C32_S106


title: NC, S11

description: Library name: S11_S22


title: NC, S18

description: Library name: S18_S10


title: E16.5 primary cortical cells, 12 hr, replicate B


title: NC, C6

description: Library name: C6_S80


title: S119


title: S121


title: E16.5 primary cortical cells, 4 hr, replicate B


title: E16.5 primary cortical cells, 2 hr, replicate B


title: RNAi SETD2 HeLa replicate 1


title: E16.5 primary cortical cells, 0 hr, replicate B


title: NC, C31

description: Library name: C31_S105


title: NC, S19

description: Library name: S19_S11


title: S118


title: NC, C30

description: Library name: C30_S104


title: NC, C2

description: Library name: C2_S76


title: E16.5 primary cortical cells, 12 hr, replicate A


title: NC, C22

description: Library name: C22_S96


title: S117

source_name: Liver metastasis


title: NC, C21

description: Library name: C21_S95


title: E16.5 primary cortical cells, 8 hr, replicate A


title: S116


title: E16.5 primary cortical cells, 4 hr, replicate A


title: NC, C20

description: Library name: C20_S94


title: S115


title: S114


title: NC, C13

description: Library name: C13_S87


title: NC, C11

description: Library name: C11_S85


title: NC, C10

description: Library name: C10_S84


title: 581_dTAG_H4K20me2_T0_rep3

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

description:
Library name: Sample76
581_dTAG_H4K20me2_RRPM_merged.bw

data_processing:
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.4.2) and uniquely mapped peaks kept using samtools (v1.12)
duplicate reads were removed with picard (version 2.26.10)
bam files were processed to bigwig for RPM by bamCoverage or RRPM in SeqMonk
bigwigs: bam files were normalized to the number of million of reads (RPM) in 50 bp bins with bamCoverage
Assembly: mm10 and dm6
Supplementary files format and content: bigwigs
Library strategy: CHOR-seq

growth_protocol: ESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 °C with 5 % CO2. DMEM was supplied with fetal bovine serum (15 %), home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using Trypsin-EDTA or TrypLE. Drosophila S2-DRSC cells were cultivated in suspension in spinners using M3+BPYE media, 10% heat-inactivated FBS , and 1X penicillin/streptomycin . Cells were incubated at 25°C with 5% CO2.

extract_protocol:
After the appropriate treatment, 1% formaldehyde for 10 min. Then, glycine was added to quench the reaction and cells were subsequently lysed. Sonication was performed on isolated nuclei using a Covaris E220. DNA fragments were immunoprecipitated, purified fragments were biotinylated, libraries were prepared, EdU-biotin fragments were pulled-down and sequenced.
Libraries were costructed using the KAPA Hyperprep kit and Illumina-compatible indexed adapters (Pentabase) following manufacturer’s instruction. For the amplification step, 11 PCR cycles were used. Subsequently, the DNA underwent size selection using Agencourt AMPure XP beads (Beckman Coulter, A63881) to obtain fragments between 200-700 bp. Libraries were validated using Agilent Fragment Analyzer.

treatment_protocol: Cells were incubated in EdU media (f.c. 10 µm) for 10 min and then collected (T0). If treated with DMSO or dTAG, cells were incubated for 1uM dTAG or DMSO prior to incubation with EdU for 10 min and then either collected (T0).

tag: cell line

value: embryonic stem cells

value: POLE4-dTAG, MCM2-2A clone 2

tag: chip antibody


title: E14.5 primary cortical cells, 12 hr, replicate C


title: NC, C16

description: Library name: C16_S90


title: E16.5 primary cortical cells, 0 hr, replicate A


title: 581_dTAG_H4K20me2_T0_rep2

description:
Library name: Sample75
581_dTAG_H4K20me2_RRPM_merged.bw


title: S112


title: NC, C18

description: Library name: C18_S92


title: NC, C12

description: Library name: C12_S86


title: 581_dTAG_H4K20me2_T0_rep1

description:
Library name: Sample74
581_dTAG_H4K20me2_RRPM_merged.bw


title: S110


title: E14.5 primary cortical cells, 4 hr, replicate C


title: NC, C27

description: Library name: C27_S101


title: S113


title: 581_DMSO_H4K20me2_T0_rep3

description:
Library name: Sample73
581_DMSO_H4K20me2_RRPM_merged.bw


title: S109


title: 581_DMSO_H4K20me2_T0_rep2

description:
Library name: Sample72
581_DMSO_H4K20me2_RRPM_merged.bw


title: E16.5 primary cortical cells, 2 hr, replicate A


title: E14.5 primary cortical cells, 8 hr, replicate C


title: 581_DMSO_H4K20me2_T0_rep1

description:
Library name: Sample71
581_DMSO_H4K20me2_RRPM_merged.bw


title: E14.5 primary cortical cells, 2 hr, replicate C


title: S108


title: 555_dTAG_H4K20me2_T0_rep3

description:
Library name: Sample70
555_dTAG_H4K20me2_RRPM_merged.bw


title: 555_dTAG_H4K20me2_T0_rep1

description:
Library name: Sample68
555_dTAG_H4K20me2_RRPM_merged.bw


title: 555_dTAG_H4K20me2_T0_rep2

description:
Library name: Sample69
555_dTAG_H4K20me2_RRPM_merged.bw


title: S107


title: E14.5 primary cortical cells, 0 hr, replicate C


title: E14.5 primary cortical cells, 12 hr, replicate B


title: 555_DMSO_H4K20me2_T0_rep2

description:
Library name: Sample66
555_DMSO_H4K20me2_RRPM_merged.bw


title: S106


title: 555_DMSO_H4K20me2_T0_rep1

description:
Library name: Sample65
555_DMSO_H4K20me2_RRPM_merged.bw


title: E14.5 primary cortical cells, 8 hr, replicate B


title: 581_dTAG_strandedInput_T0_rep3

data_processing:
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.4.2) and uniquely mapped peaks kept using samtools (v1.12)
duplicate reads were removed with picard (version 2.26.10)
bam files were processed to bigwig for RPM by bamCoverage or RRPM in SeqMonk
Assembly: mm10 and dm6
Supplementary files format and content: bigwigs: bam files were normalized to the number of million of reads (RPM) in 50 bp bins with bamCoverage
Library strategy: CHOR-seq


title: S105


title: S104


title: 581_dTAG_H3_T0_rep3


title: 581_dTAG_H3K36me3_T0_rep3


title: E14.5 primary cortical cells, 4 hr, replicate B


title: E14.5 primary cortical cells, 2 hr, replicate B


title: 581_dTAG_strandedInput_T0_rep2


title: 581_dTAG_H3_T0_rep2


title: 581_dTAG_H3K36me3_T0_rep2


title: S103


title: S102


title: E14.5 primary cortical cells, 0 hr, replicate B


title: S101


title: E14.5 primary cortical cells, 12 hr, replicate A


title: 555_DMSO_H4K20me2_T0_rep3

description:
Library name: Sample67
555_DMSO_H4K20me2_RRPM_merged.bw


title: 581_dTAG_H3_T0_rep1


title: 581_dTAG_H3K36me3_T0_rep1


title: 581_DMSO_strandedInput_T0_rep3


title: E14.5 primary cortical cells, 8 hr, replicate A


title: 581_DMSO_H3K36me3_T0_rep3


title: E14.5 primary cortical cells, 4 hr, replicate A


title: S100


title: 581_DMSO_H3_T0_rep2


title: 581_DMSO_H3_T0_rep3


title: 581_DMSO_H3K36me3_T0_rep2


title: E14.5 primary cortical cells, 2 hr, replicate A


title: E14.5 primary cortical cells, 0 hr, replicate A


title: 581_DMSO_H3K36me3_T0_rep1


title: E11.5 primary cortical cells, 12 hr, replicate C


title: 555_dTAG_strandedInput_T0_rep3


title: 581_dTAG_strandedInput_T0_rep1


title: 555_dTAG_H3_T0_rep3


title: E11.5 primary cortical cells, 8 hr, replicate C


title: 581_DMSO_H3_T0_rep1


title: 555_dTAG_H3K36me3_T0_rep3


title: 555_dTAG_H3_T0_rep2


title: 555_dTAG_strandedInput_T0_rep2


title: 555_dTAG_H3K36me3_T0_rep2


title: E11.5 primary cortical cells, 4 hr, replicate C


title: E11.5 primary cortical cells, 2 hr, replicate C


title: 555_dTAG_strandedInput_T0_rep1


title: E11.5 primary cortical cells, 0 hr, replicate C


title: 581_DMSO_strandedInput_T0_rep2


title: 555_dTAG_H3_T0_rep1


title: 555_dTAG_H3K36me3_T0_rep1


city: Tianjin

first: Ke

last: Zhao

address: Qixiangtai Road, No.22

country: China

institute: Tianjin Medical University

description:
Library name: scMulti_CRISPRko(sgEnrich)
single-cell multiome datasets (ATAC + Gene Expression), sgRNA enrichment, CRISPRko

data_processing:
The single-cell multiome data was processed by Cell Ranger ARC v2.0.2, including aligning RNA reads to the transcriptome, mapping ATAC reads to the genome, quantifying gene expression levels, and identifying accessible chromatin peaks. The output of Cell Ranger ARC was subsequently analyzed using the R package Signac 1.11.0.In the case of sgRNA enrichment data, the enrichment reads were aligned to a reference genome using Cell Ranger v5.0.1, following the same procedure as for standard scRNA-seq data processing. Reads that failed to align to the reference genome were extracted using Samtools. These extracted reads were subsequently mapped to the sequences of the sgRNA library and its reverse complement, utilizing ACCG as the left anchor (located at the end of the U6 promoter) and GTTT as the right anchor. This mapping process allowed for the identification of sgRNA sequences and the determination of their expression levels in each cell. The resulting data, including cell barcodes and sgRNA UMI counts for each perturbed cell, were added to the dataset.
Assembly: hg19
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz; sgRNA enrichment output files: txt.

growth_protocol: HAP1 (Horizon Discovery) cells were cultured in IMDM (ThermoFisher) supplemented with 10% fetal bovine serum in 5% CO2 at 37°C.

extract_protocol:
Adherent cells were digested with 0.25% trypsin and collected in a 15mL tube containing serum-containing medium, followed by centrifugation and washing of the cell pellet with serum-free basal medium to obtain a single-cell suspension.
The library construction protocol for single-cell multiome datasets (ATAC + Gene Expression)(scMulti) was performed following the manufacturer's instructions using the Chromium Single Cell Multiome ATAC + Gene Expression Reagent Kits. Nuclei are resuspended and transposed with a Transposase to fragment DNA in open chromatin regions and add adapter sequences. The transposed nuclei are then encapsulated into Gel Beads-in-Emulsion (GEMs) with barcoded primers for both ATAC and gene expression. After GEMs are broken, the products are purified and amplified via PCR to generate sufficient material for library construction. The final ATAC and gene expression libraries are constructed by adding sample indices, size selection, and adapter ligation. Sequencing is performed on an Illumina platform with paired-end reads, capturing both ATAC and gene expression data, including barcodes, UMIs, and sample indices. Finally, the enriched sgRNA library and fragmented cDNA were sequenced on an Illumina NovaSeq6000 PE150 platform, following the standard 10x libraries configuration.

treatment_protocol: Diploid HAP1 cells were isolated from Hoechst (MCE)-stained HAP1 cells by flow sorting. Lentivirus containing dCas9-KRAB-blast and dCas9-VP64-blast were separately used to construct stably-expressing HAP1 cells with diploid cells. The activation and inhibition efficiency of single clones were verified by infection with lentivirus containing sgRNA targeting the TSS of EZH2. The two most efficient clones of each cell line were selected for perturbation.

tag: strain

value: Cas9-blast stably expressed single clone

value: transduced with lentivirus

tag: library type

value: mRNA


title: 555_DMSO_strandedInput_T0_rep3


description:
Library name: scMulti_CRISPRko(ATAC)
single-cell multiome datasets (ATAC + Gene Expression),  ATAC-seq, CRISPRko

library_source: genomic single cell

value: DNA


title: 555_DMSO_H3_T0_rep3


description:
Library name: scMulti_CRISPRko(GEX)
single-cell multiome datasets (ATAC + Gene Expression),  Gene Expression, CRISPRko


title: 581_DMSO_strandedInput_T0_rep1


title: E11.5 primary cortical cells, 8 hr, replicate B


title: 555_DMSO_H3K36me3_T0_rep3


title: 555_DMSO_strandedInput_T0_rep2


description:
Library name: scMulti_CRISPRa(sgEnrich)
single-cell multiome datasets (ATAC + Gene Expression), sgRNA enrichment, CRISPRa

value: dCas9-VP64 stably expressed single clone


title: 555_DMSO_H3_T0_rep2


title: E11.5 primary cortical cells, 4 hr, replicate B


title: 555_DMSO_H3K36me3_T0_rep2


description:
Library name: scMulti_CRISPRa(ATAC)
single-cell multiome datasets (ATAC + Gene Expression),  ATAC-seq, CRISPRa


title: 555_DMSO_strandedInput_T0_rep1


title: E11.5 primary cortical cells, 2 hr, replicate B


title: 555_DMSO_H3_T0_rep1


description:
Library name: scMulti_CRISPRa(GEX)
single-cell multiome datasets (ATAC + Gene Expression),  Gene Expression, CRISPRa

molecule: nuclear RNA


title: E11.5 primary cortical cells, 0 hr, replicate B


title: E11.5 primary cortical cells, 12 hr, replicate A


title: RNA_581_dTAG96h_T0_r1

data_processing:
Reads were quality trimmed and filtered for adapters with cutadapt (version 4.2)
reads were mapped to the mouse genome (mm10) using STAR mapper (version 2.7.11a) with special multimapping parameters --winAnchorMultimapNmax 200 and --outFilterMultimapNmax
Quantification of genes and repeat-subfamilies was performed with the TEcount tool, part of the TETranscripts (version 2.2.3) software suite using gencode (version M25) annotations and TETranscripts custom repeat annotations GRCm38_GENCODE_rmsk_TE
Differential expression analysis was performed with Deseq2. Differentially expressed (DE) genes/repeat subfamilies were defined as those with |FC| > 1.5 and FDR < 0.01
Assembly: mm10
Supplementary files format and content: fastq files and count table

extract_protocol:
After the appropriate treatment, RNA was isolated with the RNeasy Plus Mini Kit (Qiagen). Total RNA (500 ng) from each sample was depleted of rRNA using the NEBNext rRNA Depletion kit (NEB)
Strand-specific RNA libraries were prepared using the NEBNext Ultra Directional RNA Library Prep kit (NEB) following manufacturer’s instruction.

treatment_protocol: Cells were treated  with DMSO or dTAG (1uM) for 24hrs in serum+LIF conditions then either collected (T0), or treated with retinoic acid and collected after 24 hrs (T24), 48 hours (T48) or 60 hours (T60)

value: untreated

tag: time

value: RA T0 - dTAG T96


description:
Library name: scMulti_CRISPRi(sgEnrich)
single-cell multiome datasets (ATAC + Gene Expression), sgRNA enrichment, CRISPRi

value: dCas9-KRAB stably expressed single clone


title: RNA_581_DMSO96h_T0_r3

value: RA T0 - DMSO T96


title: RNA_581_DMSO96h_T0_r1


description:
Library name: scMulti_CRISPRi(ATAC)
single-cell multiome datasets (ATAC + Gene Expression),  ATAC-seq, CRISPRi


title: E11.5 primary cortical cells, 12 hr, replicate B

value: primary cortical cells

value: WT

value: 100 uM 4sU


title: RNA_581_DMSO96h_T0_r2


title: E11.5 primary cortical cells, 4 hr, replicate A


title: E11.5 primary cortical cells, 8 hr, replicate A


description:
Library name: scMulti_CRISPRi(GEX)
single-cell multiome datasets (ATAC + Gene Expression),  Gene Expression, CRISPRi


title: E11.5 primary cortical cells, 2 hr, replicate A


title: RNA_555_dTAG96h_T0_r3


title: RNA_555_dTAG96h_T0_r2


title: iRMD patient muscle biopsy 8

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

data_processing:
Paired fastq files were aligned to the human genome reference build hg38 using the STAR aligner v2.5.2b.
The aligned bam files were coordinate sorted using samtools and gene counts were calculated using the feature counts utility from subread (v1.5.1)
Assembly: hg38
Supplementary files format and content: tab delimited text files with raw counts for each sample
Supplementary files format and content: tab delimited text files with normalized gene counts for each sample

source_name: Skeletal Muscle

extract_protocol:
RNA was extracted from muscle tissue of eight iRMD patients using the AllPrep Universal Kit. Total RNA was quantified using the Quant-iT™ RiboGreen RNA Assay Kit and normalized to 5ng/ul.
2 uL of ERCC controls were spiked into each sample. 325 ng per sample was transferred into library preparation using an automated variant of the Illumina TruSeq™ Stranded mRNA Sample Preparation Kit. Oligo dT beads were used to select mRNA from the total RNA sample, followed by heat fragmentation and cDNA synthesis from the RNA template. cDNA then underwent dual-indexed library preparation: ‘A’ base addition, adapter ligation using P7 adapters, and PCR enrichment using P5 adapters. After enrichment the libraries were quantified using Quant-iT PicoGreen at a 1:200 dilution. Samples were normalized to 5 ng/uL, and the set was pooled and quantified using qPCR. All pipetting was done by either Agilent Bravo or Hamilton Starlet. Pooled libraries were normalized to 2nM and denatured using 0.1 N NaOH prior to sequencing. Flowcell cluster amplification and sequencing were performed according to the manufacturer’s protocols using the NovaSeq 6000. Each run consisted of 101bp paired-end reads with an eight-base index barcode.

value: Skeletal Muscle

tag: age of_onset

tag: age of_diagnosis

tag: biopsy site

value: Supraspin.

tag: cancer (age)

tag: cav3/cavin1 mutation

value: no

tag: achr binding_ab_positive

tag: increased insertional_activity

value: yes

tag: fibrillation potentials,_psws

tag: myopathic motor_unit_potentials


title: RNA_555_DMSO96h_T0_r3

value: embryonic stem cells

tag: genotype


title: iRMD patient muscle biopsy 7

tag: tissue

value: Triceps


title: E11.5 primary cortical cells, 0 hr, replicate A

tag: cell type

tag: treatment


title: 555_DMSO_H3K36me3_T0_rep1

tag: cell line

tag: chip antibody


title: RNA_555_DMSO96h_T0_r2


title: Cnot3;Trp53 dcKO cortex, rep 3

data_processing:
Read quality was assessed with FastQC and adapter trimming was performed using Cutadapt. Reads were aligned to the mm39 genome using STAR. Mapped reads were counted and assigned to genes using featureCounts, and differential expression in cKO and dcKO versus control samples was determined using DESeq2.
Assembly: mm39
Supplementary files format and content: csv file containing raw count data for each sample

source_name: cerebral cortex

extract_protocol:
E12.5 embryos were dissected in cold PBS and cortical tissue from single embryos were microdissected and flash frozen on dry ice. Three biological replicates were used per genotype. Tissue was homogenized in RLT buffer (Qiagen) and RNA was extracted using the RNeasy Plus Micro Kit (Qiagen).
Libraries were prepared using the TruSeq Stranded mRNA kit (Illumina) according to the manufacturer's instructions

value: cerebral cortex

value: Cnot3;p53 dcKO


title: RNA_555_DMSO96h_T0_r1


title: RNA_581_dTAG96h_T0_r3

value: POLE4-dTAG, MCM2-2A clone 2


title: repliATAC_nascent_581_DMSO_rep2

data_processing:
Samples were processed and quality controlled using the ENCODE standardized pipeline for ATAC-seq (v2.2.2), briefly, adapters were removed and reads trimmed with cutadapt, mapping was performed with bowtie2 to a hybrid mm10 and dm6 genomes and bam files were filtered, using only reads with MAPQ >= 30 and reads falling in mm10 encode blacklisted regions were removed. The bam files were downsampled to the same size as the lowest sequences library using picard (version 2.27.5) Downsamples bamfiles were merged and bigwig files for all repli-ATAC samples were computed using deepTools bamcoverage (version 3.5.1) in bins of 50bp and normalized using RPKM. Bigwig files were processed with deepTools multibigwigsummary. Enrichment plots around active TSSs were made by deepTools plotProfile.
Assembly: mm10
Supplementary files format and content: bigwigs: bam files were downsampled, filtered for subnucleosomal fragments and  normalized to the number of million of reads (RPM) in 50 bp bins with bamCoverage

source_name: Cell line

extract_protocol:
After the appropriate treatment, cells were trypsinized and collected in media. Samples were then processed and tagmented using TD buffer and TDE1 enzyme (Illumina). EdU-positive samples were biotinylated via Click-IT (Invitrogen) and purified with Ampure XP beads (Beckman Coulter). Biotinylated products were captured using MyOne Streptavidin T1 beads (Thermo Fisher Scientific), and the unbound fraction in the supernatant from streptavidin pulldown was purified using the MinElute Reaction Cleanup kit (Qiagen). Steady state samples were purified following tagmentation using the MinElute PCR Purification Kit (Qiagen). Samples were amplified using NEBNext High-Fidelity 2x PCR Master Mix (NEB) and final libraries were purified using Ampure XP beads.
Repli-ATAC-seq libraries were PCR amplified with the following reaction mix: 50 nM primer 1, 50 nM indexed primer 2, 1X NEBNext High-Fidelity PCR Master Mix (NEB, M0541).

value: Cell line

value: POLE4-dTAG MCM2-2A


title: repliATAC_nascent_581_DMSO_rep1


title: iRMD patient muscle biopsy 5

value: Vastus Lat.


title: Cnot3;Trp53 dcKO cortex, rep 2


title: repliATAC_nascent_581_2hdTAG_rep2


title: iRMD patient muscle biopsy 4

value: Biceps


title: RNA_581_dTAG96h_T0_r2

value: untreated

value: RA T0 - dTAG T96


title: RNA_555_dTAG96h_T0_r1


title: repliATAC_nascent_555_DMSO_rep2


title: Cnot3;Trp53 dcKO cortex, rep 1


title: repliATAC_nascent_555_DMSO_rep1


title: iRMD patient muscle biopsy 3


title: repliATAC_nascent_555_2hdTAG_rep2


title: repliATAC_nascent_581_2hdTAG_rep1


title: repliATAC_nascent_555_2hdTAG_rep1


title: iRMD patient muscle biopsy 2


title: iRMD patient muscle biopsy 1

value: breast (76)

value: yes*


title: WT_unt_rep3

description: WT Mouse ES cell line

data_processing:
SLAM-seq analyses were performed following a previously established protocol, using the SLAMdunk pipeline (v0.4.3). Briefly, reads were trimmed and mapped to the mouse genome (mm10) with NextGenMap, which accepts multiple mismatches. Reads were filtered to keep those with unique 3’UTR alignments. T-to-C SNPs were excluded (using ‘no 4SU negative controls’ as background). Total and T-to-C conversion counts were generated for each 3’UTR transcript region. The 3′ UTR counts were then imported into R and analyzed with edgeR (v3.42.2) for differential analysis. Total counts were used for steady-state expression analysis. For nascent RNAs, the conversion counts were normalized to total counts for nascent RNAs. The threshold for significant differential expression was set at p < 0.05 and absolute fold change >1.5.
To assess post-transcriptional regulation using SLAM-seq data, we then compared RNA fold changes of steady-state gene expression and nascent RNA regulation. This method was adapted from a previously established protocol using exonic and intronic reads in RNA-seq as proxy for steady-state and nascent RNA regulation, respectively.
Assembly: GRCm38/mm10
Supplementary files format and content: Count file

source_name: Mouse ES cells WT untreated Rep-3

growth_protocol: WT and Dnmt1 KO mouse ESCs were cultured in high-glucose DMEM-containing 15% FBS, 1mM sodium pyruvate, 1% non-essential amino acids, 1% glutaMAX™, 1% penicillin and streptomycin, 0.1mM β-mercaptoethanol (Gibco), and 1000 units/ml recombinant mouse leukemia inhibitory factor (LIF) (Millipore) on tissue culture plates coated with 0.1% gelatin and feeder cells (irradiated mouse embryonic fibroblasts).

extract_protocol:
RNA was extracted with TriPure (Roche), according to the instructions of the SLAM–seq Kit (Lexogen). Alkylation of incorporated S4U nucleotides was performed from 4 µg labeled RNA.
A sequencing library was prepared from 200 ng converted RNA with the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit with UDI (Lexogen) and sequenced on the Illumina NextSeq 2000 platform in SR100 mode.

treatment_protocol: WT or Dnmt1 KO ESCs were incubated with 265 µM 4SU for 2 hours before collection in the dark. For Mettl3 inhibitor treatment, WT ESCs were treated with 50 μM STM-2457 or vehicle for 24 h, with addition of 4SU to the medium at 265 µM for the last 2 hours of treatment.

tag: cellline

value: Mouse ES cell line

tag: knockedout or drug

value: WT untreated


title: Cnot3 cKO cortex, rep 1

value: Cnot3 cKO


title: iRMD patient muscle biopsy 6

value: Skeletal Muscle

tag: age of_onset

value: no

value: yes**

value: yes


title: WT_unt_rep2

description: WT Mouse ES cell line

source_name: Mouse ES cells WT untreated Rep-2


title: p24098-s012_IF3

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing
Alignment was performed using STAR version 2.7.9a
Transcript abundance estimates were calculated using STAR --quantMode GeneCounts via the algorithm of htseq-count
Assembly: GRCh38, Ensembl annotation v107
Supplementary files format and content: comma delimited text containing the gene symbol and raw counts for each sample (in columns) for each annotated transcript (in rows).

source_name: hiPSC-CMs

extract_protocol:
RNA was isolated using Aurum total RNA mini kit (Bio‐Rad) according to manufacturer’s instructions.
RNA quality was assessed using a TapeStation 4200 (Agilent) and then ten nanograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed barcodes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000, yielding ~25 million reads per sample on average.

value: hiPSC-CMs

tag: condition

value: Spaceflight


title: WT_SP_rep3

description: WT Mouse ES cell line

source_name: Mouse ES cells WT (Dnmt1KO Control) Rep-3

value: WT


title: p24098-s011_IF2


title: Ctrl cortex, rep 3

value: cerebral cortex


title: WT_SP_rep1

description: WT Mouse ES cell line

source_name: Mouse ES cells WT (Dnmt1KO Control) Rep-1


title: WT_SP_no4SU

description: WT Mouse ES cell line

source_name: Mouse ES cells WT (Dnmt1KO Control) without 4SU


title: WT_SP_rep2

description: WT Mouse ES cell line

source_name: Mouse ES cells WT (Dnmt1KO Control) Rep-2


title: p24098-s010_IF1


title: WT_no4SU

description: WT Mouse ES cell line

source_name: Mouse ES cells WT (Mettl3i Control) without 4SU


title: M3i_rep3

description: M3i Mouse ES cell line

source_name: Mouse ES cells Mettl3i Rep-3

value: WT Mettl3i


title: p24098-s009_IG3

value: Ground control


title: Cnot3 cKO cortex, rep 3


title: p24098-s008_IG2


title: M3i_rep2

description: M3i Mouse ES cell line

source_name: Mouse ES cells Mettl3i Rep-2


title: M3i_rep1

description: M3i Mouse ES cell line

source_name: Mouse ES cells Mettl3i Rep-1


title: Ctrl cortex, rep 1


title: D1KO_rep2

description: D1-KO Mouse ES cell line

source_name: Mouse ES cells Dnmt1KO Rep-2


title: p24098-s007_IG1


title: Cnot3 cKO cortex, rep 2


title: D1KO_rep1

description: D1-KO Mouse ES cell line

source_name: Mouse ES cells Dnmt1KO Rep-1


title: WT-3-P2

city: Suzhou

first: Pengchao

last: Zhang

address: 199 Ren'ai Road

institute: Soochow University

data_processing:
Raw sequencing reads were assessed for quality using FastQC.
The clean-tag reads were aligned to the reference genome and reference genes using HISAT2 and Bowtie2.
The transcripts were assembled using Stringtie.
Assembly: Ensembl_release106
Supplementary files format and content: Excel file includes raw counts for each Sample.
Supplementary files format and content: Excel file includes FPKM values for each Sample.

source_name: peritoneal macrophages

extract_protocol:
Total RNA was extracted using TRIzol reagent.
A sequencing library was prepared using the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit according to the manufacturer’s instructions.

value: peritoneal macrophages


title: WT_unt_rep1

description: WT Mouse ES cell line

source_name: Mouse ES cells WT untreated Rep-1


title: D1KO_rep3

description: D1-KO Mouse ES cell line

source_name: Mouse ES cells Dnmt1KO Rep-3


title: DU145 xeno_TT3 LLN-CasRx/pre-gE2F8_rep3

first: Qianben

last: Wang

address: 905 S. Lasalle Street

data_processing:
RNA-seq quality control was performed by Trim Galore and samtools
For RNA-seq analysis of DU145 xenografts after indicated treatments, raw RNA-seq reads were filtered by XenofilteR. Raw reads were mapped to human hg19 genome by HISAT2
The expression counts were computed by htseq-count or featureCounts
The Differentially Expressed Genes were identified by DESeq2 or Limma-Voom
assembly: hg19
processed data files format and content: Tab-delimited text files include raw counts for each sample

source_name: xenograft

extract_protocol:
RNeasy Mini Kit from Qiagen following manufacturer's instructions
Libraries were prepared with NEBNext®Ultra™II Directional RNA Library Prep Kit for Illumina following manufacturer's instructions

value: xenograft

value: prostate cancer cells

value: E2F8 knockdown

value: LLN intratumoral treatment


title: SCAR2_555_dTAG_stranded_input_Me0_T0

description: IDT xGen UDI-UMI adapters

data_processing:
*library strategy: SCAR-seq (Sister Chromatids After Replication)
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.4.2) and uniquely mapped peaks kept using samtools (v1.12)
duplicate reads were removed with picard (version 2.26.10)
bam files were split into forward and reverse strands according to the SAM flag, using samtools view (version 1.5) -F 20 and -f 16, respectively
For each strand the SCAR normalized signal (CPM) was computed in 1kb bins and smoothed in a uniform blur considering the neighboring 30 bins on each side. For each 1kb window, the signal from its corresponding SCAR input was subtracted and negative values were set to zero
Assembly: mm10
Supplementary files format and content: SCAR-seq Partition scores in bigwig format

source_name: Cell line

growth_protocol: ESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 °C with 5 % CO2. DMEM was supplied with fetal bovine serum (15 %), home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using Trypsin-EDTA or TrypLE.

extract_protocol:
After the appropriate treatment, cells were collected by scraping and nuclei were isolated. Chromatin was digested with MNase. Sequentially, mononucleosomal fragments were immunoprecipitated, purified fragments were biotinylated, libraries were prepared, EdU-biotin fragments were pulled-down and sequenced.
Libraries were costructed using the KAPA Hyperprep kit and Illumina-compatible indexed adapters (IDT, 10005903) following manufacturer’s instruction. For the amplification step, 11 PCR cycles were used. Subsequently, the DNA underwent size selection using Agencourt AMPure XP beads (Beckman Coulter, A63881) to obtain fragments between 200-700 bp. Libraries were validated using Agilent Fragment Analyzer.

value: Cell line

value: embryonic stem cells


title: WT-2-P1


title: WT-2-P2


title: Ctrl cortex, rep 2

source_name: cerebral cortex


title: DU145 xeno_TT3 LLN-CasRx/pre-gE2F8_rep2


title: SCAR2_555_dTAG_stranded_input_Me2_T0

description: IDT xGen UDI-UMI adapters


title: SCAR2_555_DMSO_stranded_input_Me2_T0

description: IDT xGen UDI-UMI adapters


title: DU145 xeno_TT3 LLN-CasRx/pre-gE2F8_rep1


title: SCAR2_555_dTAG_H4K20me0_T0

description: IDT xGen UDI-UMI adapters


title: WT-1-P1


title: SCAR2_555_DMSO_H4K20me0_T0

description: IDT xGen UDI-UMI adapters


title: WT-3-P1


title: DU145 xeno_TT3 LLN-CasRx/pre-gCtrl_rep6


title: AKO-3-O2

source_name: peritoneal cells

value: peritoneal cells


title: DU145 xeno_TT3 LLN-CasRx/pre-gCtrl_rep5


title: RNA_581_dTAG_T60_r3

data_processing:
Reads were quality trimmed and filtered for adapters with cutadapt (version 4.2)
reads were mapped to the mouse genome (mm10) using STAR mapper (version 2.7.11a) with special multimapping parameters --winAnchorMultimapNmax 200 and --outFilterMultimapNmax
Quantification of genes and repeat-subfamilies was performed with the TEcount tool, part of the TETranscripts (version 2.2.3) software suite using gencode (version M25) annotations and TETranscripts custom repeat annotations GRCm38_GENCODE_rmsk_TE
Differential expression analysis was performed with Deseq2. Differentially expressed (DE) genes/repeat subfamilies were defined as those with |FC| > 1.5 and FDR < 0.01
Assembly: mm10
Supplementary files format and content: count table

value: POLE4-dTAG, MCM2-2A clone 2

value: retinoic acid

tag: time


title: SCAR2_555_dTAG_H4K20me2_T0

description: IDT xGen UDI-UMI adapters


title: SCAR2_555_DMSO_H4K20me2_T0

description: IDT xGen UDI-UMI adapters


title: DU145 xeno_TT3 LLN-CasRx/pre-gCtrl_rep4


title: RNA_581_dTAG_T60_r1


title: AKO-1-O2


title: RNA_581_dTAG_T24_r3


title: RNA_581_dTAG_T24_r2


title: DU145 xeno_TT3 LLN-CasRx/pre-gCtrl_rep3


title: D1KO_no4SU

description: D1-KO Mouse ES cell line

source_name: Mouse ES cells Dnmt1KO without 4SU

value: Mouse ES cell line


title: RNA_581_dTAG_T24_r1


title: DU145 xeno_TT3 LLN-CasRx/pre-gCtrl_rep2


title: RNA_581_dTAG_T12_r3


title: WT-2-O2


title: RNA_581_dTAG_T12_r2


title: DU145 xeno_TT3 LLN-CasRx/pre-gCtrl_rep1


title: WT-2-O1


title: RNA_581_dTAG_T12_r1


title: WT-1-P2


title: SCAR2_555_DMSO_stranded_input_Me0_T0

description: IDT xGen UDI-UMI adapters


title: RNA_581_dTAG_T0_r2

value: untreated


title: WT-1-O2


title: AKO-3-O1


title: RNA_581_dTAG_T60_r2


title: RNA_581_dTAG_T0_r1


title: RNA_581_dTAG_T0_r3


title: 293FT_pre-gE2F8_rep2

value: human embryonal kidney cells

value: E2F8 knockdown cells

value: transfection


title: RNA_581_DMSO_T60_r3


title: WT-1-O1


title: AKO-1-O1


title: 293FT_pre-gE2F8_rep1


title: RNA_581_DMSO_T60_r2


title: RNA_581_DMSO_T60_r1


title: RNA_581_DMSO_T24_r3


title: AKO-LPS-3


title: RNA_581_DMSO_T24_r2


title: RNA_581_DMSO_T24_r1


title: 293FT_pre-gCtrl_rep2

value: Control cells


title: AKO-LPS-2


title: RNA_581_DMSO_T12_r3


title: AKO-LPS-1


title: 293FT_pre-gE2F8_rep3


title: 293FT_pre-gCtrl_rep1


title: RNA_581_DMSO_T12_r2


title: RNA_581_DMSO_T12_r1


title: RNA_581_DMSO_T0_r3


title: DU145_siE2F8_rep3 72h


title: RNA_581_DMSO_T0_r2


title: AKO-MOCK-2


title: RNA_581_DMSO_T0_r1


title: RNA_555_dTAG_T60_r3


title: RNA_555_dTAG_T60_r2


title: DU145_siE2F8_rep2 72h


title: DU145_siE2F8_rep1 72h


title: 293FT_pre-gCtrl_rep3


title: WT-LPS-3


title: RNA_555_dTAG_T24_r3


title: WT-LPS-2


title: DU145_siCtrl_rep3 72h


title: RNA_555_dTAG_T24_r2


title: DU145_siCtrl_rep2 72h


title: RNA_555_dTAG_T24_r1


title: RNA_555_dTAG_T12_r2


title: WT-LPS-1


title: RNA_555_dTAG_T12_r1


title: RNA_555_dTAG_T12_r3


title: DU145_siCtrl_rep1 72h


title: WT-MOCK-3


title: AKO-MOCK-3


title: PC3_siE2F8_rep3 72h


title: RNA_555_dTAG_T0_r2


title: RNA_555_dTAG_T0_r3


title: RNA_555_dTAG_T0_r1


title: RNA_555_DMSO_T60_r3


title: PC3_siE2F8_rep2 72h


title: AKO-MOCK-1


title: RNA_555_dTAG_T60_r1


title: PC3_siE2F8_rep1 72h


title: WT-MOCK-1


title: RNA_555_DMSO_T60_r2


title: RNA_555_DMSO_T60_r1


title: PC3_siCtrl_rep3 72h


title: RNA_555_DMSO_T24_r3


title: M-MC3

city: 上海

first: 艳群

last: 罗

state: --- Select One ---

address: Cailun Road 1200

institute: shanghai university of traditional Chinese medicine

data_processing:
illumina NovaSeq 6000
Rawreads were obtained following mRNA-Seq sequencing.
The adapter sequences were removed using the Cutadapt program.
The data quantity of the clean data was quantified using the FastQC program, including the proportions of bases with quality scores of Q20 and Q30.
The clean data were aligned to the reference genome using the HISAT2 program.
Reads were assembled into transcripts and gene expression levels were analyzed using the StringTie program.
Expression analysis of differentially expressed genes was conducted using edgeR or DEGseq.
GO and KEGG pathway analyses of differentially expressed genes were performed using the clusterProfiler.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: -

source_name: liver

growth_protocol: Mice were housed in a temperature-controlled environment (22±2) °C with a twelve/twelve-hour light/dark cycle. Male mice aged six to eight weeks were included in the experiments.

extract_protocol:
After the final administration, mice were subjected to fasting for 12 hours before euthanasia. Tissues, including serum, liver, intestine tissues, and intestinal contents, were collected, weighed, photographed, and rapidly frozen in liquid nitrogen before storage at -80°C.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: A murine model of non-alcoholic steatohepatitis (NASH)  was established by feeding mice a MCD diet for 8 weeks.

tag: treatment group

value: LKO-MCD

value: liver

tag: strain

tag: age

value: 6 to 8 weeks

tag: Sex

value: male

value: MCD diet


title: RNA_555_DMSO_T24_r2


title: M-MC2


title: RNA_555_DMSO_T12_r3


title: RNA_555_DMSO_T12_r2


title: M-MC1


title: PC3_siCtrl_rep1 72h

value: prostate cancer cells


title: DU145_E2F8 ChIP_rep3

data_processing:
The raw reads were aligned to the reference genome (hg19) using Bowtie2 with default parameter settings
Peak calling was performed against IgG control files using MACS2 and Partek Genomics Suite (v7), with P value < 0.01 as the cutoff
Reproducible peaks from three biological replicates were used, and the ChIP-seq signal was generated from combined replicates
assembly: hg19
processed data files format and content: bigwig

extract_protocol:
1-2×107 cells were fixed with 1% formaldehyde for 10 min at room temperature. After cell lysis, chromatin was collected by sonication using Cell Sonicator (Branson Ultrasonics™ Sonifier™)
Libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina following manufacturer's instructions

value: WT

value: E2F8 antibody ab109596


title: RNA_555_DMSO_T0_r2

value: embryonic stem cells


title: RNA_555_DMSO_T12_r1


title: PC3_siCtrl_rep2 72h


title: DU145_E2F8 ChIP_rep2


title: M-MF2

value: FLOX-MCD


title: RNA_555_DMSO_T0_r1


title: M-MF1


title: ES-WT-3

description: RNA WT ES Cells

data_processing:
Raw sequencing data were first analysed with "FastQC". Low-complexity reads were removed with the "AfterQC" tool with default parameters. To get rid of reads originating from rRNA or tRNA, the reads were mapped to mouse tRNA and rRNA sequences with "Bowtie2". Reads that did not map to tRNA or rRNA sequences were then further processed with "Trimmomatic" using default parameters to remove adapter sequences.
The resulting fastq data were again analysed with "FastQC" to ensure that no further processing was needed.
The processed fastq reads were mapped to the mouse reference genome (GRCm38/mm10) using the "STAR" algorithm with Ensembl v99 reference transcriptome. Gene expression was evaluated using "HTseq" count.
Assembly: GRCm38/mm10
Supplementary files format and content: HTSeq raw count table

source_name: Mouse ES cells WT Rep-3

growth_protocol: ESCs were cultured on tissue culture plates coated with 0.1% gelatin and feeder cells, in high glucose DMEM-containing 15% FBS, 1 mM sodium pyruvate, 1% non-essential amino acids, 1% glutaMAX™, 0.1 mM β-mercaptoethanol, and 1000 units/ml recombinant mouse LIF at 37°C under 5% CO2. To generate EBs, 4 × 106 ESCs were seeded in 15 ml EB medium (without LIF) and maintained for 8 days. Cells were precipitated by gravity, resuspended, and cultured with fresh medium every two days.

extract_protocol:
Total RNA was extracted with RNeasy kit according to the manufacturer's instructions. Residual DNA removal was performed using the RNase-Free DNase Set.
The library preparation was performed using TruSeq Stranded Total RNA with Ribo-Zero Gold following the manufacturer’s instructions.

treatment_protocol: Mettl14 KO and WT E14TG2a mouse ESCs (gift from Laixin Xia, Southern Medical University, Guangzhou, China). For Mettl14-rescued cells, a Mettl14WT or Mettl14ΔRGG cDNA was cloned into plasmid pLV-EF1a-IRES (Blasticidin S resistant) and used, along with packaging vectors (pMD2.G and psPAX2), to co-transfect HEK293/T cells with Lipofectamine™ 3000, according to the manufacturer's protocol. Supernatant containing lentivirus particles was collected 48 and 72 hours post-transfection, supplemented with polybrene, and used to infect Mettl14 KO ESCs. After two rounds of infection, cells were selected for 7 days with 10 μg/ml blasticidin S48 and the surviving cells were pooled as stably rescued cell lines.

tag: knockedout


title: RNA_555_DMSO_T0_r3


title: ES-WT-2

description: RNA WT ES Cells

source_name: Mouse ES cells WT Rep-2


title: WT-MOCK-2

value: peritoneal macrophages


title: DU145_E2F8 ChIP_rep1


title: ES-WT-1

description: RNA WT ES Cells

source_name: Mouse ES cells WT Rep-1

value: Mouse ES cell line


title: M-CC3

value: LKO-NC

value: control


title: DU145_IgG ChIP_rep3

value: Rabbit IgG ab37415


title: ES-Mettl14KOR442K-3

description: RNA Mettl14-KO rescued by R442K mutant ES Cells

source_name: Mouse ES cells Mettl14KOR442K Rep-3


title: DU145_IgG ChIP_rep2


title: ES-Mettl14KOR442K-2

source_name: Mouse ES cells Mettl14KOR442K Rep-2


title: RNA_555_DMSO_T24_r1

value: retinoic acid


title: ES-Mettl14KO-2

description: RNA Mettl14-KO ES Cells

source_name: Mouse ES cells Mettl14KO Rep-2


title: ES-Mettl14KOR442K-1

source_name: Mouse ES cells Mettl14KOR442K Rep-1


title: DU145_IgG ChIP_rep1


title: ES-Mettl14KO-3

description: RNA Mettl14-KO ES Cells

source_name: Mouse ES cells Mettl14KO Rep-3


title: M-CF3

value: FLOX-NC


title: ES-Mettl14KO-1

description: RNA Mettl14-KO ES Cells

source_name: Mouse ES cells Mettl14KO Rep-1


title: M-MF3


title: M-CC1


title: PC3_E2F8 ChIP_rep3


title: M-CF2


title: EBd8-WT-2

description: RNA WT EB Cells

source_name: Mouse EB cells (day 8) WT Rep-2

value: Mouse EB cell line


title: EBd8-WT-1

description: RNA WT EB Cells

source_name: Mouse EB cells (day 8) WT Rep-1


title: PC3_E2F8 ChIP_rep2


title: EBd8-Mettl14KOR442K-3

description: RNA Mettl14-KO rescued by R442K mutant EB Cells

source_name: Mouse EB cells (day 8) Mettl14KOR442K Rep-3


title: EBd8-Mettl14KOR442K-2

source_name: Mouse EB cells (day 8) Mettl14KOR442K Rep-2


title: PC3_E2F8 ChIP_rep1


title: M-CF1

value: liver


title: EBd8-Mettl14KO-3

description: RNA Mettl14-KO EB Cells

source_name: Mouse EB cells (day 8) Mettl14KO Rep-3


title: EBd8-Mettl14KOR442K-1

source_name: Mouse EB cells (day 8) Mettl14KOR442K Rep-1


title: H-MC3

data_processing:
illumina NovaSeq 6000
Rawreads were obtained following mRNA-Seq sequencing.
The adapter sequences were removed using the Cutadapt program.
The data quantity of the clean data was quantified using the FastQC program, including the proportions of bases with quality scores of Q20 and Q30.
The clean data were aligned to the reference genome using the HISAT2 program.
Reads were assembled into transcripts and gene expression levels were analyzed using the StringTie program.
Expression analysis of differentially expressed genes was conducted using edgeR or DEGseq.
GO and KEGG pathway analyses of differentially expressed genes were performed using the clusterProfiler.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: Mice were housed in a temperature-controlled environment (22±2) °C with a twelve/twelve-hour light/dark cycle. Male mice aged eight to ten weeks were included in the experiments.

extract_protocol:
mRNA was extracted using the KAPA Stranded mRNA-Seq Kit.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: A murine model of non-alcoholic steatohepatitis (NASH)  was established by feeding mice a HFHS diet(30% sucrose, 70% water) for 16 weeks.

value: LKO-HFHS

value: 8 to 10 weeks

value: HFHS diet


title: PC3_IgG ChIP_rep3

value: prostate cancer cells


title: EBd8-Mettl14KO-2

description: RNA Mettl14-KO EB Cells

source_name: Mouse EB cells (day 8) Mettl14KO Rep-2


title: PC3_IgG ChIP_rep2

value: WT


title: H-MC2

source_name: liver

value: male


title: H-MC1


title: M-CC2

value: 6 to 8 weeks


title: PC3_IgG ChIP_rep1


title: EBd8-WT-3

description: RNA WT EB Cells

source_name: Mouse EB cells (day 8) WT Rep-3


title: ES-m6A-3h-2.2

data_processing:
Raw sequencing data were first analysed with "FastQC". Low-complexity reads were removed with the "AfterQC" tool with default parameters. To get rid of reads originating from rRNA or tRNA, the reads were mapped to mouse tRNA and rRNA sequences with "Bowtie2". Reads that did not map to tRNA or rRNA sequences were then further processed with "Trimmomatic" using default parameters to remove adapter sequences. The resulting fastq data were again analysed with "FastQC" to ensure that no further processing was needed.
The processed fastq reads were mapped to the human reference genome (GRCm38/mm10) using the "STAR" algorithm with Ensembl v99 reference transcriptome. Gene expression was evaluated using "HTseq" count on input samples. m6A sites were identified by applying the "m6aViewer" peak-calling tool onto immunoprecipitated (IP) samples, using their input counterpart to estimate background noise. Sites showing significant enrichment in all replicates and present on genes showing an expression level of at least 1TPM were considered for further analyses.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include m6Aseq list of reproducible peaks across replicates for genes expressed at least 1 TPM

source_name: mouse ES cells WT m6A-seq 3h-2.2

growth_protocol: ESCs were cultured on tissue culture plates coated with 0.1% gelatin and feeder cells, in high glucose DMEM-containing 15% FBS, 1 mM sodium pyruvate, 1% non-essential amino acids, 1% glutaMAX™, 0.1 mM β-mercaptoethanol, and 1000 units/ml recombinant mouse LIF at 37°C under 5% CO2. To generate EBs, 4 × 10^6 ESCs were seeded in 15 ml EB medium (without LIF) and maintained for 8 days. Cells were precipitated by gravity, resuspended, and cultured with fresh medium every two days.

extract_protocol:
Total RNA was extracted with RNeasy kit according to the manufacturer's instructions. Residual DNA removal was performed using the RNase-Free DNase Set. Polyadenylated RNA was enriched from 500 µg total RNA by one round of oligo-dT selection using the GenElute mRNA miniprep kit (Sigma-Aldrich). (m6A-immunoprecipitation) RNA was fragmented by mixing 90 µl RNA (at 0.9 µg/µl) and 10 µl fragmentation buffer 10X (100 mM Tris-HCl and 100 mM ZnCl2) in thin-walled 200-μl PCR tubes, then incubated at 94°C for 40 s in a pre-heated thermocycler block with the heated lid opened. 10 µl of 0.5 M EDTA was added and the tubes were placed on ice. RNA was then subjected to sodium acetate precipitation and resuspended in 300 μl RNase-free water. RNA fragmentation size was assessed by running 0.25 µg RNA on a 2100 Bioanalyzer (Agilent) with the RNA Nano kit (Agilent). Furthermore, 2-5 µg of fragmented RNA was kept at -80°C to later serve as input control. The RNA was denatured by heating (70°C for 5 min, then put on ice) and the immunoprecipitation mix was prepared as follows: polyA enriched fragmented RNA from cultured cells in 290 µl, 10µl proteinases inhibitors (Roche), 5 µl (200 units) RNasin® Ribonuclease Inhibitors (Promega), 5 µl of 200 mM Ribonucleoside Vanadyl Complex (RVC) (Sigma), 100 µl IP buffer 5X (50 mM Tris-HCl, 750 mM NaCl, 0.5% (vol/vol) Igepal), 3.5 µl anti-m6A antibody (Synaptic System, #202003) and 86.5 µl RNase-free water. The mix was incubated overnight at 4°C on a rotating wheel. The next day, 50 µl Dynabeads™ Protein G (Invitrogen, #10004D) were washed twice with IP buffer 1x supplemented with antiproteases (Roche) and blocked by incubating the beads in wash buffer supplemented with 0.5 mg/ml BSA for 1 h on a rotating wheel. The beads were washed again twice, then added to the immunoprecipitation mix and incubated for 2 h at 4°C on a rotating wheel. Then, the beads were washed three times with 1 ml washing buffer supplemented with 10 µl RNasin® and 10 µl RVC, and elution was performed by TriPure (Roche) extraction, so the RNA was resuspended in 9 µl RNase-free water.
The sequence library was prepared with SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) for both input and IP samples.

treatment_protocol: (Mettl3KO) Mettl3 knockout J1 ESCs were generated by Howard Y. Chang, Stanford University, USA (Batista et al, Cell Stem Cell, 2014). (Differentiation).The transition from naïve to formative pluripotency was adapted from previous protocols5,7. Briefly, 2×10⁶ naïve pluripotent ESCs were cultured on tissue culture plates coated with 0.1% gelatin, in “naïve medium” (2i/LIF serum-free N2B27 medium, see “Cell lines” section). After 12 hours, the medium was replaced with FBS-containing medium (high-glucose DMEM containing 15% FBS, 1 mM sodium pyruvate, 1% non-essential amino acids, 1% glutaMAX™, 1% penicillin and streptomycin, 0.1mM β-mercaptoethanol (Gibco)) to induce formative pluripotency. Cells cultured under these conditions were collected after 3 or 24 hours for further analysis.

tag: cells

value: mouse ES cells

tag: library

value: IP


title: H-MF3

value: FLOX-HFHS

tag: tissue

tag: genotype


title: H9, cR hESC, bio rep 3

city: Cincinnati

first: Kentaro

last: Iwasawa

state: OH

address: 3333 BURNET AVENUE

department: Division of Gastroenterology, Hepatology and Nutrition

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequencing was performed on NovaSeq6000 to target 26.7M reads per samples (13.3M pairs) (4Gb/sample).
Clean data were generated from the raw data by using Trimmomatic.
Trimmed sequence reads were mapped to GRCh38 and GRCm38 by using STAR.
Mapped mouse reads were removed by using XenofilterR.
Count matrix and TPM of human reads was generated with featureCounts.
Assembly: GRCh38
Supplementary files format and content: tab-separated value file includes raw counts for each sample.

extract_protocol:
RNA was harvested using FastGene RNA Premium Kit (NIPPON Genetics).
Library construction was performed with NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext UltraTMII Directional RNA Library Prep Kit (New England Biolabs).

tag: cell type

value: Human embryonic stem cells

tag: treatment

value: Chemical resetting and culture in naïve state


title: H-MF2


title: ES-m6A-24h-3.2

source_name: mouse ES cells WT m6A-seq 24h-3.2


title: ES-m6A-3h-3.1

source_name: mouse ES cells WT m6A-seq 3h-3.1


title: ES-m6A-3h-1

source_name: mouse ES cells WT m6A-seq 3h-1


title: ES-m6A-24h-3.1

source_name: mouse ES cells WT m6A-seq 24h-3.1


title: ES-m6A-3h-3.2

source_name: mouse ES cells WT m6A-seq 3h-3.2


title: ES-m6A-24h-2.2

source_name: mouse ES cells WT m6A-seq 24h-2.2


title: H-MF1


title: ES-m6A-3h-2.1

source_name: mouse ES cells WT m6A-seq 3h-2.1


title: H9, cR hESC, bio rep 1

tag: cell line


title: ES-m6A-24h-2.1

source_name: mouse ES cells WT m6A-seq 24h-2.1


title: H-CC3

value: LKO-NC

value: control


title: ES-m6A-24h-1

source_name: mouse ES cells WT m6A-seq 24h-1


title: H9, coculture-derived converted hESC, bio rep 3

value: Coculture in naïve state following coculture


title: ES-m6A-0h-3.2

source_name: mouse ES cells WT m6A-seq 0h-3.2


title: ES-m6A-0h-3.1

source_name: mouse ES cells WT m6A-seq 0h-3.1


title: EBd8-Mettl14KO-1

description: RNA Mettl14-KO EB Cells

source_name: Mouse EB cells (day 8) Mettl14KO Rep-1

tag: cellline

value: Mouse EB cell line


title: H9, coculture-derived converted hESC, bio rep 2


title: ES-m6A-0h-2.2

source_name: mouse ES cells WT m6A-seq 0h-2.2


title: H-CC1

value: liver


title: H9, coculture-derived converted hESC, bio rep 1


title: ES-m6A-0h-2.1

source_name: mouse ES cells WT m6A-seq 0h-2.1


title: ES-m6A-0h-1

source_name: mouse ES cells WT m6A-seq 0h-1


title: ES-INP-3h-3

source_name: mouse ES cells WT INPUT-3h-3

value: INPUT


title: ES-INP-3h-2

source_name: mouse ES cells WT INPUT-3h-2


title: H-CF2

source_name: liver

value: FLOX-NC

value: 8 to 10 weeks


title: ES-INP-3h-1

source_name: mouse ES cells WT INPUT-3h-1


title: ES-INP-24h-3

source_name: mouse ES cells WT INPUT-24h-3


title: ES-INP-24h-2

source_name: mouse ES cells WT INPUT-24h-2


title: H-CF3


title: H9, hESC cocultured with mESC, bio rep 2

value: Coculture with mouse ESC


title: H9, hESC cocultured with mESC, bio rep 3


title: H9, hESC cocultured with mESC, bio rep 1


title: ES-INP-24h-1

source_name: mouse ES cells WT INPUT-24h-1

value: WT


title: ES-INP-0h-3

source_name: mouse ES cells WT INPUT-0h-3


title: JF-F30-M6

treatment_protocol: A model of  alcoholic liver injury was established by feeding mice an NIAAA diet.

value: LKO-ALD

value: male

value: NIAAA diet


title: H9, primed hESC, bio rep 3

value: Culture in primed state


title: ES-INP-0h-2

source_name: mouse ES cells WT INPUT-0h-2

value: mouse ES cells


title: JF-F30-M5


title: H9, primed hESC, bio rep 2

value: Human embryonic stem cells


title: H-CC2


title: JF-F30-M4


title: H9, primed hESC, bio rep 1


title: ES-WTclon5-2-m6A

source_name: mouse ES cells WT-2 m6A-seq

value: IP


title: ES-WTclon5-3-m6A

source_name: mouse ES cells WT-3 m6A-seq


title: ES-INP-0h-1

source_name: mouse ES cells WT INPUT-0h-1


title: ES-WTclon5-3-INP

source_name: mouse ES cells WT-3 INPUT


title: ES-WTclon5-2-INP

source_name: mouse ES cells WT-2 INPUT


title: JF-F30-M2

value: FLOX-ALD


title: Donor 214, CARalone, Cycle 6

city: Houston

first: Antonino

last: Montalbano

state: TX

address: 1102 Bates Ave

institute: Baylor School of Medicine

data_processing:
Adapters of the sequenced reads were trimmed using Trimmomatic; reads shorter than 36 nucleotides were discarded.
Reads were then aligned to the human reference GRCh38 using Star aligner. Reads with an alignment score below 30 were discarded using samtools.
The counts per transcript were calculated using featureCounts.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files includes raw counts for each sample.

source_name: T cells

growth_protocol: Peripheral blood of healthy donors was purchased from Gulf Coast Regional Blood Center. PBMCs were isolated from buffy coats by Ficoll density gradient centrifugation (GE Healthcare). NKTs were purified using anti-iNKT microbeads according to the manufacturer’s instructions (Miltenyi Biotec, 130-094-842), and the negative PBMC fraction was irradiated (40 Gy) and aliquoted at 40x106 cells/ml for each donor. Approximately 1x106 NKTs were stimulated with an aliquot of 5x106 autologous PBMCs pulsed with α-galactosylceramide (αGalCer; 100 ng/mL; Avanti Polar Lipids, 86700P-1mg) per well in a 24-well plate. The culture was supplemented every other day with recombinant IL2 (200 U/mL; National Cancer Institute/TECIN™, 23-6019) in complete RPMI. NKTs were expanded for 10 to 12 days and then restimulated at a 1:5 NKT to autologous PBMC ratio in a 6-well G-rex. For retroviral transduction, 24–well, non-tissue culture treated plates were coated with RetroNectin (Takara Bio, T100B) overnight.

extract_protocol:
RNA was isolated from all NKT cell samples using the RNeasy Plus Mini Kit (QIAGEN, 74134). The BCM Genomic and RNA Profiling Core performed library synthesis and paired-end sequencing on isolated RNA samples using Illumina PE150 technology.
The BCM Genomic and RNA Profiling Core performed library synthesis and paired-end sequencing on isolated RNA samples using Illumina PE150 technology.

treatment_protocol: NKTs transduced with either the CRISPR or shRNA lentiviral plasmid were co-cultured with mCherryhigh CD1d+ J32 cells or GFPhigh CHLA255 cells in the presence of IL2 (50 U/mL) and αGalCer (100 ng/mL) at a 1:1 ratio for six rounds of 3-4 days each. At the end of each round, the cell mixture was stained for Vα24-Jα18 and GD2.CAR and cell numbers were determined using a Cellometer Auto 2000 cell viability counter. Fresh J32 cells and αGalCer or CHLA255 cells were added to the culture according to NKT numbers to re-establish the 1:1 E:T ratio at the start of each cycle for a total of six cycles.

value: T cells

value: No shRNA control, only CAR expression

value: Cycle 6

value: paired-end


title: H-CF1

value: liver

value: control


title: JF-F30-M3

value: 8 to 10 weeks


title: ES-WTclon5-1-m6A

source_name: mouse ES cells WT-1 m6A-seq


title: ES-WTclon5-1-INP

source_name: mouse ES cells WT-1 INPUT

value: INPUT


title: ES-WT-3,2-m6A

source_name: mouse ES cells WT-3.2 m6A-seq

value: WT


title: Donor 214, shRNAscramble, Cycle 6

value: shRNA scramble control


title: JF-F30-C10

value: LKO-NC

value: male


title: Donor 214, shRNAPRDM1, Cycle 6

value: PRDM1 knockdown


title: ES-WT-3-INPUT

value: mouse ES cells


title: JF-F30-M1

value: NIAAA diet


title: ES-WT-2-m6A

value: IP


title: ES-WT-1-m6A


title: Donor 71, shRNAscramble, Cycle 6


title: ES-WT-1-INPUT


title: ES-WT-2-INPUT


title: JF-F30-C4


title: Donor 71, CARalone, Cycle 6


title: Donor 71, shRNAPRDM1, Cycle 6


title: EBd8-WT-3-INPUT (2)

source_name: mouse EB cells (day 8)  WT-3 INPUT

value: mouse EB cells


title: EBd8-WT-3.2-m6A

source_name: mouse EB cells (day 8) WT-3.2 m6A-seq


title: JF-F30-C3

source_name: liver

value: FLOX-NC


title: EBd8-WT-3.1-m6A

source_name: mouse EB cells (day 8) WT-3.1 m6A-seq


title: EBd8-WT-2-INPUT (2)

source_name: mouse EB cells (day 8)  WT-2 INPUT


title: Donor GT3, CARalone, Cycle 6

value: T cells

value: No shRNA control, only CAR expression


title: JF-F30-C2


title: EBd8-WT-2.2-m6A

source_name: mouse EB cells (day 8) WT-2.2 m6A-seq


title: ES-WT-3,1-m6A

source_name: mouse ES cells WT-3.1 m6A-seq


title: Donor GT3, shRNAscramble, Cycle 6

value: Cycle 6

value: paired-end


title: JF-F30-C6

value: liver

value: control


title: JF-F30-C1

value: 8 to 10 weeks


title: Donor GT3, shRNAPRDM1, Cycle 6


title: EBd8-WT-1.2-m6A

source_name: mouse EB cells (day 8) WT-1.2 m6A-seq

value: WT


title: Donor 6, CARalone, Cycle 6


title: ES-WT-NT-3

description: ActinoD WT HeLa Cells

data_processing:
Raw sequencing data were first analysed with "FastQC". Low-complexity reads were removed with the "AfterQC" tool with default parameters. To get rid of reads originating from rRNA or tRNA, the reads were mapped to human tRNA and rRNA sequences with "Bowtie2". Reads that did not map to tRNA or rRNA sequences were then further processed with "Trimmomatic" using default parameters to remove adapter sequences. The resulting fastq data were again analysed with "FastQC" to ensure that no further processing was needed.
Pre-processed reads (cf. previous section) from ESCs and EBs were mapped against the mouse reference genome (GRCm38/mm10), also using the STAR algorithm (v2.6.1d) in single-end mode. The reference transcriptome based on Ensembl (v99) was used as reference transcriptome (referred to hereafter as mouse Ensembl). Gene expression was evaluated on the basis of HTseq counts (v0.9.1)
Assembly: GRCm38/mm10
Supplementary files format and content: HTSeq count file

source_name: Mouse ES cells WT non treated Rep-3

growth_protocol: Mettl14 KO and WT E14TG2a mouse ESCs were cultured on tissue culture plates coated with 0.1% gelatin, in N2B27 medium (50% DMEM/F12 and 50% Neurobasal Medium (Gibco), containing 0.1mM β-mercaptoethanol (Gibco), 2 mM L-glutamine (Gibco), B-27 serum-free supplement (Gibco), N2 supplement (Gibco), 1% penicillin and streptomycin), supplemented with 1000 units/ml recombinant mouse leukemia inhibitory factor (LIF) (Millipore), and a mixture, here called “2i”, of the small-molecule inhibitors CHIR99021 (3μM, Axon Medchem) and PD0325901 (1 μM, Axon Medchem).

treatment_protocol: WT and Mettl14 KO ESCs were treated with 5 µg/ml actinomycin-D (Sigma) or vehicle for 0, 2, 4, 8 hours.

value: Mouse ES cell line


title: peri-injured region 15_young ozone SP-C wild type lung tissue (immune)

city: Salt Lake City

first: Alessandro

last: Venosa

state: UT

department: Pharmacology and Toxicology

institute: University of Utah

description: peri-injured region 15_young ozone SP-C wild type (immune)

data_processing:
Raw sequencing files were processed using Nanostring GeoMx NGS pipeline to generate DCC files
Sequences were aligned to mm10 genome within the NGS pipeline using NanoString oligo RTS_ID alignment
Aligned sequences were deduplicatedaccording to Nanostring oligo UNI sequences to generate final DCC
Assembly: mm10
Supplementary files format and content: 89_old SP-Cmutant ozone (top) - 91_young SP-Cmutant ozone (bottom) [JPG]: tissue_hiresolution_image
Supplementary files format and content: 332_young SP-CWT air (top) - 333_young SP-CWT ozone (bottom) [JPG]: tissue_hiresolution_image
Supplementary files format and content: file with barcodes, matrix, features

source_name: lung

growth_protocol: all animals were kept in a germ free facility for the duration of their lives. Food and water was provided ad libitum. Sacrifice was performed according to IACUC protocol. Lungs were perfused through the heart with saline solution (0.9% sodium chloride). Lungs were then inflated with 10% Neutral buffered formalin at steady state pressure (25cmH2O). Tissue embedding in paraffin blocks was followed by sectioning immediately prior to immunofluorescent staining (CD45, CD68, DNA). Regions of interested were selected and staining threshold standardized across of samples.

extract_protocol:
Paraffin embedded blocks were sectioned at 6um of thickness
Spatial transcriptome sequencing libraries  were prepared with NanoString Mouse Whole Transcriptome Kit (v1.0) and Reagents according to Nanostring protocols

treatment_protocol: Whole body ozone exposure (0.8ppm 3h) - study termination was perfoemd 72 h post exposure. Filtered air exposure for the control.

value: lung

value: SP-C wild type

tag: time point

value: ozone exposure

tag: study id_name


title: ES-WT-NT-2

description: ActinoD WT HeLa Cells

source_name: Mouse ES cells WT non treated Rep-2


title: ES-WT-NT-1

description: ActinoD WT HeLa Cells

source_name: Mouse ES cells WT non treated Rep-1


title: EBd8-WT-2.1-m6A

source_name: mouse EB cells (day 8) WT-2.1 m6A-seq


title: Donor 6, shRNAscramble, Cycle 6

source_name: T cells

value: shRNA scramble control


title: ES-WT-8h-3

description: ActinoD WT HeLa Cells

source_name: Mouse ES cells WT 8h Rep-3


title: healthy region 12_young air SP-C wild type lung tissue (immune)

description: healthy region 12_young air SP-C wild type (immune)

value: air


title: Donor 72, shRNAPRDM1, Cycle 6

value: PRDM1 knockdown


title: ES-WT-8h-1

description: ActinoD WT HeLa Cells

source_name: Mouse ES cells WT 8h Rep-1


title: EBd8-WT-1.1-m6A

source_name: mouse EB cells (day 8) WT-1.1 m6A-seq

value: mouse EB cells

value: IP


title: peri-injured region 15_young ozone SP-C wild type lung tissue (non immune)

description: peri-injured region 15_young ozone SP-C wild type (non immune)


title: healthy region 11_young air SP-C wild type lung tissue (non immune)

description: healthy region 11_young air SP-C wild type (non immune)


title: Donor 70, CARalone, Cycle 6

value: T cells


title: ES-WT-4h-2

description: ActinoD WT HeLa Cells

source_name: Mouse ES cells WT 4h Rep-2


title: EBd8-WT-1-INPUT (2)

source_name: mouse EB cells (day 8)  WT-1 INPUT

value: INPUT


title: ES-WT-4h-1

description: ActinoD WT HeLa Cells

source_name: Mouse ES cells WT 4h Rep-1


title: healthy region 11_young air SP-C wild type lung tissue (immune)

description: healthy region 11_young air SP-C wild type (immune)


title: Donor 70, shRNAscramble, Cycle 6

value: Cycle 6


title: ES-WT-4h-3

description: ActinoD WT HeLa Cells

source_name: Mouse ES cells WT 4h Rep-3


title: ES-WT-2h-2

description: ActinoD WT HeLa Cells

source_name: Mouse ES cells WT 2h Rep-2


title: healthy region 12_young air SP-C wild type lung tissue (non immune)

description: healthy region 12_young air SP-C wild type (non immune)


title: healthy region 10_young air SP-C wild type lung tissue (non immune)

description: healthy region 10_young air SP-C wild type (non immune)


title: ES-WT-8h-2

description: ActinoD WT HeLa Cells

source_name: Mouse ES cells WT 8h Rep-2


title: Donor 70, shRNAPRDM1, Cycle 6

value: paired-end


title: ES-M14KO-NT-3

description: ActinoD Mettl14-KO HeLa Cells

source_name: Mouse ES cells Mettl14KO non treated Rep-3


title: ES-M14KO-NT-2

description: ActinoD Mettl14-KO HeLa Cells

source_name: Mouse ES cells Mettl14KO non treated Rep-2


title: Donor 6, shRNAPRDM1, Cycle 6


title: healthy region 10_young air SP-C wild type lung tissue (immune)

description: healthy region 10_young air SP-C wild type (immune)


title: Donor 71, CARalone, Cycle 1

value: No shRNA control, only CAR expression

value: Cycle 1


title: ES-WT-2h-3

description: ActinoD WT HeLa Cells

source_name: Mouse ES cells WT 2h Rep-3


title: ES-M14KO-8h-3

description: ActinoD Mettl14-KO HeLa Cells

source_name: Mouse ES cells Mettl14KO 8h Rep-3


title: ES-M14KO-NT-1

description: ActinoD Mettl14-KO HeLa Cells

source_name: Mouse ES cells Mettl14KO non treated Rep-1


title: H9, cR hESC, bio rep 2

value: Human embryonic stem cells

value: Chemical resetting and culture in naïve state


title: ES-M14KO-8h-2

description: ActinoD Mettl14-KO HeLa Cells

source_name: Mouse ES cells Mettl14KO 8h Rep-2

value: Mouse ES cell line


title: injured region 9_young ozone SP-C wild type lung tissue (immune)

description: injured region 9_young ozone SP-C wild type (immune)

source_name: lung

value: lung


title: Donor 71, shRNAscramble, Cycle 1

source_name: T cells


title: ES-M14KO-8h-1

description: ActinoD Mettl14-KO HeLa Cells

source_name: Mouse ES cells Mettl14KO 8h Rep-1


title: injured region 9_young ozone SP-C wild type lung tissue (non immune)

description: injured region 9_young ozone SP-C wild type (non immune)

value: SP-C wild type


title: Donor 71, shRNAPRDM1, Cycle 1


title: ES-M14KO-4h-3

description: ActinoD Mettl14-KO HeLa Cells

source_name: Mouse ES cells Mettl14KO 4h Rep-3


title: healthy region 8_young air SP-C wild type lung tissue (non immune)

description: healthy region 8_young air SP-C wild type (non immune)

value: ozone exposure


title: Donor GT3, CARalone, Cycle 1


title: ES-M14KO-4h-2

description: ActinoD Mettl14-KO HeLa Cells

source_name: Mouse ES cells Mettl14KO 4h Rep-2


title: ES-M14KO-4h-1

description: ActinoD Mettl14-KO HeLa Cells

source_name: Mouse ES cells Mettl14KO 4h Rep-1


title: ES-WT-2h-1

description: ActinoD WT HeLa Cells

source_name: Mouse ES cells WT 2h Rep-1

value: WT


title: ES-M14KO-2h-3

description: ActinoD Mettl14-KO HeLa Cells

source_name: Mouse ES cells Mettl14KO 2h Rep-3


title: healthy region 8_young air SP-C wild type lung tissue (immune)

description: healthy region 8_young air SP-C wild type (immune)

value: air


title: Donor GT3, shRNAscramble, Cycle 1

value: shRNA scramble control


title: ES-M14KO-2h-2

description: ActinoD Mettl14-KO HeLa Cells

source_name: Mouse ES cells Mettl14KO 2h Rep-2


title: Donor GT3, shRNAPRDM1, Cycle 1

value: PRDM1 knockdown


title: peri-injured region 7_young ozone SP-C wild type lung tissue (non immune)

description: peri-injured region 7_young ozone SP-C wild type (non immune)


title: ES-M14KO-2h-1

description: ActinoD Mettl14-KO HeLa Cells

source_name: Mouse ES cells Mettl14KO 2h Rep-1


title: Donor 6, CARalone, Cycle 1


title: 16w_TDM_03

city: Tsukuba city

first: Kozaburo

last: Tanuma

state: Ibaraki

address: Tennodai 2-1-1

department: Urology

country: Japan

institute: University of Tsukuba

description: TUL_028_08 (GE)

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench (Version 10.1.1; Qiagen, Redwood City, CA).
Assembly: mm10
Supplementary files format and content: 6samples_2groups_quantile_totalcpunt_transformed_subexperiment_N49585.xlsx
Supplementary files format and content: CON_vs_TDM_16w_N=6.xlsx

source_name: bladder tissue

extract_protocol:
Total RNA from excised whole bladders was isolated using a NucleoSpin RNA kit (TaKaRa).
For RNA sequencing, 500 ng total RNA were rRNA-depleted using the NEBNext rRNA Depletion Kit (New England Biolabs) according to the manufacturer's instructions. Library preparation was performed using an NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).

value: bladder tissue

value: Wild type

value: Lip-TDM


title: peri-injured region 7_young ozone SP-C wild type lung tissue (immune)

description: peri-injured region 7_young ozone SP-C wild type (immune)


title: Donor 6, shRNAscramble, Cycle 1

value: T cells


title: 16w_TDM_02

description: TUL_028_07 (GE)


title: peri-injured region 6_young ozone SP-C wild type lung tissue (immune)

description: peri-injured region 6_young ozone SP-C wild type (immune)


title: peri-injured region 6_young ozone SP-C wild type lung tissue (non immune)

description: peri-injured region 6_young ozone SP-C wild type (non immune)


title: 16w_CON_01

description: TUL_028_01 (GE)

value: Lip-CON


title: ES-WT-3-RNA

description: mRNA for WT ES cells Rep-3

data_processing:
Raw sequencing data were first analysed with "FastQC". Low-complexity reads were removed with the "AfterQC" tool with default parameters. To get rid of reads originating from rRNA or tRNA, the reads were mapped to mouse tRNA and rRNA sequences with "Bowtie2". Reads that did not map to tRNA or rRNA sequences were then further processed with "Trimmomatic" using default parameters to remove adapter sequences. The resulting fastq data were again analysed with "FastQC" to ensure that no further processing was needed.
The processed fastq reads were mapped to the human reference genome (GRCm38/mm10) using the "STAR" algorithm with Ensembl v99 reference transcriptome. Gene expression was evaluated using "HTseq" count on input samples. m6A sites were identified by applying the "m6aViewer" peak-calling tool onto immunoprecipitated (IP) samples, using their input counterpart to estimate background noise. Sites showing significant enrichment in all replicates and present on genes showing an expression level of at least 1TPM were considered for further analyses.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include (m6Aseq) list of reproducible peaks across replicates for genes expressed at least 1 TPM or (RNAseq) read count by genes

source_name: mouse ES cells WT

treatment_protocol: Mettl3 knockout J1 ESCs were generated by Howard Y. Chang, Stanford University, USA (Batista et al, Cell Stem Cell, 2014)

value: mouse ES cells

tag: differentiation days

value: RNA


title: peri-injured region 5_young ozone SP-C wild type lung tissue (non immune)

description: peri-injured region 5_young ozone SP-C wild type (non immune)


title: 16w_TDM_01

description: TUL_028_06 (GE)


title: Donor 6, shRNAPRDM1, Cycle 1

value: Cycle 1

value: paired-end


title: ChOR4_H3K27me3_557_dTAG_clicked_input

data_processing:
*library strategy: CHOR-seq
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.4.2) and uniquely mapped peaks kept using samtools (v1.12)
duplicate reads were removed with picard (version 2.26.10)
bam files were processed to bigwig for RPM or RRPM signal by bamCoverage
Assembly: mm10 and dm6
Supplementary files format and content: bigwigs: bam files were normalized to the number of million of reads (RPM) in 50 bp bins with bamCoverage
Supplementary files format and content: bed: bedfiles were generated from 50bp bigwig files and filtered for regions over peaks

extract_protocol:
After the appropriate treatment, 1% formaldehyde for 10 min. Then, glycine was added to quench the reaction and cells were subsequently lysed. Sonication was performed on isolated nuclei using a Covaris E220. DNA fragments were immunoprecipitated, purified fragments were biotinylated, libraries were prepared, EdU-biotin fragments were pulled-down and sequenced.
Libraries were costructed using the KAPA Hyperprep kit and Illumina-compatible indexed adapters (Pentabase) following manufacturer’s instruction. For the amplification step, 11 PCR cycles were used. Subsequently, the DNA underwent size selection using Agencourt AMPure XP beads (Beckman Coulter, A63881) to obtain fragments between 200-700 bp. Libraries were validated using Agilent Fragment Analyzer.

value: embryonic stem cells

value: POLE4-dTAG, MCM2-2A clone 1

tag: antibody


title: Donor 72, CARalone, Cycle 1

value: No shRNA control, only CAR expression


title: ES-WT-1-RNA

description: mRNA for WT ES cells Rep-1


title: ChOR4_H3K27me3_557_DMSO_clicked_input


title: Donor 72, shRNAscramble, Cycle 1


title: ES-WT-2-RNA

description: mRNA for WT ES cells Rep-2


title: injured region 4_young ozone SP-C wild type lung tissue (non immune)

description: injured region 4_young ozone SP-C wild type (non immune)

value: lung

value: SP-C wild type

value: ozone exposure


title: EBd8-METTL3KO-3-RNA

description: mRNA from METTL3 KO EB cells Rep-3

source_name: mouse EB cells (day 8) METTL3KO

value: mouse EB cells


title: injured region 4_young ozone SP-C wild type lung tissue (immune)

description: injured region 4_young ozone SP-C wild type (immune)


title: EBd8-METTL3KO-2-RNA

description: mRNA from METTL3 KO EB cells Rep-2


title: Donor 70, CARalone, Cycle 1


title: Donor 72, shRNAPRDM1, Cycle 1

value: PRDM1 knockdown


title: 16w_CON_03

description: TUL_028_03 (GE)

value: bladder tissue


title: injured region 3_young ozone SP-C wild type lung tissue (non immune)

description: injured region 3_young ozone SP-C wild type (non immune)


title: ChOR4_H3K27me3_557_DMSO

description: ChOR_double_DMSO_H3K27me3_spike_chor_merged.bw


title: 16w_CON_02

description: TUL_028_02 (GE)

value: Wild type


title: injured region 3_young ozone SP-C wild type lung tissue (immune)

description: injured region 3_young ozone SP-C wild type (immune)


title: Donor 70, shRNAPRDM1, Cycle 1


title: Donor 70, shRNAscramble, Cycle 1

value: shRNA scramble control


title: injured region 2_young ozone SP-C wild type lung tissue (non immune)

description: injured region 2_young ozone SP-C wild type (non immune)


title: EBd8-WT-3-INPUT

description: INPUT for WT EB cells Rep-3

source_name: mouse EB cells (day 8) WT

value: WT

value: INPUT(RNA)


title: peri-injured region 5_young ozone SP-C wild type lung tissue (immune)

description: peri-injured region 5_young ozone SP-C wild type (immune)


title: EBd8-METTL3KO-1-RNA

description: mRNA from METTL3 KO EB cells Rep-1


title: ChOR3_H3K27me3_581_DMSO_clicked_input

value: POLE4-dTAG, MCM2-2A clone 2


title: ChOR3_H3K27me3_555_dTAG_clicked_input


title: EBd8-WT-1-INPUT

description: INPUT for WT EB cells Rep-1


title: Donor 56, gRNA PRDM1_2, Cycle6

value: T cells

value: PRDM1 knockout, gRNA 2

value: Cycle 6


title: ChOR3_H3K27me3_555_DMSO_clicked_input

value: embryonic stem cells


title: Donor 56, gRNA B2M, Cycle6

value: B2M knockout

value: paired-end


title: ChOR3_H3K27me3_581_dTAG

description: ChOR_double_dTAG_H3K27me3_spike_chor_merged.bw


title: no template control #2

description: no template control #2


title: EBd8-WT-3-m6A

description: m6A-seq from WT EB cells Rep-3

value: IP


title: Donor 56, gRNA PRDM1_1, Cycle6

value: PRDM1 knockout, gRNA 1


title: ChOR4_H3K27me3_557_dTAG

value: POLE4-dTAG, MCM2-2A clone 1


title: injured region 12_old ozone SP-C mutant lung tissue (non immune)

description: injured region_012_CD45- "other" old ozone

value: lung

value: SP-CI73T mutant

value: ozone exposure


title: EBd8-WT-2-m6A

description: m6A-seq from WT EB cells Rep-2

value: mouse EB cells


title: Donor 199, gRNA PRDM1_2, Cycle6


title: ChOR3_H3K27me3_581_dTAG_clicked_input


title: EBd8-WT-1-m6A

description: m6A-seq from WT EB cells Rep-1


title: injured region 12_old ozone SP-C mutant lung tissue (immune)

description: injured region_012_CD68+ old ozone


title: ChOR3_H3K27me3_555_dTAG


title: Donor 199, gRNA B2M, Cycle6


title: peri-injured region 11_old  ozone SP-C mutant lung tissue (non immune)

description: peri-injured region_011_CD45- "other" old ozone


title: EBd8-WT-2-INPUT

description: INPUT for WT EB cells Rep-2


title: Donor 193, gRNA PRDM1_2, Cycle6


title: ChOR3_H3K27me3_555_DMSO