title: bisulf.9888.rep3

description:
CG.methylation.32_accessions.Araport11_PC_TE.genebody.txt
CG.methylation.32_accessions.Araport11_PC_TE.promoter.txt
CG.methylation.32_accessions.our_annotation.genebody.txt
CG.methylation.32_accessions.our_annotation.promoter.txt
CHG.methylation.32_accessions.Araport11_PC_TE.genebody.txt
CHG.methylation.32_accessions.Araport11_PC_TE.promoter.txt
CHG.methylation.32_accessions.our_annotation.genebody.txt
CHG.methylation.32_accessions.our_annotation.promoter.txt
CHH.methylation.32_accessions.Araport11_PC_TE.genebody.txt
CHH.methylation.32_accessions.Araport11_PC_TE.promoter.txt
CHH.methylation.32_accessions.our_annotation.genebody.txt
CHH.methylation.32_accessions.our_annotation.promoter.txt

data_processing:
raw data reads were trimmed and then the data was aligned to the TAIR10 genome exactly as described in doi: https://doi.org/10.1101/2022.12.04.519028.
Methylation was called exactly as described in doi: https://doi.org/10.1101/2022.12.04.519028.
The methylation level per locus for each context was determined by dividing the number of methylated reads by the total number of reads covering the cytosines in the CG, CHG or CHH context. Thus, the values of methylation of the locus were ranging from 0 to 1 and roughly correspond to the ratio of methylated to total cytosines in the locus (we did not take the average of the ratios for each cytosine to avoid high error rates caused by low read coverage).
Assembly: TAIR10
Supplementary files format and content: CG.methylation.32_accessions.Araport11_PC_TE.genebody.txt  contains a table with CG methylation levels calculated over the full locus for Araport11 genes and TEs for every bisulfite-seq sample
Supplementary files format and content: CG.methylation.32_accessions.Araport11_PC_TE.promoter.txt   contains a table with CG methylation levels calculated over promoter (TSS+/-200bp)  for Araport11 genes and TEs for every bisulfite-seq sample
Supplementary files format and content: CG.methylation.32_accessions.our_annotation.genebody.txt contains a table with CG methylation levels calculated over the full locus for 5 gene types in the new annotation created in the study (PC genes, AS lncRNAs, TE genes, lincRNAs and AS_to_TEgenes lncRNAs) for every bisulfite-seq sample
Supplementary files format and content: CG.methylation.32_accessions.our_annotation.promoter.txt contains a table with CG methylation levels calculated over the promoter (TSS+/-200bp)  for 5 gene types in the new annotation created in the study (PC genes, AS lncRNAs, TE genes, lincRNAs and AS_to_TEgenes lncRNAs) for every bisulfite-seq sample
Supplementary files format and content: CHG.methylation.32_accessions.Araport11_PC_TE.genebody.txt   contains a table with CHG methylation levels calculated over the full locus for Araport11 genes and TEs for every bisulfite-seq sample
Supplementary files format and content: CHG.methylation.32_accessions.Araport11_PC_TE.promoter.txt  contains a table with CHG methylation levels calculated over the promoter (TSS+/-200bp) for Araport11 genes and TEs for every bisulfite-seq sample
Supplementary files format and content: CHG.methylation.32_accessions.our_annotation.genebody.txt contains a table with CHG methylation levels calculated over the full locus for 5 gene types in the new annotation created in the study (PC genes, AS lncRNAs, TE genes, lincRNAs and AS_to_TEgenes lncRNAs) for every bisulfite-seq sample
Supplementary files format and content: CHG.methylation.32_accessions.our_annotation.promoter.txt contains a table with CHG methylation levels calculated over the promoter (TSS+/-200bp) for 5 gene types in the new annotation created in the study (PC genes, AS lncRNAs, TE genes, lincRNAs and AS_to_TEgenes lncRNAs) for every bisulfite-seq sample
Supplementary files format and content: CHH.methylation.32_accessions.Araport11_PC_TE.genebody.txt  contains a table with CHH methylation levels calculated over the full locus for Araport11 genes and TEs for every bisulfite-seq sample
Supplementary files format and content: CHH.methylation.32_accessions.Araport11_PC_TE.promoter.txt  contains a table with CHH methylation levels calculated over the promoter (TSS+/-200bp)  for Araport11 genes and TEs for every bisulfite-seq sample
Supplementary files format and content: CHH.methylation.32_accessions.our_annotation.genebody.txt contains a table with CHH methylation levels calculated over the full locus for 5 gene types in the new annotation created in the study (PC genes, AS lncRNAs, TE genes, lincRNAs and AS_to_TEgenes lncRNAs) for every bisulfite-seq sample
Supplementary files format and content: CHH.methylation.32_accessions.our_annotation.promoter.txt contains a table with CHH methylation levels calculated over the promoter (TSS+/-200bp) for 5 gene types in the new annotation created in the study (PC genes, AS lncRNAs, TE genes, lincRNAs and AS_to_TEgenes lncRNAs) for every bisulfite-seq sample

source_name: leaves

extract_protocol:
DNA was extracted from the frozen leaf tissue (14-leaf rosettes) using Nuclear Mag Plant kit (Machery-Nagel)
100bp PE

value: leaves


title: bisulf.9588.rep4

status: Public on Mar 15 2023

type: SRA

city: Vienna

first: Aleksandra

last: Kornienko

state: Vienna

address: Dr. Bohrgasse 3

country: Austria

institute: Gregor Mendel Institute

library_source: genomic

molecule: genomic DNA

organism: Arabidopsis thaliana

growth_protocol: 21 degrees Celcius, on soil, long-day conditions (16h light, 8h dark)

treatment_protocol: no treatment

tag: tissue

tag: developmental stage

tag: genotype


title: bisulf.9905.rep4


title: bisulf.9888.rep4


title: bisulf.9845.rep1


title: bisulf.9905.rep3


title: bisulf.9888.rep1


title: AEP1 (WT), Q-modified; 6.25µM dCTP

city: Berlin

first: Ann

middle: E.

last: Ehrenhofer-Murray

address: Philippstr. 13

department: Institut für Biologie

country: Germany

institute: Humboldt-Universität zu Berlin

description:
total RNA
column in processed data file: mm_ratio

library_source: transcriptomic

data_processing:
Adapter-trimming was performed using Skewer version 0.2.2 and trimming of PCR primers, selection of high-quality reads and sorting of the reads based on the sequence in the degenerate region of the RT-primerwas performed using Bioconductor package ShortRead. Reads were trimmed to the expected size of the transcript using Cutadapt version 3.7.
Alignment to RNA sequences from S. pombe (https://www.pombase.org/) and Shigella flexneri (http://www.ensembl.org/) was achieved using Samtools version 1.12 and Bowtie version 2.2.5. Settings were chosen to allow up to one mismatch in seed with a seed length of 6.
Misincorporation was determined using CoverageAnalyzer.
Assembly: S.pombe genome version ASM294v2.29
Supplementary files format and content: excel-files include position, refbase, coverage, total mismatch ratio (mm_ratio), mismatch ratio of single nucleotides (a_mism, g_mism, t_mism and c_mism) and arrest_ratio.

molecule: total RNA

organism: Schizosaccharomyces pombe

source_name: cells were incubated with queuine; RT via RT-KTq I614Y using 6.25 µM dCTP

growth_protocol: S. pombe strain AEP1 was grown in full medium (YES) with or without 0.1 µM queuine at 30°C. S. flexneri WT and tgt∆ strains were grown in full medium (TSB) at 37°C. Cultures were inoculated at an OD600 of 0.2 and grown to an optical density of 1.

extract_protocol:
Total RNA was isolated from 50 OD of cells. Cells were harvested and after addition of 1 mL of phenol, glass beads and vigorous shaking for 5 min, samples were centrifuged at 20.000 g for 5 min to clear the cell debris. Equal volume of phenol/chloroform/isoamylalcohol was added to the aqueous phase and centrifuged at 20.000 g for 5 min. After mixing the upper phase with an equal volume of chloroform followed by centrifugation at 20.000 g for 5 min, the RNA was precipitated.
Extraction of the RNA was performed as described in the "SAMPLEs" section. 500 ng RNA was hybridized to 500 nM of the respective stemloop-primer with the following thermocycling program: 95 °C for 2 min, 65 °C for 30 sec, ramp down to 4 °C with 5 °C/30 sec. After hybridization and incubation on ice for 1 min, 100 µM of each dNTP and 100 nM RT-KTq I614 DNA polymerase were added. The reverse transcription was carried out in reaction buffer (50 mM Tris-HCl (pH 9.2), 16 mM (NH4)2SO4, 25 mM MgCl2, 0.1% Tween 20) in a total volume of 20 µL. For experiments using decreased dCTP concentrations, 25 µM, 12.5 µM and 6.25 µM dCTP were added to the RT reaction. Following incubation at 55 °C for 1 h and incubation on ice for 10 min, the cDNA was amplified using Taq polymerase. Amplification was performed with 5 µL cDNA in reaction buffer containing 2.5 µM dNTPs, 2 mM MgCl2, 1 x Taq buffer+ KCl and 1.25 U Taq polymerase (Thermo Fisher) in a total volume of 200 µL. Primers binding at the 3’ end contained a barcoded sequence for multiplexing the PCR products. Samples were separated on a 2% agarose gel, and the respective PCR products were gel-purified using the QIAquick Gel Extraktion Kit (Qiagen) according to the manufacturer’s protocol.
Library preparation of amplified tRNAs for deep sequencing was performed using the NEXTflexR qRNA-SeqTM Kit v2 – Set C (Bioo Scientific) according to the manufacturer's protocols.

tag: strain

value: AEP1 (WT)

tag: treatment

value: growth in full medium (YES) at 30°C with 0.1 µM queuine


title: T-47D H3K27me3 E2

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

country: USA

institute: University of Utah

data_processing:
ChIP-seq reads were aligned to hg19 using bowtie v1.1.2 with parameters -m 1 –t –best -q -S -l 32 -e 80 -n 2
Peaks were called using macs2 V 2.1.0.20140616 with the following arguments: macs2 callpeak -B --SPMR --pvalue=1e-10 --mfold 15 100.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

organism: Homo sapiens

growth_protocol: RPMI 1640 medium (Gibco) with 10% fetal bovine serum (Gibco) and 1% penicillin–streptomycin (Gibco)

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 minutes at room temperature and then treated with 125 mM Glycine for 5 minutes to stop crosslinking. Crosslinked cells were then washed with cold PBS and scraped to harvest.
ChIP and library construction was performed as described in Reddy et al, Genome Research, 2009.

treatment_protocol: Cells were treated with vehicle (DMSO) or 17beta-estradiol (E2) at a final concentration of 10nM for either 1 hour for transcription factor ChIP-seqs, or 8 hours for histone marker ChIP-seqs

tag: cell line

tag: cell type

value: Breast; Ductal Carcinoma

tag: chip antibody

value: H3K27me3 (Active Motif AB_2561020)

value: 10 nM 17beta-estradiol

tag: time

value: 8 hour


title: AEP1 (WT), unmodified; 6.25µM dCTP

source_name: unmodified; RT via RT-KTq I614Y using 6.25 µM dCTP

value: growth in full medium (YES) at 30°C


title: Ishikawa TAF1 DMSO

source_name: Ishikawa

value: Ishikawa

value: Endometrial Adenocarcinoma

value: TAF II p250/TAF1 (Santa Cruz sc-735)

value: DMSO (veh)

value: 1 hour


title: bisulf.9588.rep3


title: F.9537.rep2.batch2

description:
150bp PE
TPMs.4_tissues.our_annotation.bed
TPMs.4_tissues.Araport11_annotation.bed

data_processing:
raw RNA-seq reads were aligned to the TAIR10 genome using STAR (v.2.7.1.). First the genomebuild was performed for TAIR10 accounting for the genome size and not providing the annotated splice junctions. The genomebuild command: STAR --runMode genomeGenerate  --genomeSAindexNbases 12.5 --genomeDir $stargenomedir --genomeFastaFiles genome.fasta . The command used for alignment:  STAR --readFilesIn  $fastq.gz  --readFilesCommand zcat --runThreadN 4 --alignIntronMax 6000 --alignMatesGapMax 6000 --genomeDir $stargenomedir --outFilterIntronMotifs RemoveNoncanonical --outFilterMismatchNoverReadLmax 0.1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --outFilterMultimapNmax 10 --outReadsUnmapped None --alignSJoverhangMin 8 --outSAMattributes NH HI AS nM NM MD jM jI XS --outSAMtype BAM SortedByCoordinate  --runMode alignReads --twopassMode Basic --outFileNamePrefix $out
read counts were calculated using featurecounts from the subread package (v.2.0.0). Command used: featureCounts  -T 4 -p  -F SAF -O -s 2  -t exon -g gene_id -a $saf -o $out.txt $bam
TPMs were calculated by dividing the raw counts number by the total number of raw counts in the sample (in million reads) and the length (in kb). Command used  sum=`cat $out.txt| awk -v OFS="\t" '{ sum += $7} END {print sum}'`  cat $out.txt| grep -v Geneid| awk -v OFS="\t" -v sum="$sum" ' {print $1,$6,$7,$7*1000000*1000/($6*sum)}' > $out.counts_tpm.bed
Assembly: TAIR10
Supplementary files format and content: TPMs.4_tissues.our_annotation.bed contains a table with TPMs for 5 gene types in the new annotation (PC genes, AS lncRNAs, TE genes, lincRNAs and AS_to_TEgenes lncRNAs) for every RNAseq sample
Supplementary files format and content: TPMs.4_tissues.Araport11_annotation.bed contains a table with TPMs for Araport11 annotated genes and TEs for every RNAseq sample

molecule: polyA RNA

source_name: flowers and flower buds

growth_protocol: 22 degrees Celcius, on soil, long-day conditions (16h light, 8h dark)

extract_protocol:
RNA was isolated and DNAse I (NEB) treated using a KingFisher Robot with an in-house magnetic RNA isolation kit. RNA was diluted in nuclease free water (Ambion) and stored at -80oC.
TruSeq Stranded mRNA

value: flowers and flower buds


title: bisulf.9588.rep2


title: AEP1 (WT), unmodified; 12.5µM dCTP

source_name: unmodified; RT via RT-KTq I614Y using 12.5 µM dCTP


title: AEP1 (WT), Q-modified; 12.5µM dCTP

source_name: cells were incubated with queuine; RT via RT-KTq I614Y using 12.5 µM dCTP


title: F.9537.rep1.batch1


title: Ishikawa RARA DMSO

value: RARA (Santa Cruz sc-515796)


title: bisulf.9588.rep1


title: F.9075.rep1.batchCT


title: Ishikawa c-MYC E2

value: c-MYC (Santa Cruz sc-40)


title: bisulf.9518.rep4


title: F.8236.rep2.batch2


title: F.9543.rep1.batchCT


title: Ishikawa c-MYC DMSO


title: bisulf.9518.rep2


title: F.8236.rep1.batch1


title: bisulf.9518.rep1


title: Ishikawa MAX E2

value: MAX (Santa Cruz sc-8011)


title: AEP1 (WT), Q-modified; 100µM dCTP

source_name: cells were incubated with queuine; RT via RT-KTq I614Y using 100 µM dCTP


title: AEP1 (WT), unmodified; 100µM dCTP

source_name: unmodified; RT via RT-KTq I614Y using 100 µM dCTP


title: AEP1 (WT), unmodified; 25µM dCTP

source_name: unmodified; RT via RT-KTq I614Y using 25 µM dCTP


title: in vitro-transcribed tRNA Asp, 100% Q

description:
in vitro-transcribed tRNA
column in processed data file: mm_ratio

source_name: mixing of unmodified and Q-modified tRNA-Asp to 2% Q-modification RT via RT-KTq I614Y using 6.25 µM dCTP

extract_protocol:
The pJET1 vector carrying the tRNA-Asp and tRNA-Asn sequence, respectively, was linearized with NcoI, and 2.5 µg of the linear vector was used for in vitro transcription using the TranscriptAid T7 High Yield Transcription Kit (ThermoFisher) according to the manufacturer’s instructions. Following an 8 hour incubation at 37 °C with nucleotides and the T7 RNA polymerase and subsequent DNase I treatment, the respective tRNA was purified from the reaction using phenol/chloroform extraction followed by gel filtration with Sephadex G50 (GE Healthcare). For in vitro modification of tRNA with queuine, 10 µM of in vitro transcribed tRNA was incubated with 200 nM hTGT (QTRT1:QTRT2) and 5 µM queuine in reaction buffer (50 mM Tris-HCl pH 7.5, 20 mM NaCl, 5 mM MgCl2 and 2 mM dithiothreitol) for 5 h at 37 °C. The RNA was purified using phenol/chloroform extraction and precipitated with 1/10 volume of ammonium acetate and three volumes of 100% ethanol.
Extraction of the RNA was performed as described in the "SAMPLEs" section. 500 ng RNA was hybridized to 500 nM of the respective stemloop-primer with the following thermocycling program: 95 °C for 2 min, 65 °C for 30 sec, ramp down to 4 °C with 5 °C/30 sec. After hybridization and incubation on ice for 1 min, 100 µM of each dNTP and 100 nM RT-KTq I614 DNA polymerase were added. The reverse transcription was carried out in reaction buffer (50 mM Tris-HCl (pH 9.2), 16 mM (NH4)2SO4, 25 mM MgCl2, 0.1% Tween 20) in a total volume of 20 µL. For experiments using decreased dCTP concentrations, 25 µM, 12.5 µM and 6.25 µM dCTP were added to the RT reaction. Following incubation at 55 °C for 1 h and incubation on ice for 10 min, the cDNA was amplified using Taq polymerase. Amplification was performed with 5 µL cDNA in reaction buffer containing 2.5 µM dNTPs, 2 mM MgCl2, 1 x Taq buffer+ KCl and 1.25 U Taq polymerase (Thermo Fisher) in a total volume of 200 µL. Primers binding at the 3’ end contained a barcoded sequence for multiplexing the PCR products. Samples were separated on a 2% agarose gel, and the respective PCR products were gel-purified using the QIAquick Gel Extraktion Kit (Qiagen) according to the manufacturer’s protocol.
Library preparation of amplified tRNAs for deep sequencing was performed using the NEXTflexR qRNA-SeqTM Kit v2 – Set C (Bioo Scientific) according to the manufacturer's protocols.

value: in-vitro transcribed

value: in vitro modification with queuine


title: bisulf.9518.rep3

value: leaves


title: F.6966.rep2.batch2


title: F.6966.rep1.batch1


title: in vitro-transcribed tRNA Asp, 75% Q

source_name: mixing of unmodified and Q-modified tRNA-Asp to 3% Q-modification RT via RT-KTq I614Y using 6.25 µM dCTP


title: Ishikawa MAX DMSO


title: bisulf.9512.rep2


title: F.6909.rep2.batch2


title: Ishikawa LSD1 E2

value: KDM1/LSD1 (Abcam ab17721)


title: Ishikawa RARA E2


title: Ishikawa LSD1 DMSO


title: F.6909.rep1.batch1


title: AEP1 (WT), Q-modified; 25µM dCTP

source_name: cells were incubated with queuine; RT via RT-KTq I614Y using 25 µM dCTP

value: AEP1 (WT)

value: growth in full medium (YES) at 30°C with 0.1 µM queuine


title: in vitro-transcribed tRNA Asp, 50% Q

source_name: mixing of unmodified and Q-modified tRNA-Asp to 5% Q-modification RT via RT-KTq I614Y using 6.25 µM dCTP


title: bisulf.9470.rep4


title: Ishikawa c-JUN E2

value: c-JUN (BD Biosciences 558036)

value: 10 nM 17beta-estradiol


title: bisulf.9470.rep3


title: F.6244.rep1.batchCT


title: T-47D c-MYC DMSO

value: Breast; Ductal Carcinoma

value: c-MYC (sc-40)


title: bisulf.9412.rep4


title: Ishikawa c-JUN DMSO

value: Ishikawa

value: Endometrial Adenocarcinoma


title: in vitro-transcribed tRNA Asp, 25% Q

source_name: mixing of unmodified and Q-modified tRNA-Asp to 10% Q-modification RT via RT-KTq I614Y using 6.25 µM dCTP


title: in vitro-transcribed tRNA Asp, 15% Q

source_name: mixing of unmodified and Q-modified tRNA-Asp to 15% Q-modification RT via RT-KTq I614Y using 6.25 µM dCTP


title: Ishikawa Input Paired-end

value: none (input)


title: bisulf.9412.rep3


title: F.6024.rep1.batchCT

value: flowers and flower buds


title: Ishikawa H3K4me3 E2

value: H3K4me3 (Cell Signaling 9751S)

value: 8 hour


title: F.22007.rep1.batchCT


title: Ishikawa H3K4me3 DMSO

value: DMSO (veh)


title: in vitro-transcribed tRNA Asp, 10% Q

source_name: mixing of unmodified and Q-modified tRNA-Asp to 25% Q-modification RT via RT-KTq I614Y using 6.25 µM dCTP

value: in-vitro transcribed


title: bisulf.9057.rep4

source_name: leaves


title: bisulf.9057.rep3


title: F.22006.rep1.batchCT


title: bisulf.8366.rep3


title: in vitro-transcribed tRNA Asp, 5% Q

source_name: mixing of unmodified and Q-modified tRNA-Asp to 50% Q-modification RT via RT-KTq I614Y using 6.25 µM dCTP

value: in vitro modification with queuine


title: F.22005.rep2.batch2


title: Ishikawa H3K4me1 E2

value: H3K4me1 (Cell Signaling 5326S)


title: Ishikawa H3K4me1 DMSO


title: in vitro-transcribed tRNA Asp, 3% Q

source_name: mixing of unmodified and Q-modified tRNA-Asp to 75% Q-modification RT via RT-KTq I614Y using 6.25 µM dCTP


title: in vitro-transcribed tRNA Asp, 2% Q

source_name: 100% Q-modified (in vitro); RT via RT-KTq I614Y using 100 µM dCTP


title: bisulf.8366.rep2

value: leaves


title: in vitro-transcribed tRNA Asp, 0% Q

extract_protocol:
The pJET1 vector carrying the tRNA-Asp and tRNA-Asn sequence, respectively, was linearized with NcoI, and 2.5 µg of the linear vector was used for in vitro transcription using the TranscriptAid T7 High Yield Transcription Kit (ThermoFisher) according to the manufacturer’s instructions. Following an 8 hour incubation at 37 °C with nucleotides and the T7 RNA polymerase and subsequent DNase I treatment, the respective tRNA was purified from the reaction using phenol/chloroform extraction followed by gel filtration with Sephadex G50 (GE Healthcare).
Extraction of the RNA was performed as described in the "SAMPLEs" section. 500 ng RNA was hybridized to 500 nM of the respective stemloop-primer with the following thermocycling program: 95 °C for 2 min, 65 °C for 30 sec, ramp down to 4 °C with 5 °C/30 sec. After hybridization and incubation on ice for 1 min, 100 µM of each dNTP and 100 nM RT-KTq I614 DNA polymerase were added. The reverse transcription was carried out in reaction buffer (50 mM Tris-HCl (pH 9.2), 16 mM (NH4)2SO4, 25 mM MgCl2, 0.1% Tween 20) in a total volume of 20 µL. For experiments using decreased dCTP concentrations, 25 µM, 12.5 µM and 6.25 µM dCTP were added to the RT reaction. Following incubation at 55 °C for 1 h and incubation on ice for 10 min, the cDNA was amplified using Taq polymerase. Amplification was performed with 5 µL cDNA in reaction buffer containing 2.5 µM dNTPs, 2 mM MgCl2, 1 x Taq buffer+ KCl and 1.25 U Taq polymerase (Thermo Fisher) in a total volume of 200 µL. Primers binding at the 3’ end contained a barcoded sequence for multiplexing the PCR products. Samples were separated on a 2% agarose gel, and the respective PCR products were gel-purified using the QIAquick Gel Extraktion Kit (Qiagen) according to the manufacturer’s protocol.
Library preparation of amplified tRNAs for deep sequencing was performed using the NEXTflexR qRNA-SeqTM Kit v2 – Set C (Bioo Scientific) according to the manufacturer's protocols.


title: Ishikawa H3K27me3 E2

source_name: Ishikawa

value: H3K27me3 (Active Motif AB_2561020)


title: F.22005.rep1.batchCT

source_name: flowers and flower buds


title: in vitro-transcribed tRNA Asp + Q


title: bisulf.8366.rep1


title: F.22007.rep2.batch2


title: Ishikawa H3K27me3 DMSO


title: in vitro-transcribed tRNA Asp


title: F.22004.rep1.batchCT


title: bisulf.8244.rep2


title: in vitro-transcribed tRNA Asn + Q


title: bisulf.6966.rep4


title: in vitro-transcribed tRNA Asn


title: bisulf.8244.rep1


title: F.22002.rep1.batch1


title: F.22002.rep2.batch2


title: MCF10 CA1a cells, sgControl, rep2

city: Shanghai

first: Xin

last: Hu

address: No.688 Hong-Qu Road

country: China

institute: Fudan University Shanghai Cancer Center

data_processing:
The FASTQ data was mapped to the human genome (hg19) using TopHat2
index generation was performed using SAMtools and Picard.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: MCF10 CA1a

growth_protocol: DMEM/F12 (BasalMedia, China) containing 5% horse serum (Gibco), 1% penicillin-streptomycin (BasalMedia, China), 10 μg/mL insulin (BasalMedia, China), 100 ng/mL cholera toxin (Sigma, USA), 0.5 μg/mL hydrocortisone (Sigma, USA) and 20 ng/mL EGF (PeproTech, USA).  Cells were cultured at 37C at 5% CO2.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen, USA)
RNA-seq library construction was performed using the VAHTS mRNA-seq V2 Library Prep Kit for Illumina (Vazyme, China) according to the manufacturer's instructions, followed by double-ended 150 nt sequencing using the Illumina NovaSeq 6000 platform.

value: MCF10 CA1a

value: Human malignant breast epithelial cells

value: Control


title: MCF10 CA1a cells, sgSNRPC, rep1

value: SNRPC knockdown


title: MCF10 CA1a cells, sgSNRPC, rep2


title: bisulf.6966.rep3


title: bisulf.6966.rep2


title: MCF10 CA1a cells, sgControl, rep1


title: MDA_CA1a_WT_SNRPC_IgG_rep3

data_processing:
Library construction and sequencing were completed by GENEWIZ Biotechnology Corporation.
Cutadapt (version 1.9.1) was utilized to preprocess the FASTQ data and filter the low-quality data. Bowtie2 (Version 2.2.6) software was utilized to map the clean data to the human genome (hg19).
Peak calling was completed using the MACS2.0 software, with a P-value <0.01 as the cutoff to call peaks from the aligned results.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes.
ChIP-seq libraries were prepared using the SimpleChIP® Enzymatic Chromatin IP Kit (Agarose Beads) (CST, #9002) and rabbit monoclonal anti-SNRPC (1:1000, ab192028, Abcam) according to the manufacturer's instructions.

value: Wild type

tag: antibody


title: VD3_W34

city: Lake Alfred

first: Xiaokang

last: Zhuo

state: Florida

address: 700 Experiment Station Rd

department: Citrus Research and Education Center

institute: University of Florida

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software
Trimmed sequence reads were mapped to mapped to Citrus clementina genome v1.0 (JGI) using HISAT2 software
StringTie was used to assemble transcripts of each sample, merge transcripts to get a consensus transcriptome assembly, and compute the abundance of transcripts for each sample

organism: Citrus sinensis

source_name: leaf midrib

extract_protocol:
Total RNA was extracted using TRIzol® Reagent and purified using an RNeasy Mini Kit following the manufacturer’s protocol
Ribosomal RNA was removed from the total RNA using a Ribo-Zero rRNA removal kit  for using plant seed/plant leaf following the manufacturer’s protocol. Subsequently, 50 ng of the purified RNA from each sample were used for library construction utilizing an Epicentre ScriptSeq v2 RNA-Seq library preparation kit according to the user’s guide.

value: leaf midrib

tag: infection

value: CLas infection

value: Week 34


title: VD3_W17

value: Week 17


title: bisulf.6966.rep1


title: MDA_CA1a_WT_SNRPC_IgG_rep2


title: bisulf.6911.rep2


title: F.22001.rep1.batch1

value: flowers and flower buds


title: F.1741.rep1.batchCT


title: F.22003.rep1.batchCT


title: VD3_W0

value: Week 0


title: F.10024.rep2.batch2


title: bisulf.6911.rep1


title: MDA_CA1a_WT_SNRPC_IgG_rep1


title: F.10024.rep1.batch1


title: VD2_W34


title: VD3_W7

value: Week 7


title: MDA_CA1a_WT_SNRPC_rep3

value: SNRPC


title: bisulf.6909.rep4


title: F.10015.rep4.batch2


title: F.22001.rep2.batch2


title: VD2_W7


title: bisulf.6909.rep3


title: F.10015.rep3.batch1


title: VD2_W0


title: F.10015.rep2.batch2


title: bisulf.6909.rep2


title: MDA_CA1a_WT_SNRPC_rep1


title: MDA_CA1a_WT_Pol_II_IgG_rep3


title: bisulf.6909.rep1


title: VD1_W34


title: MDA_CA1a_WT_Pol_II_IgG_rep2


title: F.10015.rep1.batch1


title: MDA_CA1a_WT_Pol_II_IgG_rep1


title: F.10002.rep2.batch2


title: bisulf.6244.rep3


title: VD1_W17


title: VD1_W7


title: MDA_CA1a_WT_Pol_II_rep3


title: F.10002.rep1.batch1


title: bisulf.6220.rep3


title: MDA_CA1a_WT_Pol_II_rep2


title: MDA_CA1a_WT_SNRPC_rep2


title: VD2_W17


title: VH3_W34

value: Mock-infection


title: bisulf.6220.rep4


title: VD1_W0


title: bisulf.6220.rep2


title: MDA_CA1a_WT_Pol_II_rep1


title: bisulf.6244.rep4


title: MDA_CA1a_WT_H3K4me3_IgG_rep3


title: MDA_CA1a_WT_H3K4me3_IgG_rep2


title: bisulf.6220.rep1


title: VH3_W7


title: acc.9905.rep4

description: 125bp PE

data_processing:
raw RNA-seq reads were aligned to the TAIR10 genome using STAR (v.2.7.1.). First the genomebuild was performed for TAIR10 accounting for the genome size and not providing the annotated splice junctions. The genomebuild command: STAR --runMode genomeGenerate  --genomeSAindexNbases 12.5 --genomeDir $stargenomedir --genomeFastaFiles genome.fasta . The command used for alignment:  STAR --readFilesIn  $fastq.gz  --readFilesCommand zcat --runThreadN 4 --alignIntronMax 6000 --alignMatesGapMax 6000 --genomeDir $stargenomedir --outFilterIntronMotifs RemoveNoncanonical --outFilterMismatchNoverReadLmax 0.1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --outFilterMultimapNmax 10 --outReadsUnmapped None --alignSJoverhangMin 8 --outSAMattributes NH HI AS nM NM MD jM jI XS --outSAMtype BAM SortedByCoordinate  --runMode alignReads --twopassMode Basic --outFileNamePrefix $out
read counts were calculated using featurecounts from the subread package (v.2.0.0). Command used: featureCounts  -T 4 -p  -F SAF -O -s 2  -t exon -g gene_id -a $saf -o $out.txt $bam
TPMs were calculated by dividing the raw counts number by the total number of raw counts in the sample (in million reads) and the length (in kb). Command used  sum=`cat $out.txt| awk -v OFS="\t" '{ sum += $7} END {print sum}'`  cat $out.txt| grep -v Geneid| awk -v OFS="\t" -v sum="$sum" ' {print $1,$6,$7,$7*1000000*1000/($6*sum)}' > $out.counts_tpm.bed
Assembly: TAIR10
Supplementary files format and content: Kornienko_et_al_annotation.TPMs.28accessions.rosette.txt contains a table with TPMs for 5 gene types in the new annotation (PC genes, AS lncRNAs, TE genes, lincRNAs and AS_to_TEgenes lncRNAs) for every RNAseq sample
Supplementary files format and content: BED files:  The 13 bed files are gene annotations created and used in the study (for example they are used to create the table with expression values (TPMs): Kornienko_et_al_annotation.TPMs.28accessions.rosette.txt).

growth_protocol: 22 degrees Celsius, on soil, long-day conditions (16h light, 8h dark)

tag: accession


title: acc.1254.rep4

description: 125bp PE


title: acc.1254.rep3

description: 125bp PE


title: acc.9905.rep3

description: 125bp PE


title: acc.9905.rep2

description: 125bp PE


title: VH3_W0


title: MDA_CA1a_WT_H3K4me3_IgG_rep1


title: acc.9905.rep1

description: 125bp PE


title: bisulf.6189.rep3


title: VH2_W34


title: MDA_CA1a_WT_H3K4me3_rep3


title: bisulf.6184.rep4


title: acc.9888.rep4

description: 125bp PE


title: MDA_CA1a_WT_H3K4me3_rep2


title: acc.9888.rep3

description: 125bp PE


title: bisulf.6076.rep4


title: VH2_W0


title: MDA_CA1a_WT_H3K4me3_rep1


title: VH3_W17


title: bisulf.6189.rep4


title: VH2_W7


title: bisulf.6069.rep4


title: MDA_CA1a_KO_Pol_II_IgG_rep2


title: acc.9888.rep1

description: 125bp PE


title: bisulf.6076.rep3


title: MDA_CA1a_KO_Pol_II_IgG_rep3


title: MDA_CA1a_KO_Pol_II_IgG_rep1


title: bisulf.6069.rep3


title: MDA_CA1a_KO_Pol_II_rep3


title: bisulf.6024.rep4


title: acc.9588.rep3

description: 125bp PE


title: VH2_W17


title: bisulf.6184.rep3


title: VH1_W0


title: bisulf.6024.rep3


title: acc.9588.rep1

description: 125bp PE


title: bisulf.6021.rep4


title: VH1_W7


title: MDA_CA1a_KO_Pol_II_rep1


title: acc.9888.rep2

description: 125bp PE


title: acc.9518.rep4

description: 125bp PE


title: SCID_3.1_scRNAseq

city: Haifa

first: Nadav

last: Sharon

address: Technion, Israel Institute of Technology

department: Faculty of biology

country: Israel

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: pancreas

extract_protocol:
Each pancreas was  perfused with 5ml RPMI containing collagenase (8ul/ml) through the bile duct. The pancreas was separated and incubated in 37C for 10 minutes, followed by vigorous shaking. Debris was separated using density-gradient (histopaq 1077 and 1119, 30 min at 4C) and the top layer was extracted to obtain the purified islets. The latter were dissociated into single cells using TrypLE (37C, 5min).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells from dissociated islets were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and sample indices were added.

value: islets of Langerhans

value: NOD-SCID

tag: age

value: 10-11 weeks

tag: Sex

value: female

tag: disease state

value: non-diabetic


title: MDA_10A_WT_SNRPC_IgG_rep3

value: Human normal breast epithelial cells


title: VH1_W34


title: acc.9518.rep3

description: 125bp PE

value: leaves


title: bisulf.6021.rep3


title: VH1_W17


title: MDA_10A_WT_SNRPC_IgG_rep2

value: Wild type


title: bisulf.6021.rep2


title: bisulf.6021.rep1


title: acc.9588.rep2

description: 125bp PE


title: acc.9518.rep2

description: 125bp PE


title: SCID_2.3_scRNAseq

institute: Technion, Israel Institute of Technology

description: 10x Genomics


title: MDA_CA1a_KO_Pol_II_rep2

value: Human malignant breast epithelial cells

value: SNRPC knockdown


title: acc.9518.rep1

description: 125bp PE


title: bisulf.5856.rep4


title: acc.9470.rep4

description: 125bp PE


title: SCID_2.6_scRNAseq

description: 10x Genomics


title: MDA_10A_WT_SNRPC_IgG_rep1


title: MDA_10A_WT_SNRPC_rep2


title: acc.9470.rep3

description: 125bp PE


title: bisulf.5856.rep3


title: bisulf.5856.rep2


title: MDA_10A_WT_SNRPA_IgG_rep3


title: MDA_10A_WT_SNRPC_rep1


title: acc.9412.rep4

description: 125bp PE


title: normal RGC cells 2

city: Chengdu

first: Li

last: Chen

state: Sichuann

address: No.17, South Renmin Road

institute: Sichuan University West China Hospital

data_processing:
Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: retinal ganglion cells

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.

value: retinal ganglion cells

value: WT


title: aging RGC cells with USCs conditioned medium 3


title: normal RGC cells 1


title: normal RGC cells 3


title: bisulf.5856.rep1


title: aging RGC cells with USCs conditioned medium 1


title: bisulf.5784.rep4


title: MDA_10A_WT_SNRPA_IgG_rep2


title: acc.9412.rep3

description: 125bp PE


title: MDA_10A_WT_SNRPC_rep3


title: acc.9057.rep4

description: 125bp PE


title: MDA_10A_WT_SNRPA_IgG_rep1


title: bisulf.5784.rep3


title: aging RGC cells 2


title: acc.9057.rep3

description: 125bp PE


title: MDA_10A_WT_SNRPA_rep3

value: SNRPA


title: aging RGC cells with USCs conditioned medium 2


title: bisulf.5784.rep2


title: acc.8366.rep3

description: 125bp PE


title: MDA_10A_WT_SNRPA_rep2


title: aging RGC cells 1


title: bisulf.5784.rep1


title: bisulf.5779.rep3


title: acc.8244.rep2

description: 125bp PE


title: Rpl3l KO m6A-seq 3

city: Chikusa-ku, Nagoya, Aichi

first: Kazuya

last: Ichihara

address: Furo-cho

country: Japan

institute: Nagoya University

data_processing:
Adaptor sequences were trimmed from raw reads with the use of cutadapt.
Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit.
Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCm38.p6) and human genome (mm10) also with the use of STAR.
Assembly: mm10
Supplementary files format and content: Counts for each tRNA isodecoders or m6A peaks

source_name: Heart

extract_protocol:
The heart tissues were flash frozen in liquid nitrogen and lysed in a lysis buffer with the use of Multi beads shocker (YASUI KIKAI). The lysates were centrifuged at 20,380 × g for 10 min at 4°C, and the resulting supernatants were collected, assayed for RNA concentration with a Qubit RNA BR Assay Kit (Thermo Fisher Scientific), incubated with RNase I (20 U per 10 μg of RNA, Epicentre) for 45 min at 25°C, and placed on ice before the addition of SUPERase•In RNase inhibitor (Invitrogen). The samples were then loaded on a 1 M sucrose cushion [containing 20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, SUPERase•In (10 U/ml), 1 mM dithiothreitol, and cycloheximide (100 μg/ml)], and the gradients were centrifuged at 100,000 rpm (417,200 × g) for 1 h at 4°C in a Beckman TLA110 rotor. The resulting pellets were suspended in ribosome splitting buffer [20 mM Tris-HCl (pH 7.5), 300 mM NaCl, 5 mM EDTA, SUPERase•In (20 U/ml), 1 mM dithiothreitol, and 1% Triton X-100] and subjected to purification with the use of an Amicon Ultra filtration device (100-kDa cutoff, Millipore) to deplete rRNAs.
Total RNA was extracted from tissue lysates with the use of a PureLink RNA Mini Kit (Thermo Fisher Scientific), and the quality of the purified RNA was assessed with a 2100 Bioanalyzer (Agilent).
The purified RNA was subjected to selection on the basis of a size range of 17 to 34 nt for Ribo-seq and 50 to 80 nt for Disome-seq by electrophoresis through a 15% polyacrylamide and Tris-borate-EDTA (TBE)–urea gel (SuperSep RNA, Fujifilm). The footprint fragments were treated with T4 polynucleotide kinase (New England Biolabs) to repair the 2'-3' cyclic phosphates, a DNA linker including barcode sequences (NI-810 to NI-817) was ligated with the use of T4 RNA ligase 2, truncated K227Q (New England Biolabs), and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. Ribosomal RNAs were further depleted with the use of RiboZero Gold (Illumina). Reverse transcription (RT) was performed with the NI-802 primer, and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. The purified cDNAs were circularized with circLigase II (Lucigen), and index sequences were then added by amplification with the polymerase chain reaction (PCR) as performed with the common primer (NI-798) and primers including index sequences (NI-799 and NI-822 to NI-826). Products of the desired size were purified on a 15% polyacrylamide nondenaturing gel (SuperSep DNA, Fujifilm), and the libraries were sequenced with a NovaSeq 6000 system (Illumina).
tRNA-seq library construction protocol
Periodic oxidation of 10   g of total RNA extracted from mouse heart was carried out in 100 mM NaOAc/HOAc (pH 4.8) and 50 mM NaIO4 for 30 min at room temperature. Then, 1 M glucose was added to a final concentration of 100 mM, left at room temperature for 5 minutes, and RNA was purified using Micro Bio-Spin P-6 Columns (Bio-Rad). The RNA was treated with 60 mM sodium borate (pH 9.5) at 45  C for 90 min for deacylation, and purified again with Micro Bio-Spin P-6 Columns. Purified RNA was selected according to size in the range of 70 to 90 nt by electrophoresis in a 15% polyacrylamide and TBE-urea gel, and demethylated using demethylase supplied with the rtStarTM tRNA-optimized First-Strand cDNA Synthesis Kit (Filgen). The resulting sample was then subjected to dephosphorylation, DNA linker ligation, and rRNA depletion with RiboZero Gold as described for the Ribo-seq protocol. RT was performed with the use of the SI-019 primer, and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. The second linker (SI-018) was ligated by incubation overnight at 25  C with T4 RNA Ligase 1 (ssRNA Ligase), High Concentration (New England Biolabs). The products were then amplified by PCR with the same primers as used for the Ribo-seq protocol, and those of the desired size were purified by electrophoresis through a 15% polyacrylamide nondenaturing gel.
m6A-seq library construction protocol
m6A-seq libraries were prepared with the use of EpiNext CUT&RUN RNA m6A-Seq Kit (EpiGentek) according to the manufacturer's protocol. Briefly, 5   g of total RNA extracted from mouse heart was immunoprecipitated with m6A antibody and cleaved on beads. The beads were then washed, RNA was purified from the beads, reverse transcribed, and the resulting cDNA was amplified by PCR.

value: Rpl3l KO


title: acc.8366.rep2

description: 125bp PE


title: MDA_10A_WT_SNRPA_rep1


title: bisulf.5779.rep2


title: Rpl3l KO m6A-seq 2


title: aging RGC cells 3


title: acc.8244.rep1

description: 125bp PE


title: MDA_10A_WT_Pol_II_IgG_rep1


title: bisulf.5772.rep4


title: MDA_10A_WT_Pol_II_IgG_rep2


title: Rpl3l KO m6A-seq 1


title: acc.6966.rep4

description: 125bp PE


title: acc.9588.rep4

description: 125bp PE


title: bisulf.5779.rep1


title: MDA_10A_WT_Pol_II_rep3


title: bisulf.5772.rep3


title: WT m6A-seq 1


title: acc.6966.rep3

description: 125bp PE


title: MDA_10A_WT_Pol_II_rep2


title: bisulf.5772.rep2


title: acc.8366.rep1

description: 125bp PE


title: MDA_10A_WT_Pol_II_IgG_rep3


title: acc.6966.rep2

description: 125bp PE


title: Rpl3l KO tRNA-seq 3

description: tRNA.xlsx


title: MDA_10A_WT_Pol_II_rep1


title: bisulf.5486.rep2


title: acc.6966.rep1

description: 125bp PE


title: Rpl3l KO tRNA-seq 2

description: tRNA.xlsx


title: Rpl3l KO tRNA-seq 1

description: tRNA.xlsx


title: bisulf.5210.rep4


title: acc.6911.rep2

description: 125bp PE


title: MDA_10A_OE_SNRPA_IgG_rep2

value: SNRPC overexpression


title: bisulf.5210.rep3


title: WT m6A-seq 2


title: WT tRNA-seq 3

description: tRNA.xlsx


title: acc.6909.rep4

description: 125bp PE


title: WT tRNA-seq 2

description: tRNA.xlsx


title: acc.6911.rep1

description: 125bp PE


title: acc.6909.rep3

description: 125bp PE


title: bisulf.5772.rep1


title: acc.6909.rep2

description: 125bp PE


title: bisulf.5210.rep1


title: MDA_10A_OE_SNRPA_rep1


title: MDA_10A_OE_SNRPA_rep2


title: WT tRNA-seq 1

description: tRNA.xlsx


title: acc.6909.rep1

description: 125bp PE


title: MDA_10A_OE_SNRPA_IgG_rep3


title: MDA_10A_OE_SNRPA_IgG_rep1


title: bisulf.4807.rep3


title: bisulf.4807.rep4


title: MDA_10A_OE_Pol_II_IgG_rep3


title: MDA_10A_OE_SNRPA_rep3


title: acc.6244.rep4

description: 125bp PE


title: MDA_10A_OE_Pol_II_IgG_rep2


title: bisulf.5210.rep2


title: bisulf.4807.rep1


title: bisulf.4807.rep2


title: Biotin-Rbbp7_oe_rep2

city: Guangzhou

first: Wang

middle: Fang

last: Ping

state: Guangdong

address: 190 Kaiyuan Avenue

department: Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
not provided
Assembly: not provided
Supplementary files format and content: *.tab: Tab-delimited text files include TPM values.

growth_protocol: mESCs were cultured on 0.1% gelatin-coated plates with the mES medium containing high-glucose Dulbecco’s modified Eagle’s medium (DMEM, HyClone), 15% fetal bovine serum (Gibco), 1 × GlutaMAX (Gibco), 1 × nonessential amino acids (NEAA, Gibco), 1 × sodium pyruvate (Gibco), 1 mM 2-mercaptoethanol (Gibco), 3 μM Chir99021 (Selleck), 1 μM PD0325901 and 1,000 U Leukemia Inhibitory Factor/LIF.

extract_protocol:
Total RNAs were extracted with TRIzol. 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA sequencing libraries were constructed by using a VAHTS mRNA-seq V3 Library Prep Kit (Vazyme Biotech, NR611) according to the manufacturer’s instructions.

value: embryonic stem cells

value: stably expressed biotin-Rbbp7

value: no


title: 46C_ctrl_rep2

value: stably expressed biotin tag alone


title: Biotin-Rbbp4_oe_rep2

value: stably expressed biotin-Rbbp4


title: acc.6220.rep4

description: 125bp PE


title: WT m6A-seq 3


title: bisulf.1741.rep4


title: acc.6244.rep3

description: 125bp PE


title: Biotin-Rbbp4_oe_rep1


title: Biotin-Rbbp7_oe_rep1


title: acc.6220.rep3

description: 125bp PE


title: MDA_10A_OE_Pol_II_IgG_rep1


title: MDA_10A_OE_Pol_II_rep1


title: acc.6220.rep1

description: 125bp PE


title: MDA_10A_OE_Pol_II_rep3


title: acc.6220.rep2

description: 125bp PE


title: bisulf.1254.rep4


title: Rbbp4-AID 24h_MNase_rep2

data_processing:
none provided by the submitter
Assembly: none provided by the submitter

growth_protocol: mESCs were cultured on 0.1% gelatin-coated plates with the mES medium containing high- glucose Dulbecco’s modified Eagle’s medium (DMEM, HyClone), 15% fetal bovine serum (Gibco), 1 × GlutaMAX (Gibco), 1 × nonessential amino acids (NEAA, Gibco), 1 × sodium pyruvate (Gibco), 1 mM 2-mercaptoethanol (Gibco), 3 μM Chir99021 (Selleck)，1 μM PD0325901 and 1,000 U Leukemia Inhibitory Factor/LIF.

extract_protocol:
1 x 106 cells were harvested and transferred into lysis buffer. Nuclei were then pelleted, washed and resuspended in digestion buffer containing 2 mM CaCl2 and 2,500 gel units micrococcal nuclease (NEB, M0247S) with shaking at 37℃ for 5 min.  The reaction was stopped by EDTA and protease was added to digest proteins. Then fragmented and naked genomic DNA were released.
The sequencing libraries were prepared from 10 ng of purified mono-nucleosome-DNAs using the VAHTS® Universal DNA Library Prep Kit (Vazyme, ND607) with 10 cycles of PCR.

treatment_protocol: For induction of the auxin-inducible RBBP4 degradation, indole-3-acetic acid (IAA, Sigma) was added in the medium at 500 µM.

value: Rbbp4-AID, Tir1

value: auxin-induced degradation of RBBP4 24h


title: bisulf.1741.rep2


title: MDA_10A_OE_Pol_II_rep2

value: Human normal breast epithelial cells


title: Rbbp4-AID 0h_MNase_rep2

value: auxin-induced degradation of RBBP4 0h


title: bisulf.1741.rep1

value: leaves


title: acc.6189.rep4

description: 125bp PE


title: 46C_ctrl_rep1


title: Rbbp4-AID 0h_MNase_rep1


title: Rbbp4-AID 24h_MNase_rep1


title: bisulf.1254.rep3


title: acc.6189.rep3

description: 125bp PE


title: Rbbp4-AID 24h_H3K9me2_rep2

extract_protocol:
CUT&Tag assay was done as described in Kaya-Okur et al (2019) with slight modifications. 1 × 105 cells were harvested and bound to Concanavalin A-coated beads, then incubated with individual primary antibody at 4°C overnight. pG-Tn5 (Vazyme, S602) enzyme was added to each sample followed by incubation 1 hour at RT. pG-Tn5 was actived by 10 mM MgCl2 at 37℃ for 1 hour. The DNA released into the supernatant were purified and subjected to library preparation and next-generation sequencing.
The sequencing libraries were prepared using NEBNext High-Fidelity 2x PCR Master Mix (NEB, M0541S) for 13 cycles.


title: bisulf.10012.rep4


title: acc.6184.rep3

description: 125bp PE


title: bisulf.10012.rep1


title: acc.6184.rep4

description: 125bp PE


title: bisulf.10012.rep3


title: FACS-Astrocytes

city: Montreal

first: Rhalena

middle: Amber

last: Thomas

state: QC

address: 3801 rue University, Montreal Neurological Institute, NW B150

department: Neurology

country: Canada

institute: McGill University

description: 10X Genomics

data_processing:
CellRanger to create matrix, barcode and feature files filtered output files
R analysis with seurat.  Each sample was separately processed separately.
Filtering applied.  Filters differ by sample for min RNA features. nRNA features > 250 to > 500.  For all samples RNA count < 10000 and percent mitochondria < 25%
Hashtag demultiplexing to identify replicates.  Doublet removal.
After all filtering Sample1 had only 1723 cells.  Sample 2 and Sample 4 were down sampled to 2000 cells and sample 3 was downsampled to 3000 cells.  The four samples were integrated
Supplementary files format and content: CellRanger outputs: raw_feature_bc_matrix(barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)
Supplementary files format and content: Four samples combined with cell types annotated.

source_name: midbrain organoids

growth_protocol: human midbrain organoids grown in bioreacotors; suspended cultures in motion.

extract_protocol:
10X Genomics scRNAseq Chromium Next GEM Single Cell 3' kit v3.1 and 3' Feature Barcode kit
Dual Index kit TT Set A and Dual Index Kit NT Set A

value: midbrain organoids

value: astrocytes

value: healthy control


title: Rbbp4-AID 24h_H3K9me2_rep1


title: FACS-Neurons2-CD56

description: 10X Genomics

value: neurons


title: 8F TCR-T cells, Mock, donor # 579

city: Philadelphia

first: David

last: Mai

state: PA

address: 8-189 Smilow Center for Translational Research

institute: University of Pennsylvania

description: ND579 8F Mock

data_processing:
Sequence reads were trimmed for adaptor sequence, uncertain nucleotides (>10% of either read), and low quality reads (base quality <5 constitute >50% of read).
Trimmed sequence reads were mapped to GRCh38.p14 using the salmon algorithm.
Supplementary files format and content: GRCh38.p14
Supplementary files format and content: comma-separated values files including average normalized counts values for genes for each experimental condition

source_name: Primary T cells

growth_protocol: Primary human T cells were maintained in R10 media in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were pelleted in RNALater (Invitrogen) and frozen at -20C until processing. Total RNA was harvested using RNeasy mini kit (Qiagen). At least 400ng of total RNA was used for the construction of sequencing libraries, per Novogene's input requirements.
RNA libraries for bulk RNA-seq was outsourced to Novogene, specifying Eukaryotic RNA-Seq as the library type.

treatment_protocol: Regnase-1, Roquin-1, both Regnase-1 and Roquin-1, or neither gene, were genetically disrupted using CRISPR-Cas9 during expansion of CAR-T or TCR-T cells.

value: Primary T cells

value: T cells

value: WT

value: Baseline


title: Rbbp4-AID 0h_H3K9me2_rep1

value: embryonic stem cells


title: Rbbp4-AID 0h_H3K9me2_rep2


title: acc.6076.rep4

description: 125bp PE


title: 8F TCR-T cells, Roquin-1 KO, donor # 579

description: ND579 8F Roq1-KO

value: Roquin-1 knockout


title: 8F TCR-T cells, DKO, donor # 579

description: ND579 8F DKO

value: Regnase-1 and Roquin1 double knockout


title: FACS-RadialGlia

description: 10X Genomics


title: acc.6069.rep4

description: 125bp PE


title: acc.6069.rep3

description: 125bp PE


title: acc.6076.rep3

description: 125bp PE


title: M5 CAR-T cells, Mock, donor # 561

description: ND561 M5 Mock


title: Rbbp4-AID 24h_CHD4_rep1

extract_protocol:
CUT&RUN assay was done as described in Meers et al (2019) with slight modifications. 1 × 105 cells were harvested and bound to Concanavalin A-coated beads, then incubated with individual primary antibody at 4°C overnight. pAG-MNase enzyme was added to each sample followed by incubation 1 hour at 4°C. Targeted digestion was done by 30 minutes incubation on ice block (0°C) under low salt conditions.The DNA released into the supernatant were purified and subjected to library preparation and next-generation sequencing.
The sequencing libraries were prepared through VAHTS Universal DNA Library Prep Kit (Vazyme, ND607).

value: CHD4 (Abcam #ab70469)


title: mES IgG

value: Rbbp4-AID, Tir1


title: Rbbp4-AID 0h_CHD4_rep2


title: acc.6024.rep3

description: 125bp PE


title: M5 CAR-T cells, Roquin-1 KO, donor # 561

description: ND561 M5 Roq1-KO


title: sciatic nerve, P2

city: shanghai

first: Hongjin

address: NO.639 Shanghai Zhizaoju Road, Huangpu District, Shanghai, China.

institute: Shanghai Ninth People's hospital

data_processing:
CLC Genomics Workbenchv 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to NCBI_Rnor_6.0 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: NCBI_Rnor_6.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: sciatic nerve

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep kit. 1 ug of total RNA was used for the construction of sequencing libraries.

value: sciatic nerve

value: streptozotocin

value: diabetic with MA


title: dCTB_PolyI:C

type: RNA

city: Setagaya

first: Kenichiro

last: Motomura

state: Tokyo

department: Allergy and Clinical Immunology

institute: National Research Institute for Child Health and Development

hyb_protocol: Cy3-labelled cRNA was fragmented and hybridized to an Agilent SurePrint G3 Human GE 8 x 60 version 3 microarray using Agilent Gene Expression Hybridization Kit according to manufacturer’s instruction. After hybridization, the microarray was washed and dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2565CA).

data_processing: The data underwent normalization using the Subio platform version 1.24.5853 (Subio Inc) with global normalization being employed at 75th percentile. Low signal cutoff of 20, log transformation (base 2), and ratio to control samples were utilized for the data analysis.

source_name: Differentiated primary human cytotrophoblast, 9 h, Poly I:C

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from pooled total RNA using the Low Input Quick Amp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions.

growth_protocol: Purified cytotrophoblasts from term human placentas were plated onto uncoated multi-well plates and incubated for 120 h in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 IU/mL penicillin/streptomycin/amphotericin B, 10 ng/mL epidermal growth factor, and 10 µM Y-27632. After 120-h culture, the primary human cytotrophoblasts spontaneously differentiate into STB-like cells, which are evidenced by the formation of syncytia by cell-cell fusion and production of hCG.

extract_protocol: The cells were lysed with QIAzol, and the total RNA was extracted using an RNeasy Mini Kit according to the manufacturer’s instructions. Total RNAs from differentiated cytotrophoblasts from three different donors (biological replicates) were pooled.

treatment_protocol: Differentiated human primary cytotrophoblasts were cultured with poly I:C (1 µg/mL) or its vehicle control (endotoxin-free water) for 9 h.

value: Poly I:C (1 µg/mL)


title: M5 CAR-T cells, DKO, donor # 561

description: ND561 M5 DKO


title: M5 CAR-T cells, Regnase-1 KO, donor # 561

description: ND561 M5 Reg1-KO

value: Regnase-1 knockout


title: sciatic nerve, NP3

value: diabetic without MA


title: sciatic nerve, con3

value: vehicle

value: control


title: dCTB_Control

source_name: Differentiated primary human cytotrophoblast, 9 h, Vehicle

value: Vehicle


title: sciatic nerve, P3


title: acc.5856.rep4

description: 125bp PE

extract_protocol:
RNA was isolated and DNAse I (NEB) treated using a KingFisher Robot with an in-house magnetic RNA isolation kit. RNA was diluted in nuclease free water (Ambion) and stored at -80oC.
TruSeq Stranded mRNA

value: leaves


title: FACS-Neurons1-CD24

description: 10X Genomics

value: midbrain organoids

value: neurons

value: healthy control


title: Rbbp4-AID 0h_G9a_rep1

value: embryonic stem cells

value: auxin-induced degradation of RBBP4 0h


title: sciatic nerve, con1


title: acc.6024.rep4

description: 125bp PE


title: Rbbp4-AID 24h_CHD4_rep2

value: auxin-induced degradation of RBBP4 24h

value: CHD4 (Abcam #ab70469)


title: acc.6021.rep1

description: 125bp PE


title: sciatic nerve, P1

value: sciatic nerve


title: Rbbp4-AID 0h_CHD4_rep1

value: Rbbp4-AID, Tir1


title: 0.2mM_Kcr

city: Pittsburgh

first: Huairui

last: Yuan

address: 4200 Fifth Ave

institute: University of Pittsburgh

data_processing:
For ChIP-seq, raw FASTQ files were trimmed using Trim Galore and aligned to the hg38 human genome using Bowtie2 with default parameters. Samtools was used to sort and index the BAM files. For subsequent visualization of ChIP-seq signal, bigwig files were generated using the Deeptools “bamCoverage” script using default settings.
Assembly: hg38
Supplementary files format and content: For ChIP-seq, the processed data are the bigwig files generated by Deeptools “bamCoverage” script.

source_name: Glioblastoma

extract_protocol:
The procedure of ChIP assays was according to the ChIP kit (cat: 17-10085, Millipore) instruction manual provided by the manufacturer.
ChIP DNA was purified and used to prepare sequencing libraries by the NEBNext Ultra DNA Library Prep Kit for Illumina sequencing.

value: Glioblastoma

value: Glioblastoma stem cells

value: Kcr (PTM Biolab, #PTM-501)

value: 0.2mM Lysine


title: Sham_rep2

city: Changchun

first: yao

last: qu

state: Jilin

address: NO1 Xinmin Street

department: Department of Anesthesiology

institute: The First Hospital of Jilin Univeristy

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 Rattus norvegicus V101 whole genome using HISAT 2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.estimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Rattus norvegicus V101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: lumbar4-6 dorsal root ganglia

extract_protocol:
Total RNA of each sample was extracted by TRK-1002U (LC sciences, Houston, Texas, USA) according to the manufacturer’s protocol. The quality and quantity of RNA in each sample was measured by Nanodrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity number (RIN) was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) with RIN ＞7.0.  approximately 2μg of total RNA from each pooled sample was used to prepare the cDNA library of mRNA by ribosomal RNA depletion method using Ribo-Zero rRNA Removal Kit (Illumina, San Diego, CA, USA). Following purification, the ribo-minus RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ for 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.
Library for mRNA, LncRNA, cicRNA was prepared for 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China)  sequencing using standard Illumina protocols.

value: lumbar4-6 dorsal root ganglia

value: Sprague-Dawley

value: male


title: Sham_rep3


title: Rbbp4-AID 24h_G9a_rep2


title: acc.6021.rep4

description: 125bp PE

source_name: leaves

value: leaves


title: acc.6021.rep3

description: 125bp PE


title: sciatic nerve, NP2

value: streptozotocin

value: diabetic without MA


title: 8F TCR-T cells, Regnase-1 KO, donor # 579

description: ND579 8F Reg1-KO

value: Primary T cells

value: T cells

value: Regnase-1 knockout

value: Baseline


title: Sham_rep1


title: acc.5784.rep4

description: 125bp PE


title: sciatic nerve, NP1


title: 2mM_H3K27ac

value: 2mM Lysine


title: acc.6021.rep2

description: 125bp PE


title: Rbbp4-AID 24h_G9a_rep1

value: embryonic stem cells

value: auxin-induced degradation of RBBP4 24h


title: acc.5784.rep3

description: 125bp PE


title: Rbbp4-AID 0h_G9a_rep2

value: Rbbp4-AID, Tir1

value: auxin-induced degradation of RBBP4 0h


title: Rbbp4-AID 24h_H3K9me3_rep2

value: H3K9me3 (Abcam #ab8898)


title: M5 CAR-T cells, Roquin-1 KO, donor # 539

description: ND539 M5 Roq1-KO

value: Roquin-1 knockout


title: sciatic nerve, con2

value: sciatic nerve

value: vehicle

value: control


title: CCI_rep1

value: lumbar4-6 dorsal root ganglia

value: Sprague-Dawley

value: male

value: CCI to sciatic nerve


title: Rbbp4-AID 0h_KAP1_rep1

value: KAP1 (Abcam #ab109545)


title: Rbbp4-AID 0h_H3K9me3_rep2


title: M5 CAR-T cells, DKO, donor # 539

description: ND539 M5 DKO

value: Primary T cells

value: T cells

value: Regnase-1 and Roquin1 double knockout


title: M5 CAR-T cells, Regnase-1 KO, donor # 539

description: ND539 M5 Reg1-KO

value: Regnase-1 knockout

value: Baseline


title: Rbbp4-AID 24h_KAP1_rep2

value: embryonic stem cells

value: Rbbp4-AID, Tir1

value: auxin-induced degradation of RBBP4 24h


title: acc.5856.rep3

description: 125bp PE

value: leaves


title: 0.2mM_H3K27ac

value: Glioblastoma

value: Glioblastoma stem cells

value: 0.2mM Lysine


title: 2mM_Input

value: 2mM Lysine


title: shCONT_H3K9me3

value: H3K9me3 (Abcam, #ab8898)

value: WT

value: shCONT


title: acc.5772.rep3

description: 125bp PE


title: Rbbp4-AID 24h_KAP1_rep1

value: KAP1 (Abcam #ab109545)


title: Rbbp4-AID 0h_KAP1_rep2

value: auxin-induced degradation of RBBP4 0h


title: acc.5856.rep2

description: 125bp PE


title: acc.5772.rep2

description: 125bp PE


title: healthy volunteers 4

city: zhengzhou

first: Yao

last: Lu

state: henan province

address: 1 Jianshe Dong Lu, Zhengzhou City, Henan Province, China

institute: zhengzhou university

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster.
After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: The xlsx format file contains the RPKM value of gene in every sample

source_name: intestinal tissue

extract_protocol:
Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: intestinal tissue


title: Biotin-RBBP7_rep2

extract_protocol:
46C cells stably expressed BIOTIN-RBBP4 or BIOTIN-RBBP7 were crosslinked with 1% formaldehyde. After quenching and cell lysis, crosslinked cells were sonicated and diluted 10-fold with ChIP dilution buffer, and then incubated with M280 streptavidin dynabeads at 4°C for overnight.  ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols.
The sequencing libraries were prepared through VAHTS Universal DNA Library Prep Kit (Vazyme, ND607).

value: stably expressed Biotin-RBBP7


title: DMSO

first: Hana

last: Imrichova

address: Lazarettgasse 14, AKH BT 25.3

institute: CeMM, Vienna

data_processing:
Raw read files were converted to fastq format using the convert function from bamtools (v2.5.2).
Sequencing adapters were trimmed using cutadapt (v3.4) with -g CGAAACACCG and --minimum-length = 10.
The 20 bp of spacer sequence were then extracted using fastx toolkit (v0.0.14) and aligned to the respective sgRNA index using bowtie2 (v2.4.4) allowing for one mismatch in the seed sequence.
Spacers were counted using the bash command ‘cut -f 3 (0) | sort | uniq -c’ on the sorted SAM files.
Assembly: Brunello library
Supplementary files format and content: Tab-delimited text files include raw read counts mapped to the Brunello library.

source_name: chronic myelogenous leukemia (CML) cell line

growth_protocol: IMDM 10%FBS 1%P/S

extract_protocol:
Genomic DNA was isolated with the QIAamp DNA Mini Kit (Qiagen, 51306) and used as template for PCR amplification of sgRNA sequences.
Brunello library

treatment_protocol: KBM7 cells (constitutively expressing Cas9) were continuously treated for 20 days with DMSO or W7 (2x EC50 starting concentration).

value: Cancer Cell Line

tag: disease

value: CML

value: DMSO


title: 0.2mM_Input


title: acc.5856.rep1

first: Aleksandra

institute: Gregor Mendel Institute

description: 125bp PE


title: W7_rep2

data_processing:
conversion and demultiplexing: IlluminaBasecallsToMultiplexSam to generate one bam file per lane from the data on the Illumina machine, IlluminaSamDemux to demultiplex the bam file into multiple samples (https://github.com/DanieleBarreca/picard)
trimming: Trimmomatic (version 0.32) using the following parameters: HEADCROP:13 ILLUMINACLIP:epignome_adapters_2_add.fa:2:10:4:1:true SLIDINGWINDOW:4:1 MAXINFO:16:0.40 MINLEN:30
alignment: STAR aligner version 2.5.2b using the following parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate
defining genes: genome-build GRCh38.p7, genome-build-accession NCBI:GCA_000001405.22.
read counts files: htseq-count (version 0.11.2) from the HTSeq framework
Assembly: hg38 (GRCh38)
Supplementary files format and content: tab-delimited text files include raw read counts mapped to genes from the human genome

extract_protocol:
CORALL Total RNA-Seq Library Prep Kit from Lexogen
RNAsey mini kit Qiagen 74106
CORALL Total RNA-Seq Library Prep Kit (Lexogen, #095.24), poly-A enrichment.

treatment_protocol: KBM7 cells treated for 6h with DMSO & W7 (4x EC50). Triplicates per condition.

tag: replicate


title: CCI_rep3

tag: tissue

value: lumbar4-6 dorsal root ganglia

value: Sprague-Dawley

value: male

value: CCI to sciatic nerve


title: 2mM_Kcr

value: Glioblastoma

value: Glioblastoma stem cells

value: Kcr (PTM Biolab, #PTM-501)


title: healthy volunteers 3


title: Biotin-RBBP4_rep2

value: embryonic stem cells

value: stably expressed Biotin-RBBP4


title: healthy volunteers 5


title: CCI_rep2


title: acc.5210.rep4

description: 125bp PE

value: leaves

tag: developmental stage


title: Rbbp4-AID 24h_H3K9me3_rep1

tag: genotype

value: Rbbp4-AID, Tir1

value: auxin-induced degradation of RBBP4 24h

value: H3K9me3 (Abcam #ab8898)


title: DMSO_rep3


title: Biotin-RBBP4_rep1


title: acc.5784.rep1

description: 125bp PE


title: shGCDH_H3K9me3

value: H3K9me3 (Abcam, #ab8898)

value: GCDH knockdown

value: shGCDH


title: acc.5210.rep3

description: 125bp PE


title: Rbbp4-AID 0h_H3K9me3_rep1

value: auxin-induced degradation of RBBP4 0h


title: W7

value: Cancer Cell Line

value: CML


title: acc.5772.rep4

description: 125bp PE


title: acc.5210.rep2

description: 125bp PE


title: Rbbp7-AID 24h_rep2

extract_protocol:
Total RNAs were extracted with TRIzol.1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA sequencing libraries were constructed by using a VAHTS mRNA-seq V3 Library Prep Kit (Vazyme Biotech, NR611) according to the manufacturer’s instructions.

treatment_protocol: For induction of the auxin-inducible RBBP4 or RBBP7 degradation, indole-3-acetic acid (IAA, Sigma) was added in the medium at 500 µM.

value: Rbbp7-AID, Tir1

value: auxin-induced degradation of RBBP7 24h


title: DMSO_rep1

value: DMSO


title: Rbbp7-AID 24h_rep1


title: mES Input

value: WT


title: Biotin-RBBP7_rep1

value: stably expressed Biotin-RBBP7


title: IBS-D patient 4

value: intestinal tissue


title: W7_rep3


title: acc.5210.rep1

description: 125bp PE


title: Rbbp7-AID 12h_rep2

value: embryonic stem cells

value: auxin-induced degradation of RBBP7 12h


title: acc.5772.rep1

description: 125bp PE

value: leaves


title: NHA_TCPplus_A

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standard illumina base calling pipeline. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned to hg38 reference genome using STAR with default parameters
STAR was used to generate the "raw count" from an aligned bam againt transcript file
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each annotated gene for each sample

source_name: NHA

extract_protocol:
Libraries were prepared from isolated total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina from Lexogen, (Vienna, Austria). Barcoded libraries were pooled and paired end sequenced (2X75) on the Illumina HiSeq using the High output V2.5 kit (Illumina Inc., San Diego CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: normal human astrocyte cells

value: TCP

value: NHA

tag: passages


title: NHA_TCPplus_B

tag: treatment


title: IBS-D patient 3


title: healthy volunteers 2


title: IBS-D patient 2


title: NHA_TCPminus_B

value: diluent

tag: cell line


title: acc.5784.rep2

city: Vienna

last: Kornienko

address: Dr. Bohrgasse 3

description: 125bp PE


title: W7_rep1


title: Rbbp7-AID 4h_rep1

tag: cell type

value: auxin-induced degradation of RBBP7 4h


title: DMSO_rep2


title: Rbbp7-AID 0h_rep2

value: auxin-induced degradation of RBBP7 0h


title: healthy volunteers 1


title: acc.1741.rep3

description: 125bp PE


title: Rbbp7-AID 4h_rep2


title: acc.1741.rep4

description: 125bp PE


title: LNZ308_TCPplus_A

value: glioblastoma cells


title: shGCDH_Kcr

value: Glioblastoma

value: Glioblastoma stem cells

tag: chip antibody

value: Kcr (PTM Biolab, #PTM-501)

value: GCDH knockdown

value: shGCDH


title: acc.4807.rep1

description: 125bp PE


title: Rbbp7-AID 0h_rep1

value: Rbbp7-AID, Tir1


title: acc.4807.rep4

description: 125bp PE


title: Rbbp7-AID 12h_rep1


title: LNZ308_TCPminus_B


title: acc.4807.rep3

description: 125bp PE


title: LNZ308_TCPminus_A


title: Rbbp4-AID 24h_rep1

value: Rbbp4-AID, Tir1

value: auxin-induced degradation of RBBP4 24h


title: acc.1741.rep1

description: 125bp PE


title: LN18_TCPplus_B


title: IBS-D patient 5

value: intestinal tissue


title: Rbbp4-AID 12h_rep2

value: embryonic stem cells

value: auxin-induced degradation of RBBP4 12h


title: acc.4807.rep2

description: 125bp PE

value: leaves


title: IBS-D patient 1


title: LN18_TCPplus_A

value: TCP


title: LNZ308_TCPplus_B


title: M5 CAR-T cells, Mock, donor # 539

description: ND539 M5 Mock

value: Primary T cells

value: T cells

value: WT

value: Baseline


title: LN18_TCPminus_A

value: glioblastoma cells

value: diluent


title: acc.1741.rep2

description: 125bp PE


title: NHA_TCPminus_A

value: normal human astrocyte cells

value: NHA


title: DGC3028_sh2_1

data_processing:
For RNA-seq, raw FASTQ reads were trimmed using Trim Galore, followed by transcript mapping with Hisat2 to human reference genome (hg38). Samtools was used for sorting, indexing and format conversion from SAM files. Quantification and differential analysis were performed using FeatureCounts and DESeq2 with paired sample analysis.
Assembly: hg38
Supplementary files format and content: For RNA-seq, text files include gene count for each Sample.

extract_protocol:
Cellular total RNA was isolated using TRIzol (cat: 15596018; Life Technologies) followed by Direct-zol RNA Miniprep kit (cat: R2052; Zymo Research).
Total RNA was extracted and used for library construction using the Illumina TruSeq Stranded Total RNA Library Prep Kit, which was performed by Novogene.

value: Glioblastoma

value: Differentiated glioblastoma cells

value: ECHS1 knockdown


title: shGCDH_H3K27ac

value: Glioblastoma stem cells

value: GCDH knockdown

value: shGCDH


title: shGCDH_Input


title: Rbbp4-AID 24h_rep2

value: embryonic stem cells

value: Rbbp4-AID, Tir1

value: auxin-induced degradation of RBBP4 24h


title: DGC3028_sh1_1


title: LN18_LSD1WT_A

value: LSD1 WT


title: LN18_LSD1WT_B


title: shCONT_Kcr

value: Kcr (PTM Biolab, #PTM-501)

value: shCONT


title: acc.10012.rep4

description: 125bp PE

data_processing:
raw RNA-seq reads were aligned to the TAIR10 genome using STAR (v.2.7.1.). First the genomebuild was performed for TAIR10 accounting for the genome size and not providing the annotated splice junctions. The genomebuild command: STAR --runMode genomeGenerate  --genomeSAindexNbases 12.5 --genomeDir $stargenomedir --genomeFastaFiles genome.fasta . The command used for alignment:  STAR --readFilesIn  $fastq.gz  --readFilesCommand zcat --runThreadN 4 --alignIntronMax 6000 --alignMatesGapMax 6000 --genomeDir $stargenomedir --outFilterIntronMotifs RemoveNoncanonical --outFilterMismatchNoverReadLmax 0.1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --outFilterMultimapNmax 10 --outReadsUnmapped None --alignSJoverhangMin 8 --outSAMattributes NH HI AS nM NM MD jM jI XS --outSAMtype BAM SortedByCoordinate  --runMode alignReads --twopassMode Basic --outFileNamePrefix $out
read counts were calculated using featurecounts from the subread package (v.2.0.0). Command used: featureCounts  -T 4 -p  -F SAF -O -s 2  -t exon -g gene_id -a $saf -o $out.txt $bam
TPMs were calculated by dividing the raw counts number by the total number of raw counts in the sample (in million reads) and the length (in kb). Command used  sum=`cat $out.txt| awk -v OFS="\t" '{ sum += $7} END {print sum}'`  cat $out.txt| grep -v Geneid| awk -v OFS="\t" -v sum="$sum" ' {print $1,$6,$7,$7*1000000*1000/($6*sum)}' > $out.counts_tpm.bed
Assembly: TAIR10
Supplementary files format and content: Kornienko_et_al_annotation.TPMs.28accessions.rosette.txt contains a table with TPMs for 5 gene types in the new annotation (PC genes, AS lncRNAs, TE genes, lincRNAs and AS_to_TEgenes lncRNAs) for every RNAseq sample
Supplementary files format and content: BED files:  The 13 bed files are gene annotations created and used in the study (for example they are used to create the table with expression values (TPMs): Kornienko_et_al_annotation.TPMs.28accessions.rosette.txt).

value: leaves


title: Rbbp4-AID 0h_rep1

value: auxin-induced degradation of RBBP4 0h


title: shCONT_Input

value: WT


title: Rbbp4-AID 12h_rep1

value: auxin-induced degradation of RBBP4 12h


title: acc.10012.rep3

description: 125bp PE


title: Rbbp4-AID 4h_rep1

value: auxin-induced degradation of RBBP4 4h


title: DGC3028_sh2_2

value: Glioblastoma


title: LN18_TCPminus_B

value: glioblastoma cells

value: diluent


title: Rbbp4-AID 4h_rep2


title: HEK293T WT 1-3 & FUSKO 1-3

city: Copenhagen N

first: Sophia

middle: Julia

last: Häfner

address: Ole Maaløes Vej 5

department: Biotechnology Research and Innovation Centre (BRIC)

country: Denmark

institute: University of Copenhagen

description: Ion Proton platform using Ion PIChip Kit v.3

data_processing:
library strategy: RiboMeth-Seq
Reads per sequencing barcode de-multiplexed using a python script
Adaptor trimming using Cutadapt v. 1.2.1
Mapping to rRNA reference sequence using Bowtie2 v. 2.1.0
Counting of 5' and 3' read ends and calculation of RiboMeth-seq scores performed using RMS analysis python script
Assembly: Human 18S and 28S rRNA sequences, based on Human ribosomal DNA complete repeating unit (gi|555853|gb|U13369.1|HSU13369 and gi|555853|gb|U13369.1|HSU13369), corrected according to high-depth sequecing coverage as defined previously in Krogh, N. and Jannson, M. et al. Profiling of 2'-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity. Nucleic acids research 44, 7884–7895 (2016).
Supplementary files format and content: Microsoft Excel files containing 5' and 3' read counts and the calculated RMS score at each nucleotide position the 18S and 28S rRNA sequences for each of three replicate RMS libraries. 2´-O-methylated rRNA psoritons (Nm), corresponding C/D box snoRNA guide RNAs (SNORD), mean RMS score and SD for each rRNA position are also given.

source_name: HEK293T cells

growth_protocol: SH-SY5Y and HEK293T cells were grown in Dulbecco’s modified Eagle’s medium containing L-glutamine and 4.5 g/L glucose (DMEM; Lonza) and supplemented with 10% fetal calf serum (Gibco) and antibiotics (100 U/ml penicillin, 100 µg/ml streptomycin (Sigma-Aldrich)) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was isolated using the Quick-RNA MiniPrep Kit (Zymo Research, R1055) according to the manufacturer's protocol.
RiboMeth-seq library construction and sequencing were performed as previously described in Krogh, N. and Jannson, M. et al. Profiling of 2'-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity. Nucleic acids research 44, 7884–7895 (2016). Briefly, triplicate libraries were produced for each cell line or condition analysed grown to ∼70–80% confluence before harvest. 4–5 µg of total RNA or purified 18S and 28S subunit rRNA (combined at 1:2.6 weight ratios to give approximate 1:1 molar ratio) were used for input. RNA was partially degraded in alkaline at denaturing temperatures. The 20–40nt fragments were purified by polyacrylamide gel electrophoresis and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2′,3′ cyclic phosphate and 5′-phosphate ends. The libraries were sequenced on the Ion Proton platform using Ion PI™ Chip Kit v3 (Life Technologies).

treatment_protocol: SH-SY5Y wild-type, FUS KO, and FUS R495X cells were subjected to retinoic acid (RA) treatment for 10 days. All-trans RA (USP, Tretinoin, 1674004) at a final concentration of 75 µM was added to DMEM with 10% FBS. The media, along with the RA, were replaced every 3 days.

value: HEK293T cells

value: immortalised human embryonic kidney cells

value: wild-type or FUS knock-out


title: acc.10012.rep2

description: 125bp PE


title: shCONT_H3K27ac

value: Glioblastoma stem cells


title: acc.10012.rep1

description: 125bp PE


title: DGC3028_sh1_2

value: Differentiated glioblastoma cells

value: ECHS1 knockdown


title: Pool_S3

city: Helsinki

first: Toni

last: Lemmetyinen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description: Samples 1-6 & 13-18

data_processing:
Quality library metrics were assed using multiqc tool (https://multiqc.info/).  Fastq files were aligned to the mouse reference genome (GRCm38) using STAR-aligner (v2.7.8a).Samples were demultiplex and count matrix of unique molecular identifier (UMI) counts was created using the CreateDGEMatrix command from the suite of tools BRB-seqToolsv1.4 (https://github.com/DeplanckeLab/BRB-seqTools). Barcode and treatment information is in the metadata_Nrg1 file.
Differential expression analysis was performed with Deseq2 package following the pipeline

source_name: intestinal crypts

growth_protocol: Intestinal crypts were mixed with ENR media containing 50 ng/ml of EGF (PMG8041, Gibco), 100 ng/ml of Noggin (250-38, Peprotech), 250 ng/ml of R-spondin 1 (3474-RS, R&D systems), 1 µM of n-acetylcysteine (A-5131, Sigma) and 10 µM of Y-27632 (Y0503, Sigma) which was used in culture media only for the first two days. Crypts in ENR media were mixed in 1:3 ratio with Matrigel (356231, Corning) before plating 20 µl domes to 48-well plates. Organoids were overlayed with ENR media for the first 3 days followed by removal of exogenous EGF for 24h and addition of EGF, EREG or NRG1 to the culture medium for 24 hours prior to the RNA isolation.

extract_protocol:
Organoids in Matrigel were lyzed and RNA was extracted with Nucleospin RNA II isolation kit (Macherey-Nagel).
3’UTR RNAseq ”Bulkseq” is based upon Dropseq method for single-cell sequencing (Macosko et al. 2015) Saavalainen group at the University of Helsinki then developed methodology for sequencing from total RNA (Freitag et al. 2020). Method involves priming mRNA with an oligo dT primer which also contains a 12 bp “Cell barcode” and an 8 bp UMI sequence which can be used to remove PCR duplicates during data analysis. Single-stranded cDNA is then converted to ds cDNA using the template switch effect and double-stranded cDNA product is then amplified with PCR and another set of primers (SMART PCR primer). The number of PCR cycles used (9-20x) depends upon the quality and starting amount of RNA. Samples are then pooled together and PCR sequencing pools are made with Nextera i7 primers and the Dropseq P5 primer. Sequencing is then performed on the NextSeq High Output 75 cycle flow cell on the NextSeq 500 to produce (Read 1: 20 bp, Index 1 (i7): 6 bp and Read 2 (61 bp).

treatment_protocol: EGF (R&D Systems 236-EG-200), NRG1 (R&D Systems 5898-NR) and EREG (R&D Systems 968-EP-050) were used at 100ng/ml

tag: model

value: organoids

tag: strain


title: sample36

city: Lille

first: Vance

last: Gao

address: 1 Rue du Professeur Calmette

country: France

institute: Institut Pasteur de Lille

data_processing:
Libraries were aligned to the human genome (hg38) using STAR.
Low-quality reads (mapq<15) were excluded from downstream analysis.
Read counts per gene were obtained with HOMER2’s analyzeRepeats.pl script using default settings and reporting raw read counts.
Log counts normalized for sequencing depth were created using the "DESeq" and "rlog" functions in the DESeq2 R package.
Genome_build: hg38
Supplementary_files_format_and_content: "Counts RefSeq.txt" - Read counts of RefSeq sequences. Tab-delimited file
Supplementary_files_format_and_content: "Log counts Genes.txt" - Normalized, log counts generated by DESeq2. Collapsed to gene symbols by taking the highest RefSeq count for each gene. Tab-delimited file

source_name: monocytes

growth_protocol: Monocytes in circulating blood of cardiopulmonary bypass surgery patients (median age 70), collected before surgery

extract_protocol:
Classical CD14++ CD16- monocytes were sorted from blood (PBMC). Total RNA was extracted using the Direct-Zol RNA Microprep kit with on-column DNaseI treatment (Zymo Research). Whole transcriptome amplification and cDNA synthesis were performed with the Ovation RNA-seq V2 kit (NuGEN) following the manufacturer’s instructions.
Sequencing libraries were prepared using the Ovation Ultralow V2 DNA-seq Library preparation kit. Libraries were pooled and sequenced on a HiSeq4000 (Illumina) to obtain 20 million single-end 50bp reads.

tag: ChIP

value: FALSE


title: DGC23_sh1_1


title: sample35

value: TRUE


title: Rbbp4-AID 0h_rep2

value: embryonic stem cells

value: Rbbp4-AID, Tir1


title: keratinocytes from the dorsal skin of control mice treated with water, Day5 [Ctrl_H2O_2]

city: Zhunan Town

first: Liang-Tung

last: Yang

state: Miaoli County

address: No. 35, Keyan Road

country: Taiwan

institute: National Health Research Institutes

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (V 0.38) to obtain clean reads  (parameters - LEADING：3、TRAILING：3、SLIDINGWINDOW：4：20、MINLEN：36)
Clean reads  were mapped to GrCM38/mm10 using HISHAT2 (v2.1.0)
Gene expression in raw raed counts were quantified using featureCount (v2.0.0)
Data normalization and differential expression analysis were performed using DEseq2 (1.26.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: back skin epidermis

extract_protocol:
The mouse dorsal epidermis was separated from the dermis by treatment with 2.5 U/mL displase in HBSS for 3 hours at 37 oC, then keratinoocytes were isolated by Trysin-EDTA (0.25%, Invitrogen) treatment at 37 oC for 10 min.  Total RNA from keratinocytes was isolated using NucleoSpin RNA mini kit (MACHEREY-NAGEL, CO.) according to the manufacturer's protocol.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Control and Gsdma1/a3 epitheial knockout mice after topical acetone/olive oil 4:1 (AOO) or water on dorsal skin rubbing twice a day for 3 days

value: back skin epidermis

value: keratinocytes

value: wild type

value: water


title: SH-SY5Y WT DIFF 1-3 & FUSKO DIFF 1

value: thrice-cloned sub-line of bone marrow biopsy-derived line SK-N-SH

value: Differentiation using Retinoic Acid for 10 days


title: DGC3028_ctrl_2

value: Glioblastoma

value: WT

value: shCONT


title: DGC23_sh1_2


title: keratinocytes from the dorsal skin of Gsda1a3eKO mice treated with water, Day5 [Mut_H2O_2]


title: keratinocytes from the dorsal skin of control mice treated with olive oil-acetone, Day5 [Ctrl_AOO_3]

value: olive-oil/acetone


title: SH-SY5Y WT PROLI 1-3 & FUSKO PROLI 1-3

value: wild-type or FUS knock-out


title: SH-SY5Y R495X DIFF 1

value: FUS R495X


title: DGC3028_ctrl_1

value: Differentiated glioblastoma cells


title: GSC3028_2mM_2

value: Glioblastoma stem cells

value: 2mM Lysine


title: GSC3028_2mM_1


title: keratinocytes from the dorsal skin of Gsda1a3eKO mice treated with water, Day5 [Mut_H2O_1]


title: LN18_LSD1KD_A

value: glioblastoma cells

value: LSD1 KD


title: sample38

value: TRUE


title: DGC23_sh2_2

value: ECHS1 knockdown


title: sample37


title: DGC23_sh2_1


title: keratinocytes from the dorsal skin of Gsda1a3eKO mice treated with olive oil-acetone, Day5 [Mut_AOO_3]

value: back skin epidermis

value: keratinocytes


title: Pool_S4

description: Samples 7-12

value: organoids


title: Mc5r-/- LSKs, rep3

city: Chongqing

first: Naicheng

state: Chongqing

address: Gaotanyan Street 30

department: College of Preventive Medicine

institute: Third Military Medical University

description: Isolation of hematopoietic stem cells from Mc5r knock out mouse bone marrow

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
RNA-seq reads were aligned to the GRCm38 genome assembly using Hisat2 (Hierarchical Indexing for Spliced Alignment of  Transcripts, version 2.0.5).
Gene abundance was expressed as fragments per kilobase of exon per million  reads mapped (FPKM). Stringtie software was used to count the fragment within each gene,  and TMM algorithm was used for normalization
Differential expression analysis for RNA was performed using R package edgeR（3.4.3）.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: Bone marrow

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany), after which the RNA concentration and quality were determined by the Qubit®3.0 Fluorometer (Life Technologies, USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA). Integrity of total RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA), and samples with RNA integrity number (RIN) values above 7.0 were used for sequencing.
Paired-end libraries were synthesized by using the Stranded mRNA-seq Lib Prep Kit for lllumina (ABclonal, China) following Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 10 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 3.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA). The library construction and sequencing were performed by Sinotech Genomics Co., Ltd (Shanghai, China).

value: Bone marrow

value: hematopoietic stem cells

value: stem cells

value: Mc5r mutant


title: LN18_LSD1KD_B


title: Mc5r-/- LSKs, rep1


title: GSC23_2mM_1

value: Glioblastoma


title: keratinocytes from the dorsal skin of Gsda1a3eKO mice treated with olive oil-acetone, Day5 [Mut_AOO_1]

value: olive-oil/acetone


title: sample34

value: FALSE


title: keratinocytes from the dorsal skin of Gsda1a3eKO mice treated with olive oil-acetone, Day5 [Mut_AOO_2]


title: DGC23_ctrl_1

value: Differentiated glioblastoma cells

value: WT

value: shCONT


title: sample33


title: keratinocytes from the dorsal skin of control mice treated with olive oil-acetone, Day5 [Ctrl_AOO_2]

value: wild type


title: Wild type LSKs, rep3

description: Isolation of hematopoietic stem cells from littermate Wild type mouse bone marrow

value: Wild type


title: sample31

value: TRUE


title: DGC23_ctrl_2


title: GSC23_0.2mM_1

value: Glioblastoma stem cells

value: 0.2mM Lysine


title: Mc5r-/- LSKs, rep2


title: sample23


title: GSC3028_0.2mM_2


title: GSC3028_sh2_2

value: GCDH knockdown


title: sample30


title: sample20


title: sample32


title: keratinocytes from the dorsal skin of control mice treated with water, Day5 [Ctrl_H2O_1]

value: back skin epidermis

value: keratinocytes

value: water


title: Rpl3l KO heart disome-seq replicate 2-2

first: Kazuya

institute: Nagoya University

data_processing:
Adaptor sequences were trimmed from raw reads with the use of cutadapt.
Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit.
Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCm38.p6) and human genome (mm10) also with the use of STAR.
Read counting was performed with the use of featureCounts.
Assembly: mm10
Supplementary files format and content: Counts per transcript
Library strategy: disome-seq

source_name: Heart

growth_protocol: C2C12 (CRL-1772) cells were obtained from American Type Culture Collection and were checked for mycoplasma contamination with the use of MycoAlert (Lonza). The cells were cultured under an atmosphere of 5% CO2 at 37°C in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (Life Technologies) and antibiotics.

extract_protocol:
C2C12 cells were lysed with a lysis buffer [50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, 1 mM dithiothreitol, 1% Triton X-100, and EDTA-free protease inhibitor cocktail] supplemented with cycloheximide (100 μg/ml). The heart tissues were flash frozen in liquid nitrogen and lysed in a lysis buffer with the use of Multi beads shocker (YASUI KIKAI). The lysates were centrifuged at 20,380 × g for 10 min at 4°C, and the resulting supernatants were collected, assayed for RNA concentration with a Qubit RNA BR Assay Kit (Thermo Fisher Scientific), incubated with RNase I (20 U per 10 μg of RNA, Epicentre) for 45 min at 25°C, and placed on ice before the addition of SUPERase•In RNase inhibitor (Invitrogen). The samples were then loaded on a 1 M sucrose cushion [containing 20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, SUPERase•In (10 U/ml), 1 mM dithiothreitol, and cycloheximide (100 μg/ml)], and the gradients were centrifuged at 100,000 rpm (417,200 × g) for 1 h at 4°C in a Beckman TLA110 rotor. The resulting pellets were suspended in ribosome splitting buffer [20 mM Tris-HCl (pH 7.5), 300 mM NaCl, 5 mM EDTA, SUPERase•In (20 U/ml), 1 mM dithiothreitol, and 1% Triton X-100] and subjected to purification with the use of an Amicon Ultra filtration device (100-kDa cutoff, Millipore) to deplete rRNAs.
The purified RNA was subjected to selection on the basis of a size range of 17 to 34 nt for Ribo-seq and 50 to 80 nt for Disome-seq by electrophoresis through a 15% polyacrylamide and Tris-borate-EDTA (TBE)–urea gel (SuperSep RNA, Fujifilm). The footprint fragments were treated with T4 polynucleotide kinase (New England Biolabs) to repair the 2'-3' cyclic phosphates, a DNA linker including barcode sequences (NI-810 to NI-817) was ligated with the use of T4 RNA ligase 2, truncated K227Q (New England Biolabs), and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. Ribosomal RNAs were further depleted with the use of RiboZero Gold (Illumina). Reverse transcription (RT) was performed with the NI-802 primer, and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. The purified cDNAs were circularized with circLigase II (Lucigen), and index sequences were then added by amplification with the polymerase chain reaction (PCR) as performed with the common primer (NI-798) and primers including index sequences (NI-799 and NI-822 to NI-826). Products of the desired size were purified on a 15% polyacrylamide nondenaturing gel (SuperSep DNA, Fujifilm), and the libraries were sequenced with a NovaSeq 6000 system (Illumina).

value: Rpl3l KO


title: GSC3028_0.2mM_1


title: Rpl3l KO heart disome-seq replicate 3-2


title: sample19


title: Rpl3l KO heart disome-seq replicate 1-2


title: GSC3028_ctrl_1


title: WT heart disome-seq replicate 4-2


title: GSC23_2mM_2

value: 2mM Lysine


title: sample28


title: sample26


title: keratinocytes from the dorsal skin of control mice treated with olive oil-acetone, Day5 [Ctrl_AOO_1]


title: Wild type LSKs, rep1

value: Bone marrow

value: hematopoietic stem cells

value: stem cells


title: Wild type LSKs, rep2


title: sample22

value: FALSE


title: sample25


title: GSC23_sh1_1

value: Glioblastoma


title: GSC3028_sh2_1


title: Rpl3l KO heart disome-seq replicate 3-1


title: sample21


title: sample10


title: sample11


title: GSC23_0.2mM_2


title: Rpl3l KO heart disome-seq replicate 4-2


title: sample24


title: GSC3028_sh1_2


title: GSC3028_sh1_1


title: GSC3028_ctrl_2

value: WT

value: shCONT


title: sample14


title: WT heart disome-seq replicate 3-2


title: Rpl3l KO heart disome-seq replicate 4-1


title: Knockout 4 [KO_8]

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Sequencing reads were trimmed of adapters and filtered
STAR alignment was performed against mouse reference
Quantification of reads was determined by Novogene
DEG analysis was performed with DeSeq2
clusterProfiler was used to perform enrichment analyses
Assembly: mm10
Supplementary files format and content: Excel file containing results of DEG, raw counts, and FPKM counts

growth_protocol: Mice were housed at animal facilities at the National Institutes of Health, Bethesda and Frederick, MD. Animal handling was conducted in accordance with the ACUC, under protocol number 21-018.

extract_protocol:
RNA isolation was performed with a Qiagen tissue RNA isolation kit, then tested via an Agilent BioAnalyzer analysis.
Illumina paired-end total RNA-seq

treatment_protocol: All mice were age matched (20-25 weeks).

value: Heart

value: 20-25 weeks

value: ARE-/-


title: Knockout 3 [KO_7]


title: WT heart disome-seq replicate 2-1

city: Chikusa-ku, Nagoya, Aichi

address: Furo-cho


title: GSC23_sh2_2

value: Glioblastoma stem cells


title: GSC23_sh2_1

value: GCDH knockdown


title: sample06


title: sample12

value: TRUE


title: WT heart disome-seq replicate 2-2


title: sample13


title: WT heart disome-seq replicate 1-2


title: sample17


title: GSC23_sh1_2


title: Wildtype 4 [WT_6]


title: Rpl3l KO heart disome-seq replicate 2-1


title: sample09


title: sample01