title: Wnt1Cre-mTmG DRG pNSCs rep 3

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: replicate 3

data_processing:
HISAT2 was used to align the RNA-seq reads for each of the samples to the mouse reference genome GRCm38, and Cufflinks to annotate them.
The counts of aligned reads to each gene were calculated with HTSeq.
In-house software was used to merge the expression results into a single text file used in the downstream analysis in Matlab (MathWorks).
We performed quantile normalization to equalize the data and stabilized them through the log2 transform of the data plus one.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include log2 counts values for each sample

source_name: Wnt1Cre-mTmG DRG pNSCs rep 3

growth_protocol: Embryonic limb cells were derived from embryos at embryonic day 13.5. Adult brain and lung cells were derived from around 4-6 week-old wide-type (WT) or transgenic mice. Postnatal brain, lung, tail, and DRG cells were derived from around postnatal day 1-5 WT or transgenic mice. Limb, lung, tail, DRG or whole brain tissues were cut and minced using a pair of scissors, and incubated with 0.25% trypsin (Invitrogen) at 37C for 10 min. After trypsinization, 3 times volume amount of MEF medium was added, and the entire suspension was pipetted up and down to dissociate the tissues. The dissociated tissues were centrifuged and resuspended in MEF or NSCs medium, and cells were plated onto 6-well plates, and cultured in a humidified incubator at 37C under 5% CO2. Passage-4 embryonic limb cells and passage-2 adult lung cells from WT mice were maintained and passaged in MEF medium: high-glucose DMEM (Sigma) containing 10% FBS (Biochrom), 1% GlutaMAX (Gibco), 1% sodium pyruvate (Sigma), 1% nonessential amino acids (Sigma), 0.1% B-mercaptoethanol (Gibco), 1% penicillin-streptomycin (Sigma).

extract_protocol:
RNA quality was verified on an Agilent Bioanalyzer Nano Eukaryote chip. 1 mg of total RNA was used for poly-A selection with NEBNext PolyA mRNA magnetic isolation module and subsequent cDNA synthesis, Illumina Tru-seq adaptor ligation and library preparation were performed with NEBNext Ultra RNA Library Prep Kit (NEB) according to the manufacturer’s instructions.
Library quality and concentration were determined using an Agilent Bioanalyzer DNA1000 chip and a Qubit fluorometer. Libraries were sequenced on Illumina NextSeq500 in single-end mode.

treatment_protocol: Generation of pNSCs: For generation of low-pH NSCs, passage-4 embryonic limb cells, passage-2 adult lung cells from WT mice were dissociated by trypsin. The trypsin treatment was stopped by adding MEF medium. The cells were then washed 2 times in D-PBS (without calcium chloride and magnesium chloride) (Sigma). 0.5*10^6 cells were treated with 500 microL of low-pH HBSS solution (Biochrom) (titrated to different pH by hydrochloric acid) for 25 min at 37C in water bath, and then centrifuged at 1000 rpm at room temperature for 5 min. After the supernatant was removed, precipitated cells were resuspended and plated in a well of a 6-well plate without coating in simple defined NSC medium: DMEM/F-12 [1:1] (Gibco) with 2% B27 w/o Vitamin A, 1% N2 (both from Gibco), 1x GlutaMAX (Gibco), 1x penicillin-streptomycin (Sigma), supplemented with 10 ng/mL of EGF and 10 ng/mL of human bFGF (both from Invitrogen). Freshly isolated GFP- and GFP+ postnatal lung cells after FACS from Sox1-GFP mice were treated with low-pH medium in the same way and then the cells were resuspended and plated in gelatin-coated 6-well plate in NSC medium for 3 weeks. Medium was changed every 48 hours. Single pNSC cluster was manually picked and cultured in 96-well plate individually. For generation of pNSCs without low-pH treatment, freshly isolated embryonic limb cells and postnatal tail cells from WT mice, freshly isolated adult lung or postnatal tail GFP+ cells from Nes-GFP mice, freshly isolated adult lung or postnatal lung GFP+ and GFP- cells from Sox2-GFP mice, freshly isolated postnatal lung or postnatal tail GFP+ and GFP- cells from Sox1-GFP mice, freshly isolated postnatal lung or postnatal tail GFP+ and GFP- cells from Sox1-Cre-mTmG mice were cultured on gelatin-coated dishes in NSC medium for 3 weeks. Medium was changed every 48 hours. Single pNSC cluster was manually picked and cultured in 96-well plate individually. For generation of brain control NSCs, the whole brain tissues from adult or postnatal mouse were cut and minced using a pair of scissors, and incubated with 0.25% trypsin (Invitrogen) at 37C for 10 min. After trypsinization, 3 times volume amount of MEF medium was added, and the entire suspension was pipetted up and down to dissociate the tissues. The dissociated tissues were centrifuged and resuspended in NSCs medium, and cells were plated onto 6-well plates coated with gelatin, and cultured in a humidified incubator at 37C under 5% CO2. After several passages, pure brain NSCs can be established.

value: pNSC


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

status: Public on Jan 10 2025

type: SRA

city: Salt Lake City

first: Alessandro

last: Venosa

state: UT

department: Pharmacology and Toxicology

country: USA

institute: University of Utah

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

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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.

tag: tissue

value: lung

tag: genotype

value: SP-C wild type

tag: age

tag: time point

tag: treatment

value: ozone exposure

tag: study id_name


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

description: peri-injured region_011_CD68+ old ozone

value: SP-CI73T mutant


title: Donor 193, gRNA PRDM1_1, Cycle6

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.

molecule: polyA RNA

organism: Homo sapiens

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

tag: cell line

value: PRDM1 knockout, gRNA 1

tag: cell type

value: Cycle 6

value: paired-end


title: ChOR2_H3K27me3_557_dTAG_clicked_input

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

library_source: genomic

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

molecule: genomic DNA

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).

value: embryonic stem cells

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

tag: antibody


title: injured region 10_old  ozone SP-C mutant lung tissue (non immune)

description: injured region_010_CD45- "other" old ozone


title: Donor 193, gRNA B2M, Cycle6

value: B2M knockout


title: Wnt1Cre-mTmG DRG pNSCs rep 1

description: replicate 1

source_name: Wnt1Cre-mTmG DRG pNSCs rep 1

tag: strain


title: Donor 192, gRNA PRDM1_1, Cycle6


title: Wnt1Cre-mTmG brain NSCs rep 3

description: replicate 3

source_name: Wnt1Cre-mTmG brain NSCs rep 3

value: NSC


title: injured region 10_old ozone SP-C mutant lung tissue (immune)

description: injured region_010_CD68+ old ozone


title: peri-injured region 9_old  ozone SP-C mutant lung tissue (non immune)

description: peri-injured region_009_CD45- "other" old ozone


title: Donor 192, gRNA PRDM1_2, Cycle6

value: PRDM1 knockout, gRNA 2


title: ChOR2_H3K27me3_555_DMSO_clicked_input


title: ChOR3_H3K27me3_581_DMSO

description: ChOR_double_DMSO_H3K27me3_spike_chor_merged.bw

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


title: Wnt1Cre-mTmG brain NSCs rep 2

description: replicate 2

source_name: Wnt1Cre-mTmG brain NSCs rep 2


title: peri-injured region 9_old ozone SP-C mutant lung tissue (immune)

description: peri-injured region_009_CD68+ old ozone


title: Wnt1Cre-mTmG brain NSCs rep 1

description: replicate 1

source_name: Wnt1Cre-mTmG brain NSCs rep 1


title: Donor 192, gRNA B2M, Cycle6


title: DRG NCSCs rep 3

description: replicate 3

source_name: DRG NCSCs rep 3


title: ChOR2_H3K27me3_557_dTAG

description: ChOR_double_dTAG_H3K27me3_spike_chor_merged.bw


title: injured region 8_old ozone SP-C mutant lung tissue (non immune)

description: injured region_008_CD45- "other" old ozone


title: Donor 199, gRNA PRDM1_2, Cycle1

value: Cycle 1


title: ChOR2_H3K27me3_557_DMSO


title: injured region 8_old ozone SP-C mutant lung tissue (immune)

description: injured region_008_CD68+ old ozone


title: Wnt1Cre-mTmG DRG pNSCs rep 2

description: replicate 2

source_name: Wnt1Cre-mTmG DRG pNSCs rep 2


title: Donor 199, gRNA PRDM1_1, Cycle1


title: ChOR2_H3K27me3_555_dTAG


title: peri-injured region 7_old ozone SP-C mutant lung tissue (non immune)

description: peri-injured region_007_CD45- "other" old ozone


title: Donor 199, gRNA B2M, Cycle1


title: DRG NCSCs rep 1

description: replicate 1

source_name: DRG NCSCs rep 1


title: ChOR2_H3K27me3_557_DMSO_clicked_input


title: peri-injured region 7_old ozone SP-C mutant lung tissue (immune)

description: peri-injured region_007_CD68+ old ozone


title: ChOR2_H3K27me3_555_dTAG_clicked_input


title: ChOR2_H3K27me3_555_DMSO


title: Donor 193, gRNA PRDM1_2, Cycle1


title: ChOR1_H3K27me3_557_dTAG_clicked_input


title: Donor 193, gRNA PRDM1_1, Cycle1


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

description: peri-injured region_006_CD45- "other" young ozone


title: Wnt1Cre-mTmG Tail pNSCs rep 2

description: replicate 2

source_name: Wnt1Cre-mTmG Tail pNSCs rep 2


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

description: peri-injured region_006_CD68+ young ozone


title: ChOR1_H3K27me3_557_DMSO_clicked_input


title: Donor 193, gRNA B2M, Cycle1


title: Wnt1Cre-mTmG Tail pNSCs rep 1

description: replicate 1

source_name: Wnt1Cre-mTmG Tail pNSCs rep 1


title: DRG NCSCs rep 2

description: replicate 2

source_name: DRG NCSCs rep 2


title: Sox2-GFP lung pNSCs rep 3

description: replicate 3

source_name: Sox2-GFP lung pNSCs rep 3


title: Sox2-GFP lung pNSCs rep 2

description: replicate 2

source_name: Sox2-GFP lung pNSCs rep 2


title: peri-injured region 5_young ozoneSP-C mutant lung tissue (immune)

description: peri-injured region_005_CD68+ young ozone


title: ChOR1_H3K27me3_555_DMSO_clicked_input


title: ChOR1_H3K27me3_557_dTAG


title: Donor 192, gRNA PRDM1_1, Cycle1


title: Sox2-GFP lung pNSCs rep 1

description: replicate 1

source_name: Sox2-GFP lung pNSCs rep 1


title: Donor 192, gRNA PRDM1_2, Cycle1


title: ChOR1_H3K27me3_557_DMSO


title: Wnt1Cre-mTmG Tail pNSCs rep 3

description: replicate 3

source_name: Wnt1Cre-mTmG Tail pNSCs rep 3


title: peri-injured region 4_young ozoneSP-C mutant lung tissue (immune)

description: peri-injured region_004_CD68+ young ozone


title: PAS-seq srrm2+son RNAi bio rep 3

city: Irvine

first: Yoseop

last: Yoon

state: CA

address: 1002 Health Sciences Rd

institute: University of California Irvine

data_processing:
PAS-seq data analysis was conducted as described by (Wang et al., 2021).
for 4sU-seq data, adapters and low-quality reads were removed from the raw fastq files using Cutadapt (Martin, 2011). The paired-end reads were aligned to the human genome using STAR (Dobin et al., 2013).
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: All HEK293T cell lines were cultured in DMEM (Dulbecco's Modified Eagle Medium, high glucose, pyruvate) (Gibco, 11995065) supplemented with 10% FBS (fetal bovine serum) (Sigma, F0926-100ML).

extract_protocol:
TRIZOL
1µg of total RNA was used for PAS-seq library preparation, adhering to the protocol detailed in our methodological paper (Yoon et al., 2021). For 4sU-seq, biotinylated RNAs were used for library construction  using the TruSeq Stranded mRNA Library Prep kit (illumina, 20020595)

treatment_protocol: To deplete RBBP6, 500nM dTAGv-1 (TOCRIS, 6914) was added to the media for the desired duration. For RNAi, siRNA transfection was  performed to achieve a final concentration of 10 nM using Lipofectamine RNAi MAX Transfection Reagent (Invitrogen, 13778100), and cells were incubated for 48 hrs

value: human embryonic kidney cell

value: srrm2/son knockdown

value: siRNA


title: Donor 192, gRNA B2M, Cycle1


title: ChOR1_H3K27me3_555_dTAG


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

description: peri-injured region_004_CD45- "other" young ozone

value: lung


title: Sox2-GFP brain NSCs rep 2

description: replicate 2

source_name: Sox2-GFP brain NSCs rep 2


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

description: injured region_003_CD45- "other" young ozone

source_name: lung

value: ozone exposure


title: ChOR1_H3K27me3_555_DMSO


title: Sox2-GFP brain NSCs rep 1

description: replicate 1

source_name: Sox2-GFP brain NSCs rep 1


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

description: injured region_003_CD68+ young ozone

value: SP-CI73T mutant


title: PAS-seq srrm2+son RNAi bio rep 2


title: SCAR2_581_dTAG_stranded_input_Me0_T0

description: Pentabase 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

tag: chip antibody


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

description: injured region_002_CD45- "other" young ozone


title: ChOR1_H3K27me3_555_dTAG_clicked_input


title: PAS-seq son RNAi bio rep 3

value: son knockdown


title: Lung rep 2

description: replicate 2

source_name: Lung rep 2

value: Lung


title: SCAR2_581_DMSO_stranded_input_Me0_T0

description: Pentabase adapters


title: injured region 2_young ozone SP-C mutant lung tissue (immune)

description: injured region_002_CD68+ young ozone


title: PAS-seq son RNAi bio rep 2


title: Lung rep 1

description: replicate 1

source_name: Lung rep 1


title: injured region 1_young ozoneSP-C mutant lung tissue (non immune)

description: injured region_001_CD45- "other" young ozone


title: Lung-pNSC rep 2

description: replicate 2

source_name: Lung-pNSC rep 2

value: pNSC


title: SCAR2_581_dTAG_stranded_input_Me2_T0

description: Pentabase adapters

value: embryonic stem cells


title: Sox2-GFP brain NSCs rep 3

description: replicate 3

source_name: Sox2-GFP brain NSCs rep 3


title: PAS-seq son RNAi bio rep 1


title: SCAR2_581_DMSO_stranded_input_Me2_T0

description: Pentabase adapters


title: Lung-pNSC rep 1

description: replicate 1

source_name: Lung-pNSC rep 1


title: SCAR2_581_dTAG_H4K20me0_T0

description: Pentabase adapters


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

description: peri-injured region_005_CD45- "other" young ozone


title: injured region 1_young ozone SP-C mutant lung tissue (immune)

description: injured region_001_CD68+ young ozone


title: PAS-seq srrm2 RNAi bio rep 3

value: srrm2 knockdown


title: no template control #1

description: no template control #1


title: PAS-seq srrm2 RNAi bio rep 2


title: PAS-seq srrm2+son RNAi bio rep 1


title: T3_Rep3

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description: WT Mouse ES cell line

data_processing:
The raw fastq data were trimmed with Cutadapt (v1.14) and Trimmomatic (v0.33) and then aligned with either the mm10 or dm3 genome using bowtie2. The strand-specific single nucleotide ends of aligned reads were constructed using BEDTools with genomecov. Bedgraph data were normalized to the number of reads mapped to the spike-in dm3 genome before being converted into bigwig data for further analysis. Bigwig files were then averaged for each condition with deepTools using bigwigCompare, with –operation set at ‘mean’. Visualization was performed with computeMatrix and plotProfile from deepTools.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig file

source_name: Mouse ES cells WT time 3h Rep-3

growth_protocol: WT 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:
Total RNA was extracted and fragmented in 0.2 M NaOH for 10 minutes on ice. Biotinylated nascent RNAs were then purified on M-280 streptavidin beads (Invitrogen). Enzymatic steps were conducted with RppH (NEB) and PNK (NEB) to remove the 5' cap, repair the triphosphate, and repair the 5' hydroxyl ends.
Adapter ligation and reverse transcription were performed with SuperScript III (Invitrogen), followed by PCR amplification. Libraries were size-selected with AMpure XP (Beckman Coulter)

treatment_protocol: Nuclear run-on assays were performed on 10×106 nuclei, incubated for 3 minutes at 30°C with 25 μM Biotin-11-ATP/UTP/CTP/GTP (PerkinElmer).

tag: cellline

value: Mouse ES cell line

tag: knockedout or drug

value: WT


title: PAS-seq srrm2 RNAi bio rep 1


title: SCAR2_581_dTAG_H4K20me2_T0

description: Pentabase adapters


title: Brain-NSC rep 2

description: replicate 2

source_name: Brain-NSC rep 2

value: NSC


title: T3_Rep2

description: WT Mouse ES cell line

source_name: Mouse ES cells WT time 3h Rep-2


title: Tail rep 1

description: replicate 1

source_name: Tail rep 1

value: Tail


title: PAS-seq control RNAi bio rep 5

value: control knockdown


title: T3_Rep1

description: WT Mouse ES cell line

source_name: Mouse ES cells WT time 3h Rep-1


title: SCAR1_557_dTAG_stranded_input_T0

description: Pentabase adapters

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


title: Brain-NSC rep 1

description: replicate 1

source_name: Brain-NSC rep 1


title: Tail-pNSC rep 1

description: replicate 1

source_name: Tail-pNSC rep 1


title: PAS-seq control RNAi bio rep 3

value: human embryonic kidney cell


title: T24_Rep2

description: WT Mouse ES cell line

source_name: Mouse ES cells WT time 24h Rep-2


title: SCAR1_557_DMSO_stranded_input_T0

description: Pentabase adapters


title: PAS-seq control RNAi bio rep 2

value: siRNA


title: SCAR2_581_DMSO_H4K20me2_T0

description: Pentabase adapters

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


title: Tail rep 2

description: replicate 2

source_name: Tail rep 2


title: SCAR2_581_DMSO_H4K20me0_T0

description: Pentabase adapters


title: SCAR1_557_dTAG_H4K20me0_T0

description: Pentabase adapters


title: T24_Rep1

description: WT Mouse ES cell line

source_name: Mouse ES cells WT time 24h Rep-1


title: PAS-seq control RNAi bio rep 1


title: T12_Rep3

description: WT Mouse ES cell line

source_name: Mouse ES cells WT time 12h Rep-3


title: Sox1-GFP+ brain cells

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

description: primary cells

library_source: transcriptomic single cell

data_processing:
Sequencing data were processed with UMI-tools (ver1.0.1)
aligned to the mouse reference genome (mm10) with STAR (version 2.7.1a)
quantified with Subread featureCounts (version 1.6.4)
Alternatively, the FASTQ format of sequencing raw data were processed with BD Rhapsody WTA Analysis pipeline (version 1.11) on SevenBridges Genomics online platform (SevenBridges).
Assembly: mm10
Supplementary files format and content: tsv or st files include UMI counts for each cell barcode and genes

source_name: Brain

extract_protocol:
lung,  tail, brain  tissues were cut and minced using a pair of scissors, and incubated with 0.25% trypsin (Invitrogen) at 37°C for 10 min. After trypsinization, 3 times volume amount of MEF medium was added, and the entire suspension was pipetted up and down to dissociate the tissues. The dissociated tissues were centrifuged, resuspended in FACS medium (D-PBS without calcium and magnesium supplemented with 0.3% BSA)and passed through a 40-µm cell strainer (Beckon Dickinson, BD). The flow cytometry was performed using either FACS Canto (BD Biosciences) or FACS Aria II (BD biosciences). After FACS sorting, the Sox2- GFP+ single cells from  lung, Sox1-GFP+ cells from tail and brain were counted using Luna-II automated cell counter (Logos Biosystems) and captured using the BD RhapsodyTM system.
After FACS sorting, the Nestin GFP+, Sox1-GFP+ or Sox2-GFP+ cells from brain, lung or tail tissue were counted using a Luna-II automated cell counter (Logos Biosystems) and Chromium (10X Genomics) for Nestin-GFP+ or BD Rhapsody Express system (BD) for Sox1-GFP+ and Sox2-GFP+ were used for the single cell capture and mRNA harvest. Single cell whole transcriptome libraries were prepared according to the manufacturer’s instructions using Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomics) or BD Rhapsody WTA Reagent kit (BD, 633802) and sequenced on the Illumina NextSeq 500 using High Output Kit v2.5 (150 cycles, Illumina) aiming sequencing depth of >20,000 reads per cell for each sample.

value: Brain

value: Sox1-GFP+ cells

value: single cell sorting by FACS


title: (experiment 2) PAS-seq RBBP6-NTD+IDR1 over-expression biol rep 3


title: Sox1-GFP+ tail cells

description: primary cells

source_name: Tail


title: SCAR1_557_DMSO_H4K20me0_T0

description: Pentabase adapters

source_name: Cell line

value: Cell line


title: PAS-seq control RNAi bio rep 4


title: Tail-pNSC rep 2

description: replicate 2

source_name: Tail-pNSC rep 2


title: SCAR1_557_dTAG_H4K20me2_T0

description: Pentabase adapters


title: Sox2-GFP+ lung cells

description: primary cells

source_name: Lung

value: Lung

value: Sox2-GFP+ cells


title: T12_Rep2

description: WT Mouse ES cell line

source_name: Mouse ES cells WT time 12h Rep-2


title: T12_Rep1

description: WT Mouse ES cell line

source_name: Mouse ES cells WT time 12h Rep-1


title: SCAR1_557_DMSO_H4K20me2_T0

description: Pentabase adapters

value: embryonic stem cells


title: SCAR1_555_dTAG_stranded_input_T0

description: Pentabase adapters


title: (experiment 2) PAS-seq RBBP6-NTD+IDR1 over-expression biol rep 1


title: Lung Nestin-GFP+ cells (single cell RNA Seq)

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
UMI-tools (v1.0.0) used for cell barcode and UMI counting
STAR (v2.7.1a) used for mouse reference genome (mm10) alignment
Subread featureCounts (v1.6.4) used for UMI quantification
Genome_build: mm10
Supplementary_files_format_and_content: tsv files include UMI counts for each cell barcode and genes

source_name: Adult mouse lung Nestin-GFP+ cells

extract_protocol:
adult  Nestin-GFP mice (C57BL/6) were sacrificed, lung and brain  tissues were cut and minced using a pair of scissors, and incubated with 0.25% trypsin (Invitrogen) at 37°C for 10 min. After trypsinization, 3 times volume amount of MEF medium was added, and the entire suspension was pipetted up and down to dissociate the tissues. The dissociated tissues were centrifuged, resuspended in FACS medium (D-PBS without calcium and magnesium supplemented with 0.3% BSA)and passed through a 40-µm cell strainer (Beckon Dickinson, BD). The flow cytometry was performed using either FACS Canto (BD Biosciences) or FACS Aria II (BD biosciences). After FACS sorting, the Nestin GFP+ single cells from brain or lung were counted using Luna-II automated cell counter (Logos Biosystems) and captured using the 10X Chromium system (10X Genomics).
Libraries were prepared according to the manufacturer’s instructions using Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomics)

value: lung

tag: developmental stage

value: ~6 weeks adult mouse


title: (experiment 2) PAS-seq RBBP6-NTD over-expression biol rep 3


title: Brain Nestin-GFP+ cells (single cell RNA Seq)

source_name: Adult mouse brain Nestin-GFP+ cells

value: brain


title: SCAR1_555_dTAG_H4K20me0_T0

description: Pentabase adapters


title: T0_Rep3

description: WT Mouse ES cell line

source_name: Mouse ES cells WT time 0h Rep-3

value: Mouse ES cell line

value: WT


title: U937 (p53-R282W) 1 μM DAC for 48 hr

city: Shanghai

first: Jiale

last: Wu

address: Room 707, Science and Education Plaza  197 Rui Jin Er Road

country: China

institute: State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiaotong University

description: RPKM of THP-1 U937 treated with DAC.xls

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to hg38 using STAR
Read counts were calculated by using htseq count
Genome_build: hg38
Supplementary_files_format_and_content: excel file generated by htseq count. GeneSymbol, FKPM

source_name: Myeloid malignant cell line

growth_protocol: THP-1 and U937 cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (Moregate) and cultured in a humidified incubator at 37℃ under 5% CO2.

extract_protocol:
Total RNA was isolated using total RNA Purification Kit (B518651, Sangon Biotech). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: THP-1 or U937 cells expressing indicated p53 were treated with DAC for indicated durations.

tag: cell lines

tag: cell types

value: monocyte

tag: p53 status

value: 1 uM DAC for 48 hr


title: SCAR1_555_DMSO_H4K20me0_T0

description: Pentabase adapters

tag: tissue


title: T0_Rep1

description: WT Mouse ES cell line

source_name: Mouse ES cells WT time 0h Rep-1


title: U937 (p53-R282W) 5 μM DAC for 48 hr

description: RPKM of THP-1 U937 treated with DAC.xls

value: 5 uM DAC for 48 hr


title: (experiment 2) PAS-seq RBBP6-NTD over-expression biol rep 1

value: human embryonic kidney cell

tag: genotype


title: THP-1 (p53-R282W) 5 μM DAC for 48 hr

description: RPKM of THP-1 U937 treated with DAC.xls


title: T0_Rep2

description: WT Mouse ES cell line

source_name: Mouse ES cells WT time 0h Rep-2


title: (experiment 2) PAS-seq RBBP6 depletion RBBP6-NTD+IDR1 rescue biol rep 3


title: SCAR1_555_DMSO_stranded_input_T0

description: Pentabase adapters


title: U937 (p53-R282W) DMSO for 48 hr

description: RPKM of THP-1 U937 treated with DAC.xls

value: DMSO for 48 hr


title: T24_Rep3

description: WT Mouse ES cell line

source_name: Mouse ES cells WT time 24h Rep-3


title: KO.IL33.1

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the GENCODE v27 reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: tab delimited text file of RPKM normalized read counts for each gene

source_name: male epididymal visceral adipose tissue

extract_protocol:
1,000 cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

value: male epididymal visceral adipose tissue

tag: age

value: 25 weeks

value: Tregs

value: Foxp3-YFPcre Srebf2 flox/flox

value: IL-33 treated

tag: sorting markers

value: live CD3+ CD4+ YFP+ ST2+


title: KO.IL33.2

tag: treatment


title: SCAR1_555_DMSO_H4K20me2_T0

description: Pentabase adapters

value: Cell line

value: embryonic stem cells


title: (experiment 2) PAS-seq RBBP6-NTD over-expression biol rep 2


title: (experiment 2) PAS-seq RBBP6-NTD+IDR1 over-expression biol rep 2


title: KO.IL33.3


title: (experiment 2) PAS-seq RBBP6 depletion RBBP6-NTD+IDR1 rescue biol rep 1


title: (experiment 2) PAS-seq RBBP6 depletion RBBP6-NTD+IDR1 rescue biol rep 2


title: Leaf, control, 0hpw, rep3

city: Pozuelo de Alarcon

first: Miguel

middle: Angel

last: Moreno-Risueno

state: Madrid

department: Biotechnology

country: Spain

institute: Center for Plant Biotechnology and Genomics

description:
Leaf, control, 0hpw, rep3
Arabidopsis thaliana (L.) Heynh., 1842

data_processing:
Tophat2 to alignement
Cufflinks and Cuffmerge for asembly
Cuffdiff for differential expression
HTseq-count form TPMs
Assembly: Arabidopsis-TAIR10
Supplementary files format and content: tab delimited text file containing FPKM values

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: For the RNA sequencing experiment Arabidopsis plants were grown plants were grown for 21 days on MS media under short-day conditions at 23 º C. A 4 mm cut was performed on three-week-old Arabidopsis leaves with a surgical scalpel. Cuts were left uncovered or covered with a 1.6 mm diameter BC film. The samples for RNA extraction were snap frozen in liquid nitrogen 0, 3, 6 and 24 h post-wounding (hpw) and keep at -80º. Three biological replicas composed of 5-6 different pieces of leaf each were used for the analysis.

extract_protocol:
RNA extraction was performed using the QIAGEN RNeasy Micro kit (Quiagen, Hilden, Germany). RNA quality and concentration were measured using an Agilent 2100 Bioanalyzer (pico chip) (Agilent Gechnologies, Santa Clara, CA, USA).
TAKARA Low Input Library Prep Kit v2
RNA-seq, 100 bp single-end Illumina HiSeq2000

value: leaf

value: uncovered control


title: WT.IL33.3

value: Foxp3-YFPcre Srebf2 wt/wt


title: (experiment 2) PAS-seq RBBP6 depletion RBBP6-NTD rescue biol rep 3


title: THP-1 (p53-R282W) DMSO for 48 hr

description: RPKM of THP-1 U937 treated with DAC.xls


title: Leaf, BC, 24hpw, rep3

description:
Leaf, BC, 24hpw, rep3
Arabidopsis thaliana (L.) Heynh., 1842

treatment_protocol: Cuts were left uncovered or covered with a 1.6 mm diameter BC film.

value: bacterial cellulose


title: WT.IL33.2


title: (experiment 2) PAS-seq RBBP6 depletion RBBP6-NTD rescue biol rep 2


title: Leaf, BC, 24hpw, rep1

description:
Leaf, BC, 24hpw, rep1
Arabidopsis thaliana (L.) Heynh., 1842


title: (experiment 2) PAS-seq RBBP6 depletion RBBP6-NTD rescue biol rep 1


title: Leaf, BC, 24hpw, rep2

description:
Leaf, BC, 24hpw, rep2
Arabidopsis thaliana (L.) Heynh., 1842


title: ITK_SYK_Tcells_S16

type: RNA

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

hyb_protocol: Labeled fragments were hybridized to Affymetrix Mouse Gene ST 2.0 arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: Spleen CD4+ T-cells ITK-SYK

label_protocol: We used the Affymetrix WT Pico kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

growth_protocol: CD4+ T-cells and granulocytes were harvested and sorted from spleens of ITK-SYK and control mice

extract_protocol: cell sorting via CD3/CD4 for T-cells and Gr-1/CD11b for granulocytes

treatment_protocol: no treatment was performed

value: CD4+ T-cells (CD3+ CD4+)

value: Spleen

value: ITK-SYK


title: Leaf, control, 24hpw, rep3

description:
Leaf, control, 24hpw, rep3
Arabidopsis thaliana (L.) Heynh., 1842


title: KO.PBS.2

value: PBS treated


title: KO.PBS.3


title: ITK_SYK_Tcells_S13


title: Leaf, control, 24hpw, rep2

description:
Leaf, control, 24hpw, rep2
Arabidopsis thaliana (L.) Heynh., 1842


title: (experiment 2) PAS-seq RBBP6 depletion control rescue biol rep 3

value: human embryonic kidney cell


title: THP-1 (p53-R282W) 1 μM DAC for 48 hr

description: RPKM of THP-1 U937 treated with DAC.xls

value: monocyte

value: 1 uM DAC for 48 hr


title: ITK_SYK_Tcells_S10


title: WT.IL33.1

value: male epididymal visceral adipose tissue

value: 25 weeks

value: Tregs


title: ITK_SYK_neutro_S18

source_name: Spleen neutrophil granulocytes ITK-SYK mouse

value: Neutrophil granulocytes (Gr1+)


title: (experiment 2) PAS-seq RBBP6 depletion control rescue biol rep 2


title: (experiment 2) PAS-seq RBBP6 depletion control rescue biol rep 1


title: ITK_SYK_neutro_S15


title: Leaf, control, 24hpw, rep1

description:
Leaf, control, 24hpw, rep1
Arabidopsis thaliana (L.) Heynh., 1842


title: KO.PBS.1

value: Foxp3-YFPcre Srebf2 flox/flox

value: live CD3+ CD4+ YFP+ ST2+


title: WT.PBS.2


title: (experiment 2) PAS-seq rescue control biol rep 3


title: Leaf, BC, 6hpwBC, rep3

description:
Leaf, BC, 6hpwBC, rep3
Arabidopsis thaliana (L.) Heynh., 1842

value: leaf


title: WT.PBS.1


title: Leaf, BC, 6hpwBC, rep2

description:
Leaf, BC, 6hpwBC, rep2
Arabidopsis thaliana (L.) Heynh., 1842


title: (experiment 2) PAS-seq rescue control biol rep 2


title: ctl_Tcells_S7

source_name: Spleen CD4+ T-cells wt

value: CD4+ T-cells CD3+ CD4+

value: wildtype


title: EC1CRM8Δ/Δ, replicate 3, scRNAseq

city: Basel

first: Aimee

last: Zuniga

address: Mattenstrasse, 28 4058

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

description: 10x Genomics

data_processing:
used CellRanger (v.6.0.1) with the default parameters to obtain transcript count matrices aligning the sequenced reads to the mouse genome and annotations
Count matrices were further processed using the R package Seurat (v.4.3.0.1)
Assembly: mm10
Supplementary files format and content: CellRanger output files

source_name: Pair of forelimbs

growth_protocol: mice were kept in an animal facility

extract_protocol:
For enzymatic digestion, PBS was removed and exchanged for Collagenase D (20 mg/ml) in DMEM and incubated in a water bath at 37°C for 20min. Limb buds were pipetted gently using a P1000 every 5min to help dissociation. Enzymatic digestion was stopped by adding 500 μl of HBSS+ (HBSS, 5% Fetal Bovine Serum, 1% Hepes 1M, 1% Pen-Strep) and the cell suspension was filtered and transferred to a new tube using a FlowMi Cell Strainers (40μm) in combination with a P1000 tip. Tubes were centrifuged for 5 minutes at 2000g (4oC). Cells were resuspended in 100 μl HSBB+ and cell viability and numbers were assessed using a Trypan Blue assay on the cell counter.
libraries were prepared using Single cell library preparation system Chromium X (10X Genomics) and using the kit and manufacturer’s guidelines from the user guide Chromuim Next GEM Single Cell 3’ Reagent Kits v3.1
all samples were prepared in individual libraries

treatment_protocol: Mice were set for timed matings and embryos were collected in ice cold PBS at E10.75 (37-39 somites). Pairs of limb buds were dissected from selected embryos and placed into Eppendorf tubes

value: Pair of forelimbs


title: (experiment 2) PAS-seq rescue control biol rep 1


title: Leaf, BC, 6hpwBC, rep1

description:
Leaf, BC, 6hpwBC, rep1
Arabidopsis thaliana (L.) Heynh., 1842

value: bacterial cellulose


title: ctl_Tcells_S4

value: Spleen


title: EC1CRM8Δ/Δ, replicate 2, scRNAseq

description: 10x Genomics


title: (experiment 1) PAS-seq RBBP6 NTD+IDR4 over-expression biol rep 3


title: Leaf, control, 6hpw, rep3

description:
Leaf, control, 6hpw, rep3
Arabidopsis thaliana (L.) Heynh., 1842

value: uncovered control


title: SCAR1_555_dTAG_H4K20me2_T0

description: Pentabase adapters

source_name: Cell line

value: Cell line

value: embryonic stem cells


title: Leaf, control, 6hpw, rep2

description:
Leaf, control, 6hpw, rep2
Arabidopsis thaliana (L.) Heynh., 1842


title: (experiment 1) PAS-seq RBBP6 NTD+IDR4 over-expression biol rep 2

value: human embryonic kidney cell


title: EC1CRM5Δ/Δ, replicate 3, scRNAseq

description: 10x Genomics


title: ITK_SYK_neutro_S12

value: ITK-SYK


title: (experiment 1) PAS-seq RBBP6 NTD+IDR4 over-expression biol rep 1


title: Leaf, control, 6hpw, rep1

description:
Leaf, control, 6hpw, rep1
Arabidopsis thaliana (L.) Heynh., 1842


title: EC1CRM5Δ/Δ, replicate 2, scRNAseq

description: 10x Genomics


title: ctl_neutro_S9

source_name: Spleen neutrophil granulocytes wt mouse


title: (experiment 1) PAS-seq RBBP6 FL over-expression biol rep 2


title: ctl_neutro_S6


title: (experiment 1) PAS-seq RBBP6 FL over-expression biol rep 1


title: Leaf, BC, 3hpwBC, rep3

description:
Leaf, BC, 3hpwBC, rep3
Arabidopsis thaliana (L.) Heynh., 1842


title: ctl_neutro_S3


title: GF_TAC5

city: Cincinnati

first: Joo-Seop

last: Park

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie version 1.0.0 with parameters ---library-type fr-unstranded -p 6 --no-coverage-search
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cuffdiff v2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: an excel file (RPKM.xlsx) contains RPKM values for each gene.

source_name: liver

extract_protocol:
Total RNA was extracted from mouse liver tissues using Trizol reagent (Thermo, 15596018). Afterwards, mRNA was extracted from total RNA using  NEBNext® Poly(A) mRNA Magnetic Isolation Module, 24 rxns (NEB, E7490S)
RNA libraries were prepared for sequencing using ThruPLEX-FD-12 kit (Rubicon Genomics)

value: Liver

tag: gender

value: male

tag: fasted state

value: Fasted


title: Leaf, BC, 3hpwBC, rep2

description:
Leaf, BC, 3hpwBC, rep2
Arabidopsis thaliana (L.) Heynh., 1842


title: Wildtype, replicate 3, scRNAseq

description: 10x Genomics

value: Wildtype


title: GF_TAC4


title: (experiment 1) PAS-seq RBBP6 depletion RBBP6 NTD+IDR4 rescue biol rep 2

tag: cell line

tag: cell type


title: (experiment 1) PAS-seq RBBP6 depletion RBBP6 NTD+IDR4 rescue biol rep 1


title: Wildtype, replicate 2, scRNAseq

description: 10x Genomics


title: GF_TAC3

tag: strain


title: Wildtype, replicate 1, scRNAseq

description: 10x Genomics


title: Leaf, control, 3hpw, rep3

description:
Leaf, control, 3hpw, rep3
Arabidopsis thaliana (L.) Heynh., 1842


title: EC1CRM8Δ/Δ, replicate 1, scRNAseq

description: 10x Genomics


title: GF_TAC2


title: GF_TAC1


title: (experiment 1) PAS-seq RBBP6 depletion RBBP6 FL rescue biol rep 2


title: (experiment 1) PAS-seq RBBP6 depletion RBBP6 FL rescue biol rep 3


title: Leaf, control, 3hpw, rep2

description:
Leaf, control, 3hpw, rep2
Arabidopsis thaliana (L.) Heynh., 1842


title: EC1CRM5Δ/Δ, replicate 1, scRNAseq

description: 10x Genomics


title: GF_JAX5


title: Fbp1_KO_3_snRNAseq

city: La Jolla

first: Masafumi

last: Ohira

state: California

address: 9500 Gilman Drive

department: Department of Pharmacology

institute: University of California San Diego

description: 10x Genomics

data_processing:
Raw fastq files were aligned to the mouse mm10 reference genome using 10x Genomics Cell Ranger 7.1.0 with 10x Genomics Cloud Analysis.
Assembly: mm10
Supplementary files format and content: comma-separated text file includes raw counts for each sample

molecule: nuclear RNA

source_name: Liver

extract_protocol:
Live freshly collected livers nuclei were determined with Chromium Nuclei Isolation with RNase Inhibitor Kit (1000494, 10x Genomics) and 500,000 cells per sample were run on the 10x Chromium platform (10x Genomics).
Library preparation were performed using the Chromium Next GEM Single Cell 3' Kit v3.1 according to manufacturer's instructions.

value: tissue

value: MUP-uPA, Fbp1deltaHep

tag: diet

value: High fructose diet


title: Leaf, control, 3hpw, rep1

description:
Leaf, control, 3hpw, rep1
Arabidopsis thaliana (L.) Heynh., 1842

value: leaf


title: Fbp1_KO_2_snRNAseq

description: 10x Genomics


title: (experiment 1) PAS-seq RBBP6 depletion RBBP6 FL rescue biol rep 1


title: Leaf, BC, 0hpw, rep3

description:
Leaf, BC, 0hpw, rep3
Arabidopsis thaliana (L.) Heynh., 1842


title: ctl_Tcells_S1

value: CD4+ T-cells CD3+ CD4+

value: wildtype


title: (experiment 1) PAS-seq RBBP6 depletion control rescue biol rep 3


title: GF_JAX4


title: Leaf, BC, 3hpwBC, rep1

description:
Leaf, BC, 3hpwBC, rep1
Arabidopsis thaliana (L.) Heynh., 1842

value: bacterial cellulose


title: GF_JAX3


title: Leaf, BC, 0hpw, rep2

description:
Leaf, BC, 0hpw, rep2
Arabidopsis thaliana (L.) Heynh., 1842


title: (experiment 1) PAS-seq RBBP6 depletion control rescue biol rep 1


title: Leaf, control, 0hpw, rep2

description:
Leaf, control, 0hpw, rep2
Arabidopsis thaliana (L.) Heynh., 1842


title: GF_JAX2


title: GF4


title: (experiment 1) PAS-seq rescue control biol rep 2


title: (experiment 1) PAS-seq rescue control biol rep 1


title: Leaf, BC, 0hpw, rep1

description:
Leaf, BC, 0hpw, rep1
Arabidopsis thaliana (L.) Heynh., 1842


title: GF_JAX1


title: GN071

city: Budapest

first: <Up loaded by Bioinformatics core  facility>

last: <PI shown in the article>

address: Szigony st 43.

country: Hungary

institute: HUN-REN Institute of Experimental Medicine

description: SVTg

data_processing:
Trimmed adapter seq and low phredscore 3’ ends
if a read became shorter than 50 bp it and it’s pair was removed
readspairs where one seq consisted of only 3 tipe of nucleotids were removed
STAR aligner (2.7.10a) was used to alige reads to the reference and to cunt reads per genes
Assembly: Mouse genome mm39 with ensembl annotation v110 was supplemented with Addgene_pAAV-EF1a-DIO-mCherry (Plasmid #50459); Cre (NCBI/Nucleotide:NC_005856.1); and YFP (NCBI/Nucleotide:GQ221700.1).
Supplementary files format and content: both datafiles are count matrixes on a gene level consisting of genes as rows and samples as columns

source_name: Brain

growth_protocol: We used vGAT-iRES-Cre adult (at least 6 weeks-old) mice that had access to food and water ad libitum and were housed in a vivarium (3-5 mice/cage) until used in experiments. Mice were injected with AAVretro-EF1a-DIO-mCherry into bilateral LHb (60 nl per site) then were placed into separate cages. After 2-5 weeks of incubation time mice were sacrificed during the light phase and 200-250 μm thick coronal slices were made from the pontine region of the brainstem of vGAT-Cre mice.

extract_protocol:
Mice were decapitated under deep anesthesia and slices were prepared in ice-cold cutting solution (85 mM NaCl, 75 mM sucrose, 2.5 mM KCl, 25 mM glucose, 1.25 mM NaH2PO4, 4 mM MgCl2, 0.5 mM CaCl2, and 24 mM NaHCO3) using a VT1200S vibratome (Leica). Slices were incubated at 35 °C for ~30 min and then kept at room temperature until use. During recordings the slices are kept at 35 °C in continuously perfused with artificial cerebrospinal fluid (126 mM NaCl, 2.5 mM KCl, 26 mM NaHCO3, 2 mM CaCl2, 2 mM MgCl2, 1.25 mM NaH2PO4, and 10 mM glucose, saturated with carbogen,) Fluorescently labeled SVTg neurons were visualized in an upright microscope (Eclipse FN-1; Nikon) with epifluorescent illumination (Lambda FLED @ 530 nm; Sutter Instrument) combined with a CMOS camera (DaVinci 1k, RedShirtImaging). The neurons were patched with thin-wall borosilicate pipettes (pipette resistance: 3.69±0.09 MΩ, BF150-117-10, Sutter Instrument) filled with small amount (~1 µl) of intracellular solution containing 133.5 mM K-gluconate, 1.8 mM NaCl, 1.7 mM MgCl2, 0.05 mM EGTA, 10 mM HEPES, 2 mM Mg-ATP, 0.4 mM Na2-GTP, 10 mM phosphocreatine, and 8 mM biocytin (pH 7.25;  290-300 mOsm). Pipette capacitance and the bridge balance were carefully compensated in all current clamp recordings. For the RNA harvesting, the recordings were made using a HEKA EPC800 amplifier (HEKA Elektronik) digitized with a Digidata1440A A/D converter (Molecular Devices). The data acquisition was controlled by the pClamp10 software package. After patching the identified neurons, we measured the basic electrophysiological parameters of the cells including the resting membrane potential, the spontaneous synaptic activity, and the firing pattern. The length of the recording session was limited to 5 min from the break-in. The cytosol together with the nucleus was extracted from the neuron by the application of small negative pressure to the pipette. The tip of the quickly removed pipette was gently pushed into a microtube containing ice cold reaction buffer (lysis buffer with RNase inhibitor, Takara SMART-Seq HT PLUS Kit). The sample containing tubes was spun briefly and snap-frozen on dry ice. To suppress RNase contamination, the workplace including parts of the experimental setup was cleaned each day before the start of the sample collection with RNase AWAY (Thermo Fisher).
Sample collection: After electrophysiological recordings, the cells’ cytosol was aspirated via the same recording glass pipette that used for recording, and using a positive pressure, expelled into microtubes containing 1 µl of 1x lysis buffer with RNase inhibitor (SMART-Seq HT PLUS Kit, Takara). The samples were immediately frozen on dry ice and stored at -80°C until further processing. cDNA and library preparation for next-generation sequencing: Single-cell mRNA processing was performed using the SMART-Seq HT PLUS Kit (Takara) and according to manufacturer’s protocol. In brief, samples were reverse transcribed to cDNA, amplified, and purified with AMPure XP beads (Beckman Coulter). The quantity and the quality of the purified cDNA was assessed using Fragment Analyzer (Advanced Analytical). Subsequently, the cDNA was fragmented and adapters including indices for cell identification were added to the fragments. The quality and quantity were again assessed using Fragment Analyzer. For library preparation, the single cell samples with unique index adapters were pooled in equal amounts. The sequencing was performed on a NovaSeq 6000 (Illumina) instrument using 150 bp paired end configuration and a full SP-flowcell. Processing of sequencing data: After sequencing, raw reads were de-multiplexed with Illumina’s bcl2fastq2 (v2.20).

treatment_protocol: All vGAT-Cre mice were injected with AAVretro-EF1a-DIO-mCherry into bilateral LHb (60 nl per site) to label SVTg neurons.

value: Brain

value: adult (at least 6 weeks-old)


title: (experiment 1) PAS-seq RBBP6 depletion control rescue biol rep 2


title: Leaf, control, 0hpw, rep1

description:
Leaf, control, 0hpw, rep1
Arabidopsis thaliana (L.) Heynh., 1842

value: uncovered control


title: (experiment 1) PAS-seq rescue control biol rep 3


title: GF3


title: GN072

description: SVTg


title: GN070

description: SVTg


title: Fbp1_ff_3_snRNAseq

description: 10x Genomics

value: MUP-uPA, Fbp1 f/f


title: GF1


title: Fbp1_ff_2_snRNAseq

description: 10x Genomics


title: Fbp1_ff_1_snRNAseq

description: 10x Genomics


title: GN098

description: SVTg


title: PAS-seq RBBP6 depletion biol rep 2

value: human embryonic kidney cell


title: MU_1

city: Guangzhou

first: Huiting

last: Liu

state: Guangdong

address: Lujing road NO.2

institute: Dermatology Hospital, Southern Medical University

description: Library name: Sample 4

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using hisat2 (v2.0.1)
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using stringtie-2.0.6 following the protocol from Pertea et al., Nature Protocols, 2016.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for all Sample.

source_name: NHEK

growth_protocol: NHEK cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using Trizol reagent. Total RNA was quantified and qualified by Agilent 2100/2200 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: NHEK

value: SERPINB7 mutant

value: NO


title: MU_2

description: Library name: Sample 5


title: PAS-seq RBBP6 depletion biol rep 3


title: MU_3

description: Library name: Sample 6


title: GF2

value: Liver

value: male

value: Fasted


title: Fbp1_KO_1_snRNAseq

description: 10x Genomics

value: tissue

value: MUP-uPA, Fbp1deltaHep


title: WT_3

description: Library name: Sample 3

value: control


title: TAC4


title: GN069

description: SVTg


title: PAS-seq RBBP6 depletion biol rep 1


title: WT_2

description: Library name: Sample 2


title: TAC3


title: GN068

description: SVTg


title: PAS-seq control biol rep 3


title: GN066

description: SVTg


title: GN067

description: SVTg


title: TAC2


title: PAS-seq control biol rep 2


title: GN065

description: SVTg


title: TAC1


title: ESC_miR-302KO_rep2

city: San Francisco

first: Robert

last: Blelloch

address: 35 Medical Center Way

department: Dept. of Urology

institute: UC, San Francisco

description: 3'end capture

data_processing:
Data was processed from fastq to a gene count matrix using Nextflow pipeline nf-core/RNA-seq v3.2. In brief, adapters for sample FastQ files were trimmed using trimgalore v0.66 followed by alignment to the mm10 genome using STAR align v2.6.1d. Salmon v1.4.0 was used to generate a counts matrix of reads per gene. FastQC v0.11.9 and MultiQC were used to validate quality sequencing and mapping.
The gene count matrix was converted to CPM and filtered for genes greater than 1 cpm in at least two total samples. Samples were normalized using TMM. Next, Log2 CPM averages were calculated for replicates of each sample and used for UMAP, heatmaps, and cumulative distribution function plots of predicted miRNA targets . All transcriptomics analyses were conducted using CPM values from TMM normalization of all samples (including Freimer et al. 2018 data) and batch corrected via Limma::removeBatchEffect() between our data and data from Freimer etal. 2018. To conduct differential gene expression we performed DESeq2 v1.34.0 analysis using the raw gene count matrix as input for each desired comparison.
Assembly: mm10
Supplementary files format and content: csv file containing CPM values of filtered, TMM-normalized, and batch corrected genes for every sample generated and those included from Freimer et al. 2018
Supplementary files format and content: csv file of DESeq2 outputs comparing WT iPSCs to either reprogrammed 290, 302, or 290;302KO cells

source_name: ESC

extract_protocol:
Total RNA was extracted and purified from cells using Trizol followed by ethanol precipitation
RNA-seq libraries were generated using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, CAT#A01172) according to their protocol using 200ng of total RNA for input. We utilized the PCR Add-on kit for Illumina (Lexogen, CAT#M02096) to determine an appropriate number of PCR cycles to amplify libraries. Amplified libraries were quantified using Agilent Tapestation 4200. Libraries were pooled and sequenced using a HiSeq 4000 to obtain single end 50bp reads. An average of 20 million mapped reads or more per sample were obtained.

value: ESC


title: JAX4


title: ESC_miR-290KO_rep2

description: 3'end capture


title: PAS-seq control biol rep 1


title: 4sU-seq RBBP6 depletion biol rep 3


title: ESC_miR-302KO_rep1

description: 3'end capture


title: 4sU-seq RBBP6 depletion biol rep 2


title: ESC_miR-290KO_rep1

description: 3'end capture


title: JAX3


title: GN061

description: SVTg


title: 4sU-seq RBBP6 depletion biol rep 1


title: JAX1


title: iPSC_WT_rep3

description: 3'end capture

source_name: iPSC

value: iPSC

value: WT


title: JAX2


title: iPSC_WT_rep2

description: 3'end capture


title: 4sU-seq control biol rep 3


title: GN060

description: SVTg

value: Brain


title: WT_1

description: Library name: Sample 1


title: HeLa-WT-2.2-Subpolysome

description: SubPolysome 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.
The processed fastq reads were mapped to a human reference transcriptome that includes Ensembl v85 transcripts and long noncoding from LNCipedia v5.2 using the "RSEM" tool.
Assembly: GRCh37/hg19
Supplementary files format and content: HTSeq count file

source_name: HeLa cells WT SubPolysome Rep-4

growth_protocol: HeLa were maintained in DMEM supplemented with 10% FBS and 1% penicillin and streptomycin (Gibco).

extract_protocol:
RNA was extracted with TRIzol LS (Invitrogen) and purified with lithium chloride (LiCl) precipitation solution (Invitrogen) according to the manufacturer’s protocols.
The library preparation was performed using TruSeq Stranded Total RNA with Ribo-Zero Gold following the manufacturer’s instructions.

treatment_protocol: Fifteen minutes before harvest, 100 μg/ml cycloheximide (CHX) (Sigma) was added to the medium. Cells were washed twice with ice-cold PBS supplemented with 100 μg/ml CHX, scraped, and centrifuged at 4°C (500g for 5 minutes).  Cell pellets were resuspended in 500 μL lysis buffer (20 mM Tris pH 7.4, 100 mM KCl, 5 mM MgCl2, 100 μg/ml CHX, 1% Triton X- 100, supplemented with cOmplete™ Mini Protease Inhibitor Cocktail (Roche) and 40 U RNase Inhibitor (Promega)), incubated at 4°C for 20 minutes, and centrifuged (13000g for 20 minutes). The supernatant was treated with the RNase-Free DNase Set (Qiagen) according to the manufacturer’s protocol and then centrifuged at 4°C (13,000g for 15 minutes). The A260 absorbance of each sample was measured to adjust the RNA amount to 300 μg. A 10–50% w/v sucrose gradient was prepared for each sample in lysis buffer without Triton X-100 and adjusted lysates were loaded onto the sucrose gradient and centrifuged at 4°C (190,000g for 90 minutes, Beckman, rotor SW41Ti). The gradients were then fractionated into 0.4-ml fractions with an ISCO Density Gradient Fractionation system at 1ml/min speed. The A254 absorbance of each fraction was measured by the optical unit of the fractionating system. Fractions corresponding to non-polysomes (free RNA, 40S, 60S, and 80S) and polysomes were collected.

tag: cellline

value: Human HeLa cell line

tag: knockedout


title: 4sU-seq control biol rep 2


title: HeLa-WT-2.2-polysome

description: Polysome WT HeLa Cells

source_name: HeLa cells WT Polysome Rep-4


title: GN059

description: SVTg

value: adult (at least 6 weeks-old)


title: 4sU-seq control biol rep 1


title: GN029

description: SVTg


title: iPSC_WT_rep1

description: 3'end capture


title: GN064

description: SVTg


title: HeLa-WT-2.1-Subpolysome

description: SubPolysome WT HeLa Cells

source_name: HeLa cells WT SubPolysome Rep-3


title: GN026

description: SVTg


title: iPSC_miR-290KO;miR-302KO_colony2_rep1

description: 3'end capture


title: iPSC_miR-290KO;miR-302KO_colony1_rep2

description: 3'end capture


title: GN062

description: SVTg


title: miR-5681b transfected HSVSMC treated with IL1a+PDGFBB rep2

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: UNIVERSITY OF EDINBURGH

data_processing:
Gene quantification (read count and FPKM) was obtained using RSEM (options: -bowtie2 -pairedend), based on human  GRCh38 genome annotation and GENCODE transcriptome annotation (Release 25)
Assembly: GRCh38
Supplementary files format and content: Count.csv: csv file containing read count for each gene in the different samples
Supplementary files format and content: FPKM.csv: csv file containing the FPKM (fragments per kilobase of transcript per million mapped reads) expression value for each gene in the different samples

source_name: Human saphenous vein smooth muscle cell

growth_protocol: Primary human saphenous vein derived smooth muscle cells (HSVSMCs) were obtained and maintained as previously described in Ballantyne et al, 2016 Circulation. Briefly, HSVSMCs were isolated from medial explants and cultured using Smooth Muscle Cell (SMC) growth medium 2 (Promocell) were supplemented with the SMC 2 medium supplement (Promocell), 10% foetal bovine serum (FBS) (Gibco), 2 mM L-Glutamine (Invitrogen), 50 μg/ml penicillin (Invitrogen) and 50 μg/mL streptomycin (Invitrogen).

extract_protocol:
RNA was extracted and DNAse treated using the miRNeasy mini kit (Qiagen)
Library preparation was prepared after polyA mRNA selection using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB).

treatment_protocol:
Transient transfection of the 7 miRNA mimics (Dharmacon, ThermoFisher)  or the miRNA control (miR-CTRL-miRIDIAN microRNA Mimic Negative Control #1) was performed with Lipofectamine RNAiMAX (Life Technologies) following the manufacturer’s guidelines, for 6 hours in Opti-MEM (Life Technologies).
HSVSMCs were treated with 10 ng/mL IL1α and 20 ng/mL PDGF for 48h.

value: Human saphenous vein smooth muscle cell

tag: replicate/patient

tag: mimic transfection


title: GN025

description: SVTg


title: miR-5681b transfected HSVSMC treated with IL1a+PDGFBB rep3


title: iPSC_miR-290KO;miR-302KO_colony1_rep1

description: 3'end capture


title: miR-5681b transfected HSVSMC treated with IL1a+PDGFBB rep1


title: GN024

description: SVTg


title: miR-4774-3p transfected HSVSMC treated with IL1a+PDGFBB Rep3


title: iPSC_miR-302KO_colony2_rep2

description: 3'end capture


title: GN023

description: SVTg


title: miR-4774-3p transfected HSVSMC treated with IL1a+PDGFBB Rep2


title: HeLa-WT-1.1-Subpolysome

description: SubPolysome WT HeLa Cells

source_name: HeLa cells WT SubPolysome Rep-1


title: iPSC_miR-302KO_colony2_rep1

description: 3'end capture


title: GN022

description: SVTg


title: iPSC_miR-290KO;miR-302KO_colony2_rep2

description: 3'end capture


title: HeLa-WT-1.1-polysome

description: Polysome WT HeLa Cells

source_name: HeLa cells WT Polysome Rep-1


title: miR-4774-3p transfected HSVSMC treated with IL1a+PDGFBB Rep1


title: iPSC_miR-302KO_colony1_rep2

description: 3'end capture


title: HeLa-M3KO-2.2-Subpolysome

description: SubPolysome METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO SubPolysome Rep-4


title: miR-1827 transfected HSVSMC treated with IL1a+PDGFBB Rep3


title: HeLa-WT-2.1-polysome

description: Polysome WT HeLa Cells

source_name: HeLa cells WT Polysome Rep-3


title: GN021

description: SVTg


title: GN020

description: SVTg


title: HeLa-WT-1.2-Subpolysome

description: SubPolysome WT HeLa Cells

source_name: HeLa cells WT SubPolysome Rep-2


title: miR-1827 transfected HSVSMC treated with IL1a+PDGFBB Rep2


title: HeLa-M3KO-2.2-polysome

description: Polysome METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO Polysome Rep-4


title: GN018

description: SVTg


title: miR-1827 transfected HSVSMC treated with IL1a+PDGFBB Rep1


title: iPSC_miR-290KO_colony2_rep1

description: 3'end capture


title: iPSC_miR-290KO_colony2_rep2

description: 3'end capture


title: HeLa-M3KO-2.1-Subpolysome

description: SubPolysome METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO SubPolysome Rep-3


title: GN014

description: SVTg


title: HeLa-WT-1.2-polysome

description: Polysome WT HeLa Cells

source_name: HeLa cells WT Polysome Rep-2


title: miR-892b transfected HSVSMC treated with IL1a+PDGFBB Rep3


title: GN013

description: SVTg


title: iPSC_miR-290KO_colony1_rep2

description: 3'end capture


title: HeLa-M3KO-1.2-Subpolysome

description: SubPolysome METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO SubPolysome Rep-2


title: miR-892b transfected HSVSMC treated with IL1a+PDGFBB Rep2


title: iPSC_miR-290KO_colony1_rep1

description: 3'end capture


title: miR-892b transfected HSVSMC treated with IL1a+PDGFBB Rep1


title: HeLa-M3KO-1.2-polysome

description: Polysome METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO Polysome Rep-2


title: GN012

description: SVTg

source_name: Brain


title: iPSC_miR-302KO_colony1_rep1

description: 3'end capture


title: cko_female_3

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on a Miseq platform in a 301+301 base paired-end mode.
Raw FASTQ sequences were analyzed using QIIME2 (ver.2020.2).
Taxonomy was assigned based on the Greengenes 16S rRNA reference database (supplementary file: v1v2-gg-classifier_2020.2.qza).
Relative frequencies of taxonomy for each rank of the Kingdom Bacteria were calculated for each sample.
Assembly: v1v2-gg-classifier_2020.2.tar.gz
Supplementary files format and content: Level2_relative_frequency: tab delimited text file include relative frequency for Phylum rank of the Kingdom Bacteria
Supplementary files format and content: Level3_relative_frequency: tab delimited text file include relative frequency for Class rank of the Kingdom Bacteria
Supplementary files format and content: Level4_relative_frequency: tab delimited text file include relative frequency for Order rank of the Kingdom Bacteria
Supplementary files format and content: Level5_relative_frequency: tab delimited text file include relative frequency for Family rank of the Kingdom Bacteria
Supplementary files format and content: Level6_relative_frequency: tab delimited text file include relative frequency for Genus rank of the Kingdom Bacteria
Supplementary files format and content: Level7_relative_frequency: tab delimited text file include relative frequency for Species rank of the Kingdom Bacteria

organism: mouse gut metagenome

source_name: feces from Foxl1-cre; Cxcl12f/f mouse

extract_protocol:
Fecal DNA was extracted from feces in  Cxcl12f/f and Foxl1-cre; Cxcl12f/f mice.
Each library was prepared by 1st PCR with a primer set (27Fmod and 338R) targeting the V1–V2 region of the 16S rRNA gene and 2nd PCR with Nextera XT Index Kit (illumina).

value: feces from Foxl1-cre; Cxcl12f/f mouse


title: GN009

description: SVTg


title: HeLa-M3KO-1.1-Subpolysome

description: SubPolysome METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO SubPolysome Rep-1


title: wtff_female_2

source_name: feces from Cxcl12f/f mouse

value: feces from Cxcl12f/f mouse


title: miR-491-3p transfected HSVSMC treated with IL1a+PDGFBB Rep3


title: miR-491-3p transfected HSVSMC treated with IL1a+PDGFBB Rep2


title: cko_female_10


title: miR-491-3p transfected HSVSMC treated with IL1a+PDGFBB Rep1


title: GN006

description: SVTg


title: HeLa-WT-for-differential-3-INPUT

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.
The processed fastq reads were mapped to the human reference genome (GRCh37/hg19) using the "STAR" algorithm with reference transcriptome includes Ensembl v85 and long noncoding from LNCipedia v5.2. 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: GRCh37/hg19
Supplementary files format and content: tab-delimited text files include list of reproducible peaks across replicates for genes expressed at at least 1 TPM

source_name: HeLa WT-for-differential-3 INPUT

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:
(RNA purification) 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.

tag: library

value: INPUT


title: cko_male2-2


title: HeLa-M3KO-1.1-polysome

description: Polysome METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO Polysome Rep-1


title: HeLa-WT-for-differential-3-m6A

source_name: HeLa WT-for-differential-3 m6A-seq

value: IP


title: GN007

description: SVTg


title: GN005

description: SVTg


title: GN003

description: SVTg


title: HeLa-WT-for-differential-2-INPUT

source_name: HeLa WT-for-differential-2 INPUT


title: cko_male2


title: HeLa-M3KO-2.1-polysome

description: Polysome METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO Polysome Rep-3


title: miR-449b-5p transfected HSVSMC treated with IL1a+PDGFBB Rep1

source_name: Human saphenous vein smooth muscle cell


title: GN002

description: SVTg


title: HeLa-WT-for-differential-2-m6A

source_name: HeLa WT-for-differential-2 m6A-seq


title: wtff_female_13


title: HeLa-WT-for-differential-1-m6A

source_name: HeLa WT-for-differential-1 m6A-seq


title: miR-449b-5p transfected HSVSMC treated with IL1a+PDGFBB Rep3


title: miR-323a-3p transfected HSVSMC treated with IL1a+PDGFBB Rep3


title: GN008

description: SVTg


title: GN001

description: SVTg


title: wtff_male_5


title: HeLa-METTL3KO-3-m6A

source_name: HeLa METTL3KO-3 m6A-seq


title: wtf+_male_4


title: Native HSPC (Rep 2)

city: Los Angeles

first: Apeksha

last: Singh

address: 570 Boyer Hall

institute: University of California, Los Angeles

description: 10x Genomics

data_processing:
Demultiplexing, bardcode processing, feature counting, and aggregation performed with CellRanger (version 7.0; cellranger counts; --expect-cells=10000). Output from cellranger was loaded into Seurat (version 4.3.0) and cells with less than 200 features (min.features) or features with less than 3 cells (min.cells) were filtered out.  Additionally, cells with more than 10% mitochondrial transcripts were removed.  For the second replicate, an additional filter of at least 10 hashtag counts was required since there were many instances of low hashtag counts.  Gene expression and hashtag counts were normalized using the “LogNormalize” and “CLR” methods respectively.  Next DoubletFinder (version 2.0.3) was used for doublet detection and exclusion.  The first 40 principal components (PCA calculated by Seurat using the scaled top 2000 variable features (method -“vst”) were used to identify the optimal pK parameter (paramSweep_v3).  A doublet rate of 5% was assumed as input for doubletFinder_v3 along with the identified pK parameter (0.17 and 0.001 for replicate 1 and 2 respectively), and the suggested value of pN = 0.25 was used.  For demultiplexing, the Seurat function HTODemux was used (positive.quantile = 0.99; init=4 for replicate 2).  Cells identified as singlets from DoubletFinder were retained and then cells assigned doublet or negative from HTODemux were removed.  Cells from each replicate were then merged into a common dataframe for downstream analysis of the native HSPCs.  Next, a set of 115 genes related to hematopoiesis were utilized for dimensionality reduction (Table S2).  Normalized counts for these genes were scaled across all cells (deducted mean and divided by standard deviation) and input for principal component analysis.  Using the first 20 principal components, a k-nearest neighbors graph was constructed (k=15). To remove potential contaminating cells that were not LSK HSPCs, cells with likely zero Kit expression were removed.  More specifically, cells were only retained if they either had nonzero Kit expression or were assigned nonzero expression status through an iterative process that would include cells that had nonzero expression status in at least half of their neighbors.  This quality control resulted in 3721 wildtype and 3962 IκB– HSPCs for Replicate 1 and 4963 wildtype and 5383 IκB– HSPCs for Replicate 2.
Assembly: mm10
Supplementary files format and content: tab separated value and matrix files

source_name: Bone Marrow

extract_protocol:
Bone marrow from the bilateral femur and tibia was collected; red blood cells were lysed and mature hematopoietic cells were depleted using magnetic bead-based lineage antibody cocktail.  Pre-selected cells were then flow sorted to collect Lin-/Sca1+ cKithi (LSK) HSPCs. For each replicate, 30,000 cells were collected from each experimental condition, barcoded with TotalSeqB antibodies, and multiplexed for sequencing.
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1

value: Bone Marrow

value: LSK (Lin-Sca1+cKit+)


title: miR-323a-3p transfected HSVSMC treated with IL1a+PDGFBB Rep1


title: miR-449b-5p transfected HSVSMC treated with IL1a+PDGFBB Rep2


title: wtff_male_1


title: cko_male3


title: Native HSPC (Rep 1)

description: 10x Genomics


title: miRCTRL transfected HSVSMC treated with IL1a+PDGFBB Rep3

value: miRCTRL


title: cKO

data_processing:
Sequencing was performed on NovaSeq 6000 or DNBSEQ-G400 platform in a 28+90 base or 28+100 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling in NovaSeq 6000 platform.
Generated reads were input into the cellranger pipeline (Cell Ranger v.6.0.0, 10x Genomics) for UMI counting for each gene - cell (barcode) combination.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: genematrix.csv: comma-delimited text files including UMI counts for all cells detected

source_name: large intestine

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v2 User Guide.

value: large intestine

value: CD45- EpCAM+ epithelial  cells

value: Foxl1cre; Cxcl12flox/flox


title: 4 week old

tag: developmental stage

value: 4 week old

value: CD45- EpCAM- CD31- gp38+ mesenchymal cells


title: HeLa-METTL3KO-2-m6A

source_name: HeLa METTL3KO-2 m6A-seq


title: miRCTRL transfected HSVSMC treated with IL1a+PDGFBB Rep1


title: WT 5DE

tag: tissue


title: 3 week old

value: 3 week old


title: neonate

value: neonate


title: GF

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+90 or 28+91 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (Cell Ranger v.6.0.0, 10x Genomics) for UMI counting for each gene - cell (barcode) combination.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: genematrix.csv: comma-delimited text files including UMI counts for all cells detected

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 3' Reagent Kits v3.1 User Guide.

value: Balb/c


title: Mock transfected HSVSMC treated with IL1a+PDGFBB Rep3

value: Transfection reagent


title: HeLa-WT-for-differential-1-INPUT

source_name: HeLa WT-for-differential-1 INPUT

value: Human HeLa cell line

tag: genotype

value: WT


title: ff


title: miR-323a-3p transfected HSVSMC treated with IL1a+PDGFBB Rep2

value: Human saphenous vein smooth muscle cell


title: HeLa-METTL3KO-2-INPUT

source_name: HeLa METTL3KO-2 INPUT

value: INPUT


title: Mock transfected HSVSMC treated with IL1a+PDGFBB Rep2


title: HeLa-METTL3KO-1-m6A

source_name: HeLa METTL3KO-1 m6A-seq

value: IP


title: large intestine, TauGABA_6hr-3

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101 or 151-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: large intestine, TauGABA_6hr

extract_protocol:
Total RNA was extracted using RLT lysis buffer and miRNeasy Micro Kit (Qiagen).
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan). According to the SMART-Seq kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

value: CD45- EpCAM- CD31- gp38+ PDGFR{alpha}high Ly6Cneg mesenchymal cells

value: GABA and Taurine treatment, 6hr


title: HeLa-WT-8h-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.
The processed fastq reads were mapped to the human reference genome (GRCh37/hg19) using the "STAR" algorithm with reference transcriptome includes Ensembl v85 and long noncoding from LNCipedia v5.2. Gene expression was evaluated using "HTseq" count.
Assembly: GRCh37/hg19
Supplementary files format and content: HTSeq count file

source_name: HeLa cells WT 8h Rep-3

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: WT and METTL3 KO HeLa cells were treated with 1 μg/ml Actinomycin D or vehicle for 0, 4, 6, and 8 hours.


title: Mock transfected HSVSMC treated with IL1a+PDGFBB Rep1


title: large intestine, TauGABA_6hr-2


title: HeLa-METTL3KO-3-INPUT

source_name: HeLa METTL3KO-3 INPUT


title: HSVSMC treated with IL1a+PDGFBB Rep3

value: No


title: large intestine, TauGABA_6hr-1

value: large intestine


title: HeLa-WT-8h-2

description: ActinoD WT HeLa Cells

source_name: HeLa cells WT 8h Rep-2


title: HeLa-WT-8h-1

description: ActinoD WT HeLa Cells

source_name: HeLa cells WT 8h Rep-1


title: miRCTRL transfected HSVSMC treated with IL1a+PDGFBB Rep2

value: miRCTRL


title: HSVSMC treated with IL1a+PDGFBB Rep2


title: embryo

value: embryo


title: large intestine, TauGABA_0hr-3

source_name: large intestine, TauGABA_0hr

value: GABA and Taurine treatment, 0hr


title: HeLa-WT-6h-3

description: ActinoD WT HeLa Cells

source_name: HeLa cells WT 6h Rep-3


title: HeLa-WT-6h-2

description: ActinoD WT HeLa Cells

source_name: HeLa cells WT 6h Rep-2


title: large intestine, TauGABA_0hr-2


title: large intestine, TauGABA_0hr-1


title: Quiescent HSVSMC Rep3

source_name: Human saphenous vein smooth muscle cell


title: HeLa-METTL3KO-1-INPUT

source_name: HeLa METTL3KO-1 INPUT


title: Quiescent HSVSMC Rep2


title: large intestine, Foxl1-cre_Cxcl12_ff

source_name: large intestine, conditional knockout

value: Foxl1cre; Cxcl12 flox/flox


title: HeLa-WT-6h-1

description: ActinoD WT HeLa Cells

source_name: HeLa cells WT 6h Rep-1


title: Quiescent HSVSMC Rep1


title: large intestine, Cxcl12_ff

source_name: large intestine, control

value: Cxcl12 flox/flox


title: HeLa-WT-4h-2

description: ActinoD WT HeLa Cells

source_name: HeLa cells WT 4h Rep-2


title: miR-5681b transfected HSVEC rep3

source_name: Human saphenous vein endothelial cells

growth_protocol: HSVECs were obtained by enzymatic collagenase digestion of human saphenous veins and maintained in EC growth medium (EGM-2 BulletKit™) (Lonza) supplemented with foetal bovine serum (10%, Life Technologies) and Penicillin-Streptomycin (100U/ml) (Gibco).

treatment_protocol: Transient transfection of the 7 miRNA mimics (Dharmacon, ThermoFisher)  or the miRNA control (miR-CTRL-miRIDIAN microRNA Mimic Negative Control #1) was performed with Lipofectamine RNAiMAX (Life Technologies) following the manufacturer’s guidelines, for 6 hours in Opti-MEM (Life Technologies).

value: Human saphenous vein endothelial cells


title: HeLa-WT-4h-3

description: ActinoD WT HeLa Cells

source_name: HeLa cells WT 4h Rep-3


title: HFD-Treg_NCD-Tregs_CITE

first: Gregory

middle: K

last: Tharp

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

library_source: other

data_processing:
Demultiplexing, barcode processing, gene and HTO counting was done with Cellranger 7.0.1 into a single set of files for each capture
Assembly: mm10, refdata-gex-mm10-2020-A
Supplementary files format and content: Tab separated values and matrix files
Library strategy: CITE-seq

molecule: other

source_name: HTO

extract_protocol:
Labeled live CD3+ CD4+ Foxp3+ VAT Treg cells were FACS sorted and pooled; Srebf2WT/WT with Srebf2flox/flox (1:1) for one experiment and NCD with HFD (1:1) for a separate experiment. After pooling, single cell VAT Treg suspensions were loaded onto the 10X Genomics Chromium Controller using the Chromium NextGEM Single Cell 5’ Library & Gel Bead Kit v2 to capture individual cells and barcoded gel beads within droplets.
Following reverse transcription, the cDNA was prepared to create gene expression libraries and feature barcode libraries.

value: visceral adipose tissue (VAT)

value: Regulatory T (Treg)

tag: condition

value: mixed sample (NCD,HFD)

tag: hto

value: TotalSeq-C0303 Hashtag 3 NCD,TotalSeq-C0304 Hashtag 4 HFD


title: HeLa-WT-4h-1

description: ActinoD WT HeLa Cells

source_name: HeLa cells WT 4h Rep-1

value: Human HeLa cell line

value: WT


title: miR-5681b transfected HSVEC rep2


title: HFD-Treg_NCD-Tregs_GEX

data_processing:
Demultiplexing, barcode processing, gene and HTO counting was done with Cellranger 7.0.1 into a single set of files for each capture
Assembly: mm10, refdata-gex-mm10-2020-A
Supplementary files format and content: Tab separated values and matrix files

source_name: mRNA


title: HSVSMC treated with IL1a+PDGFBB Rep1

value: Human saphenous vein smooth muscle cell

tag: treatment


title: HeLa-WT-0h-3

description: ActinoD WT HeLa Cells

source_name: HeLa cells WT 0h Rep-3


title: miR-5681b transfected HSVEC rep1


title: 3 hours differentiated Wild Type mouse ES rep-3

type: genomic

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.

label_protocol: Standard Illumina Protocol

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

treatment_protocol: (Mettl3KO) Mettl3 knockout J1 ESCs were generated by Howard Y. Chang, Stanford University, USA (Batista et al, Cell Stem Cell, 2014). (Mettl14KO and rescue) Mettl14 KO E14TG2a mouse ESCs were gifted by 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.  (Mettl3i) ESCs were treated with Mettl3 inhibitor STM-2457 at 50 μM or with its vehicle control and collected 24 h post-treatment for further analysis.  (Dnmt1KO) Dnmt1 KO mouse ESCs were gifted by Fabio Spada, Ludwig Maximilians University, Germany.  (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: genotype or drug

tag: es strain

tag: replicate


title: 24 hours differentiated Wild Type mouse ES rep-2


title: HeLa-WT-0h-2

description: ActinoD WT HeLa Cells

source_name: HeLa cells WT 0h Rep-2


title: miR-4774-3p transfected HSVEC Rep2

tag: cell line


title: HeLa-WT-0h-1

description: ActinoD WT HeLa Cells

source_name: HeLa cells WT 0h Rep-1


title: Adipose-Tregs_WT-KO-mix_GEX

tag: cell type


title: VAT.KO.3

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the UCSC mm10 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: csv file of RPKM normalized read counts for each detected gene

source_name: visceral adipose tissue

extract_protocol:
Cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

value: visceral adipose tissue

value: T regulatory cells

tag: age

value: 25 week old

value: Foxp3-YFPcre Srebf2-flox/flox

tag: Sex

value: male


title: Adipose-Tregs_WT-KO-mix_CITE

value: TotalSeq-C0301 Hashtag 1 WT,TotalSeq-C0302 Hashtag 2 KO


title: miR-4774-3p transfected HSVEC Rep3


title: HeLa-M3KO-8h-3

description: ActinoD METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO 8h Rep-3

tag: cellline

tag: knockedout


title: miR-4774-3p transfected HSVEC Rep1

tag: replicate/patient

tag: mimic transfection


title: VAT.KO.2


title: miR-1827 transfected HSVEC Rep3


title: HeLa-M3KO-8h-2

description: ActinoD METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO 8h Rep-2


title: 0 hour differentiated Wild Type mouse ES rep-3


title: VAT.KO.1


title: HeLa-M3KO-8h-1

description: ActinoD METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO 8h Rep-1


title: miR-1827 transfected HSVEC Rep2


title: VAT.WT.3

value: Foxp3-YFPcre Srebf2-WT/WT


title: HeLa-M3KO-6h-3

description: ActinoD METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO 6h Rep-3


title: 3 hours differentiated Wild Type mouse ES rep-2


title: DRB treated Wild Type mouse ES rep-2

source_name: DRB treated Wild Type mouse ES

value: DRB


title: 3 hours differentiated Wild Type mouse ES rep-1


title: VAT.WT.2


title: miR-1827 transfected HSVEC Rep1


title: miR-892b transfected HSVEC Rep3


title: HeLa-M3KO-6h-2

description: ActinoD METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO 6h Rep-2


title: HeLa-M3KO-6h-1

description: ActinoD METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO 6h Rep-1


title: miR-892b transfected HSVEC Rep2


title: Untreated Wild Type mouse ES rep-6

source_name: Untreated Wild Type mouse ES


title: 24 hours differentiated Wild Type mouse ES rep-1


title: VAT.WT.1


title: Spl.KO.3

source_name: spleen

value: spleen


title: HeLa-M3KO-4h-3

description: ActinoD METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO 4h Rep-3


title: 0 hour differentiated Wild Type mouse ES rep-1


title: Mettl3i treated Wild Type mouse ES rep-2

source_name: Mettl3i treated Wild Type mouse ES


title: HeLa-M3KO-4h-1

description: ActinoD METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO 4h Rep-1


title: miR-491-3p transfected HSVEC Rep2

source_name: Human saphenous vein endothelial cells

value: Human saphenous vein endothelial cells


title: Mettl3i treated Wild Type mouse ES rep-3


title: Mettl3i treated Wild Type mouse ES rep-1


title: Untreated Wild Type mouse ES rep-5


title: 24 hours differentiated Wild Type mouse ES rep-3


title: HeLa-M3KO-0h-3

description: ActinoD METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO 0h Rep-3


title: Spl.WT.3


title: 0 hour differentiated Wild Type mouse ES rep-2


title: Spl.WT.2


title: miR-449b-5p transfected HSVEC Rep3


title: HeLa-M3KO-0h-2

description: ActinoD METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO 0h Rep-2


title: Untreated Wild Type mouse ES rep-1


title: HeLa-M3KO-4h-2

description: ActinoD METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO 4h Rep-2


title: Braf Q241R/+ ;Cre, hippocampus, No56 [PR1825_03]

city: Maebashi

first: Hiroshi

last: Ohnishi

state: Gunma

address: 3-39-22 Showa-machi

department: Department of Laboratory Sciences

institute: Gunma University Graduate School of Health Sciences

description:
n-Braf Q241R/+_3
PR1825_03

data_processing:
Sequencing analysis were performed NovaSeq Control Software v1.6.0, Real Time Analysis v3.4.4 and bcl2fastq2 v2.20.
Sequence reads were processed by the use of fastp program (v0.20.1) for quality control, adapter trimming, quality filtering, and pre-read quality cutting.
Trimmed sequence reads were aligned to GRCm/mm10 using Spliced Transcripts Alignment to a Reference (STAR) software (v2.7.6a).
Aligned data were quantified by RNA-Seq Expectation Maximization (RSEM) software (v1.3.3).
The count data were statistically processed and normalized using edgeR software (v3.36.0).
Assembly: mm10
Supplementary files format and content: Comma separated values file contain row counts sample for each samples and statistical processing data.

source_name: Hippocampus

growth_protocol: Mice were bred and maintained under specific-pathogen-free conditions. They were housed in an air-conditioned room with a 12-h light, 12-h dark cycle.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 10.0 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq®Stranded Kit and SMART-Seq®Stranded Kit Unique Dual Index Kit following SMART-Seq®Stranded Kit User Manual (022819).

value: Hippocampus

value: 34 weeks of age

value: Braf Q241R/+ ;CaMKII-Cre

tag: strain background


title: miR-491-3p transfected HSVEC Rep3


title: miR-491-3p transfected HSVEC Rep1


title: miR-449b-5p transfected HSVEC Rep2


title: Wild Type mouse ES (Mettl14 KO control) rep-2

first: Martin

last: Bizet

institute: Université Libre de Bruxelles

source_name: Wild Type mouse ES (Mettl14 KO control)