title: DG from 5N1 [LID_100757]

source_name: dentate gyrus

value: female


title: CA3 from 7L0 [LID_100751]

status: Public on Sep 26 2022

type: SRA

city: Tempe

first: Kenneth

last: Chiou

state: AZ

address: 427 E Tyler Mall

department: Center for Evolution and Medicine

country: USA

institute: Arizona State University

library_source: transcriptomic

data_processing:
Gene expression counts were quantified from RNA-seq reads using the pseudoalignment method implemented in kallisto.
Estimated counts and transcripts-per-million (TPM) values were then imported into R v4.0.2 and summarized to genes using the tximport package.
Genome_build: rhesus macaque reference genome (Mmul_10)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with transcripts per million (TPM) values for every gene and every sample

molecule: polyA RNA

organism: Macaca mulatta

source_name: cornu ammonis 3

growth_protocol: free-ranging population

extract_protocol:
Total RNA was extracted using a TRIzol-chloroform gradient followed by column isolation of RNA using the Quick-RNA Microprep kit (Zymo Research). Briefly, 1 ml of TRIzol (Invitrogen) was added to each 2-ml sample tube, along with a sterile 5-mm stainless steel grinding bead (QIAGEN cat. no. 69989). Samples were then homogenized using the Tissuelyser II system (QIAGEN) at 20 Hz in two sets of 2 minutes each, with rotation in between, and the lysate transferred to a new tube. 200 µl of chloroform were added to each sample, which was then vortexed at full speed for 15 seconds and incubated at room temperature for 2 minutes. The sample was then centrifuged at 12,000 × g for 15 minutes at 4°C. After centrifugation, the aqueous layer was transferred to a new tube and mixed with 600 µl of 70% ethanol to precipitate RNA. The resulting solution was transferred to Quick-RNA Microprep columns (Zymo Research). The remainder of the protocol followed manufacturer instructions for the Quick-RNA Microprep kit. Total RNA was eluted in 60 µl of RNase-free water.
We prepared bulk RNA-seq libraries using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) with an initial mRNA isolation step using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). We followed manufacturer instructions and guidelines for library preparation using these kits. We used 200 ng of starting RNA and set the enzymatic fragmentation time (10 minutes), first-strand synthesis incubation time (50 minutes at 42°C), and bead cleanup volume ratios for a target insert size of 400 bp. Libraries were amplified using 10 cycles of PCR and eluted in a final volume of 20 µl of RNase-free water. Libraries were quantified by Qubit 3 using the Qubit DNA HS Assay kit (Invitrogen) and library quality was assessed using the Fragment Analyzer HS NGS kit (AATI/Agilent). Libraries were pooled in equimolar quantities prior to sequencing.

treatment_protocol: Following veterinary euthanasia, a necropsy was immediately performed during which the brain was perfused by transcardial perfusion with sterile saline. The brain was then removed from the cranium and sagittally sectioned into left and right hemispheres. The left hemisphere was fixed in 10% formalin and not used for this study. The right hemisphere was further sectioned prior to cryopreservation. First, the cerebellum was separated from the cerebrum. The cerebrum was then placed on a custom mold and sectioned coronally into 11 ~0.5 cm-thick slices. All 12 slices (including the cerebellar hemisphere) were individually stored in Whirl-pak bags and flash frozen in a dry-ice/ethanol bath immediately before storage in ultralow (-80°C) freezers. Regions of interest were dissected in sterile, RNase-free conditions on dry ice to minimize RNA degradation. Six 1-mm tissue biopsies were then collected by biopsy punch.

tag: individual id

tag: tissue

value: cornu ammonis 3

tag: age

tag: Sex

tag: dominance rank

value: low


title: HepG2 spheroid, NaBut treated, day 10, replicate 1

city: Bronx

first: Ronald

last: Cutler

state: NY

address: 1925 Eastchester Road, Apt 20D, Apt 208

institute: Albert Einstein College of Medicine

data_processing:
Raw reads were trimmed to remove low quality base calls and Illumina universal adapters using Trim Galore! (Version 0.6.5) with default parameters and then assessed using fastQC (version 0.11.4) and multiqc (version 1.10.1).
Reads were then aligned to the human genome (GRCh38) using STAR with default parameters. Alignment quality control was performed using RSeQC and Qualimap.
Quantification was performed using RSEM. Quantification quality control was performed using EDASeq (version 2.3) and NOISeq (version 2.4).
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include length effective_length, expected_count, TPM, and FPKM for each sample

molecule: total RNA

organism: Homo sapiens

source_name: HepG2 spheroid

growth_protocol: HepG2 spheroids were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM, containing 4.5g/L glucose) supplemented with 10% Fetal Bovine Serum (FBS), 1% Non-Essential Amino Acids, 1% GlutaMAX and 0.5% Penicillin/Streptomycin (all Corning). Spheroids were kept in a controlled atmosphere (5% CO2 incubator at 37C) in ClinoReactors. Optimal growth conditions were achieved by exchanging media three times a week and adjusting rotation speed according to spheroids growth.

extract_protocol:
5 spheroids stored at -80C were thawed on ice and then mechanically homogenized. RNA was extracted using an RNeasy micro kit (Qiagen).
RNA libraries for RNA-seq were prepared by Novogene lncRNA seqeucning service

treatment_protocol: After 24 h, growth media was replaced by growth media containing 20 mM of NaBut for the treatment group while the non-treated group received growth media only. Spheroids and flat cells were treated for 3 days and, after collection, the treatment media was replaced by the standard growth media and spheroids were maintained for additional 7 days, until the last collection on day 10.

value: HepG2 spheroid

tag: cell line

tag: cell type

value: hepatocellular carcinoma

tag: genotype

value: WT

tag: treatment

value: NaBut

tag: time

value: day 10


title: Ctrl2-iRFP-Low

city: New York

first: Hani

last: Shayya

state: New York

address: 3227 Broadway

department: Biochemistry and Mol Biophysics

institute: Columbia University

data_processing:
Transcript annotations were downloaded from Ensembl (GRCm38, Ensembl version 92). Extended OR gene models were included from Ibarra-Soria et al., PLOS Genetics, 2014. The coding sequence for each extended OR gene model was annotated based on the Ensembl annotations for that OR. Only transcripts from a localized contig and containing an annotated coding sequence were retained in the final transcript set.
A fasta file of transcript sequences was generated using the GRCm38 (mm10) sequence, the above annotation set and custom python scripts. Sequences were indexed using salmon (verson 0.13.1, -k 31).
Demultiplexed fastq files were quantified against the reference transcriptome using Salmon (version 0.13.1, --libType A, --seqBias, --gcBias, --validateMappings).
Assembly: mm10
Supplementary files format and content: Tab-delimited quant.sf files generated by Salmon. Each row is a transcript (ENSMUST = Ensembl transcripts, CUFFORT = extended OR gene models, egfp/tdtomato/lacZ as above). Columns indicate Length (nt), EffectiveLength (as modeled by Salmon), TPM (abundance in transcripts per million) and NumReads (expected number of reads originating from each transcript).

organism: Mus musculus

source_name: Olfactory epithelium

extract_protocol:
For experiments on OSN developmental populations (INPs, iOSNs, mOSNs), cells were sorted across multiple days, pelleted (10 minutes at 800g) and frozen at -80 until the day of extraction. Lysates were prepared from roughly 1e6 cells per condition using a lysis buffer (20mM Tris pH=7.5, 150mM NaCl, 5mM MgCl2, 1mM DTT, 100ug/mL cycloheximide, 1%(v/v) Triton X-100 and 25U/mL TURBO DNAse), RNA was quantified by Quant-iT RiboGreen assay (Thermo Fisher) and lysate containing 100ng of RNA was mixed with 300uL of Trizol (Invitrogen). In all other experiments, 10-20k cells were sorted directly into 500uL of Trizol LS (Sigma). RNA was recovered from Trizol using the Direct-Zol RNA Miniprep kit (Zymo), precipitated overnight with 300mM sodium acetate and 1.5 volumes of isopropanol, digested for 30min at 37°C with TURBO DNAse (Invitrogen) and cleaned up on 1.8x Ampure Beads (Beckman Coulter). <10ng RNA was used for library prep, as measured by Quant-iT RiboGreen assay.
Libraries were prepared using the SMARTER Stranded Total RNA-seq Kit v2 - Pico Input Mammalian (Takara Bio) and the manufacturer’s instructions.

treatment_protocol: Mice were sacrificed by decapitation (if younger than postnatal day 14) or CO2 followed by cervical dislocation, and the main olfactory epithelium (MOE) was isolated by dissection into ice-cold 1xPBS without calcium or magnesium. Single-cell suspensions were prepared using a papain dissociation system (Worthington) following a modified version of the manufacturer’s protocol. Dissociations were for 30-45 minutes at 37°C, centrifugation steps for 5min at 400g and the discontinuous density gradient was not performed. Cells were re-suspended for FACS in a buffer containing 2%FBS (Gibco), 5mM MgCl2, DAPI (1:10k, Invitrogen) and the remaining DNAase I from the dissociation kit. For experiments where iRFP intensity was measured to determine stress levels in mice containing the Atf5-reporter allele, cycloheximide (Sigma, 100µg/mL) was added to all solutions during dissociation and cytometry to block new protein synthesis and minimize the effects of dissociation or sorting-related stress on these measurements. Dissociated cells were filtered through a 40µm cell strainer and analyzed on a Beckman Coulter MoFlo Astrios EQ sorter.

value: Olfactory epithelium

value: iOSN

value: Atf5(rep/+); Omp(iresGFP/+)


title: Ctrl2-iRFP-High


title: vehicle treated xenograft cells_2

city: Gothenburg

first: Cleas

middle: M.

last: Gustafsson

address: Medicinaregatan 9A

department: medical biochemistry and cell biology

country: Sweden

institute: university of Gothenburg

data_processing:
Reads were aligned to hg38 genome using Hisat2 version 2.2.1.
Number of reads mapping to each feacher were calculated using htseq-count version 0.12.4.
Assembly: Hg38
Supplementary files format and content: tab-delimited text files including raw counts for each sample.

source_name: vehicle treated xenograft cells

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen). RNA was processed as per manufacturer’s instructions.
RNAseq library preparation and RNA-sequencing was done using the SMARTer Total Stranded RNA pico kit.

value: bone marrow

value: leukemic

value: TP53 mutant

value: placebo


title: Ctrl1-iRFPGFP-Low

value: mOSN


title: HepG2 spheroid, NaBut treated, day 3, replicate 2

value: day 3


title: HepG2 spheroid, NaBut treated, day 3, replicate 3


title: CA3 from 9N0 [LID_100750]

value: female

value: high


title: CA3 from 1B7 [LID_100749]

value: cornu ammonis 3

value: male


title: Cartilage, WT

city: New Orleans

first: Yi-Ping

last: Li

state: LA

address: 1441 Canal St, Room 318

department: Pathology and Laboratory Medicine

institute: Tulane University School of Medicine

data_processing:
RNA-seq was performed using Illumina MiSeq (performed by Admera Health, LLC (South Plainfield, NJ)). The FASTQ files were checked for quality using FastQC (v0.11.3). STAR (v 2.0) with reference genome (Mouse, mmo) and annotation file (UCSC) were used for sequence alignment.
Assembly: mm0
Supplementary files format and content: Text file contains gene expression count

source_name: Cartilage

growth_protocol: Primary calvarial osteoblasts were isolated from newborn mice and BMSCs and seeded in culture at 3×10^3 cells per square centimeter.

extract_protocol:
Total mRNA was isolated using TRIzol reagent (Invitrogen Corp., Carlsbad, CA) from the osteoblasts or cartilage following the manufacturer's protocol
Admera Health (South Plainsfield, NJ) prepared the library using the NEBnext Ultra RNA—Poly-A kit.

treatment_protocol: After growing to confluence, calvarial were induced to differentiate into osteoblasts using osteogenic medium and BGJb medium (Gibco, 12591) supplemented with 10% (vol/vol) FBS, 50 μg/mL L-ascorbic acid (Sigma, A4544), and 5 mM β-glycerolphosphate (Sigma, G9891).

value: Cartilage


title: Osteoblasts, Runx1f/f;Twist2-cre, biol rep 2

source_name: Calvarial cells

value: Calvarial cells

value: osteogenic differentiation

value: 14 Days


title: Ctrl1-iRFPGFP-High

value: Olfactory epithelium


title: Cartilage, Runx1f/f;Col2α1-Cre


title: Ctrl1-iRFP-Low

value: iOSN


title: CA3 from 4N8 [LID_100748]

value: mid


title: HepG2 spheroid, NaBut treated, day 3, replicate 1

value: HepG2 spheroid

value: hepatocellular carcinoma

value: WT

value: NaBut


title: Ctrl1-iRFP-High

value: Atf5(rep/+); Omp(iresGFP/+)


title: Osteoblasts, Runx1f/fCol1α1-Cre, biol rep 1


title: Osteoblasts, Runx1f/fCol1α1-Cre, biol rep 2


title: WT_3

city: Hamburg

first: Cloe

last: de Luxán-Hernández

state: Hamburg

address: Ohnhorststraße 18

department: Molecular Plant Physiology

country: Germany

institute: University Hamburg

data_processing:
Base calling was performed with Alta-Cyclic (Erlich et al., 2008)
Quality control: Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Mapping against the Arabidopsis TAIR10 reference genome was performed using the HISAT2 software.
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Alternative splicing (AS) analysis was performed with the rMATS software.
Genome_build: TAIR10
Supplementary_files_format_and_content: Matrix table with gene counts and fkpm values for every gene and sample

organism: Arabidopsis thaliana

source_name: 12-day old complete seedlings

growth_protocol: Plants were grown on Murashige and Skoog (MS) plates containing 1% sucrose and 1% (w/v) agar in growth chambers (16 h light, 22°C/ 8 h dark, 18°C cycles) during 12 days.

extract_protocol:
Total RNA was extracted from 3 different biological replicates containing 12-day-old seedlings of WT and mdf-1 using the innuPREP Plant RNA kit (Analytik Jena Bio solutions). 1 ug of total RNA for the construction of sequencing libraries.
Library was prepared with the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB) following the manufacturer’s recommendations.

value: wild type


title: HepG2 spheroid, NaBut treated, day 2, replicate 2

value: day 2


title: CA3 from 5N1 [LID_100747]

value: female


title: CA3 from 60T [LID_100746]

value: cornu ammonis 3

value: low


title: Osteoblasts, Runx1f/f, biol rep 2


title: WT_2


title: CN from 9C6 [LID_100745]

source_name: caudate nucleus

value: caudate nucleus

value: male


title: HepG2 spheroid, NaBut treated, day 2, replicate 1


title: HepG2 spheroid, NaBut treated, day 1, replicate 3

value: day 1


title: WT_1


title: CA3 from 4N7 [LID_100744]

value: high


title: HepG2 spheroid, NaBut treated, day 1, replicate 2


title: CA3 from 2E9 [LID_100743]


title: Osteoblasts, Runx1f/f, biol rep 1

value: Calvarial cells

value: osteogenic differentiation

value: 14 Days


title: eiCLIP_sample3

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description: RNA bound to Rbfox2

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
Each raw read from the eiCLIP experiment contains a random barcode sequence in the first 7 nucleotides, where the 8th nucleotide is an A. The random barcode was moved to the header of the FASTQ file for the later removal of PCR duplicates and the 8th nucleotide was removed from the read sequence.
For the adapter removal of eiCLIP sequencing samples, we used ‘cutadapt’ tool (https://cutadapt.readthedocs.io/en/stable/) with the following parameters: ‘cutadapt -f fastq --match-read-wildcards --times 1 -e 0.1 -O 1 --quality-cutoff 6 -m 18 -a AGATCGGAAG $INPUT.fastq > $OUTPUT.adapterTrim.fastq 2> $OUTPUT.adapterTrim.metrics’.
eiCLIP samples were aligned to GENCODE assembly annotation version ‘GRCm38.VM20’ by STAR alignment tool (version 2.4.2a) (https://github.com/alexdobin/STAR) with the following parameters: ‘STAR –runThreadN 8 –runMode alignReads –genomeDir GRCm38 Gencode v20 –genomeLoad LoadAndKeep –readFilesIn read1, read2, –readFilesCommand zcat –outSAMunmapped Within –outFilterMultimapNmax 1 –outFilterMultimapScoreRange 1 –outSAMattributes All –outSAMtype BAM Unsorted –outFilterType BySJout –outFilterScoreMin 10 –alignEndsType EndToEnd –outFileNamePrefix outfile’.
For the overamplification correction of the eiCLIP samples we used a custom python script to swap random barcodes from the first 7 nts of the FASTQ sequence line to the FASTQ header line. Uniquely mapped reads with the same genomic positions and the same random barcode were then removed as PCR duplicates. At each cDNA-start position, the counts of all cDNAs were summed together and converted into in bedGraph format using a custom python script, where each number represents a unique number of crosslinking positions.
Then crosslink clusters were defined by using the cDNA-starts with counts as the input for False Discovery Rate clustering tool available by iMaps (https://imaps.genialis.com/iclip). The clusters were identified by using default parameters and Paraclu clustering algorithm (http://cbrc3.cbrc.jp/~martin/paraclu/).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph and BED6 format

source_name: Primary Mouse Hepatocytes

extract_protocol:
RNA was extracted as described and isolated with Rbfox2 antibody (RBM9 - Bethyl Laboratories). The protocol differed from the iCLIP protocol published previously (Sibley et al 2018. Individual Nucleotide Resolution UV Cross-Linking and Immunoprecipitation (iCLIP) to Determine Protein–RNA Interactions. In: Gaspar I. (eds) RNA Detection. Methods in Molecular Biology, vol 1649. Humana Press, New York, NY) by the following: The adaptor contains index 1 rather than the RT-primers thus allowing multiplexing of samples after adapter ligation. Excess adaptor is removed using recjf-deadnylase. RNA purification is carried out by column rather than overnigh ethanol precipitation. RT primer binds to the 3' of the adaptor and has a biotin attached enabling cDNA purification by Streptavidin beads. Free RT primer is ligated with a complementary primer and digested by exonuclease. There is no requirement for a ciruclarisation step. A solexa adaptor primer binds to the RT primer in advance of library preparation.
Library is constructed using Accuprime Supermix I  and P5/P7 solexa primer mix. The P5/P7 primers are also indexed with independent barcodes. 22 cycles of PCR were used in this extraction method. Size selection of the cDNA occurs after library preparation using a zymogen select-a-size kit. The P7 primer has phosphthioate bonds between the last three nucleotides of the primer.

tag: strain

value: Liver

tag: number of livers

tag: number of pellets

tag: rip antibody


title: Osteoblasts, Runx1f/f;Twist2-cre, biol rep 1


title: mdf_1_3


title: HepG2 spheroid, NaBut treated, day 2, replicate 3

value: HepG2 spheroid

value: hepatocellular carcinoma


title: eiCLIP_sample2

description: RNA bound to Rbfox2

value: Rbfox2 antibody (RBM9 - Bethyl Laboratories)


title: CN from 3A9 [LID_100742]


title: HepG2 spheroid, control, day 10, replicate 3

value: WT

value: control

value: day 10


title: eiCLIP_sample1

description: RNA bound to Rbfox2


title: CA3 from 94S [LID_100741]

value: female


title: HepG2 spheroid, control, day 10, replicate 2


title: CN from 7L0 [LID_100739]


title: HepG2 spheroid, control, day 10, replicate 1


title: HepG2 spheroid, control, day 3, replicate 3

value: day 3


title: CA3 from 7L7 [LID_100738]

value: cornu ammonis 3

value: mid


title: mdf_1_2


title: GEM

city: Seoul

first: Duk Ki

last: Kim

address: Daehakro 103

country: South Korea

institute: Seoul National University of Hospital

description: Single cell RNA sequencing data

data_processing:
HiSeq platform (Illumina) with a read length of 28 bp for read 1 (cell barcode and UMI), 8 bp index read (sample barcode), and 91 bp for read 2 (RNA read)
the Cell Ranger toolkit provided by 10X Genomics was applied to align reads and produce the gene-cell unique molecular identifier (UMI) matrix using the reference genome GRCm38.
Genome_build: GRCm38.
Supplementary_files_format_and_content: Cell ranger output

source_name: Whole live cells of Pan02 tumor

growth_protocol: After Pan02 cancer cell injection to pancreas of mice, all mice were housed in a ventillated temperature-controlled environment (median temperature 23C, humidity 65%), under a 12-hour light/dark cycle, with a free access to food and water. Mouse cages were changed weekly.

extract_protocol:
After sacrificng mice, tumors were resected from mice, and digested with Dnase, Hyaluronidase, Collagenase. Digested tissues were minced, filtered through a 70-um cell strainer, and made into single-cell suspensions. Single-cell suspensions prepared from Pan02 samples were stained with a Live/Dead fixable dye and sorted by live cells using a BD Aria III sorter.
Libraries were prepared using the Chromium controller according to the 10X Single Cell 3' v3 protocol (10x Genomics). The cell suspensions were diluted in nuclease-free water to obtain a cell count of 10,000. The cell suspension was mixed with master mix and loaded with Single-cell 3? Gel Beads and Partitioning Oil into a Single-cell 3' Chip. Transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled, and the cDNA pool was subjected to end-repair, single "A" base addition, and adapter ligation. The products were then purified and enriched via PCR to create the final cDNA library. The purified libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA) and qualified using the Agilent Technologies 4200 TapeStation (Agilent Technologies).

treatment_protocol: Gemcitabine or Ate-Grab with Gemcitabine were injected to mice 5 times every 3 days after tumor size up to 50-100mm^3

value: FACS sorted live cells of Pan02 tumor treated with Gemcitabine

value: Gemcitabine


title: ATG+GEM

description: Single cell RNA sequencing data

value: FACS sorted live cells of Pan02 tumor treated with Ate-Grab+Gemcitabine

value: Ate-Grab + Gemcitabine


title: HepG2 spheroid, control, day 3, replicate 2


title: HepG2 spheroid, NaBut treated, day 1, replicate 1

value: NaBut

value: day 1


title: CA3 from 5B6 [LID_100735]

value: high


title: CA3 from 8L6 [LID_100737]

value: male

value: low


title: HepG2 spheroid, control, day 3, replicate 1

value: HepG2 spheroid

value: hepatocellular carcinoma


title: HepG2 spheroid, control, day 2, replicate 3

value: WT

value: control

value: day 2


title: CA3 from 3A6 [LID_100734]


title: N5

city: ChangSha

first: Tang

last: Liu

state: Hunan

address: No. 139 Renmin Middle Road

department: Department of Orthopedics

country: China

institute: The Second Xiangya Hospital

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore
Trimmed sequence reads were mapped to Homo_sapiens GRCh37 using Tophat
The mapping reads were arranged using Cufflinks (http://cufflinks.cbcb.umd.edu/) to assemble transcripts and estimate their abundance
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: scar tissue approximately 4 mm in size at the bone nonunion site

extract_protocol:
We extracted total RNA using TRIzol reagent following the manufacturer’s protocol. The absorbance ratio at 260/280 nm (A260/A280) was measured using SmartSpec Plus to determine the concentration and purity of the isolated RNA. The integrity of the extracted RNA was confirmed using electrophoresis (1.5% agarose gel). The RNA was then transcribed into first-strand cDNA using the First-Strand cDNA Synthesis Kit (TAKARA) for performing gene expression analysis.
We used 3 μg RNA per sample for sample preparation. Following ribosomal RNA (rRNA) depletion, the RNA was fragmented and a cDNA library was constructed using the VAHTS Total RNA-seq (HMR) Library Prep Kit.


title: mdf_1_1


title: N14

source_name: normal healing fracture site

value: normal healing fracture site


title: CN from 5B6 [LID_100733]

value: caudate nucleus

value: female


title: N12


title: N10

source_name: scar tissue approximately 5 mm in size at the bone nonunion site


title: CA3 from 3A9 [LID_100732]

value: cornu ammonis 3


title: HepG2 spheroid, control, day 2, replicate 1


title: HepG2 spheroid, control, day 1, replicate 3


title: N2

source_name: scar tissue approximately 3 mm in size at the bone nonunion site


title: CA3 from 4J3 [LID_100740]

value: mid


title: HepG2 spheroid, control, day 1, replicate 2


title: CN from 4J0 [LID_100730]


title: STS from 9I5 [LID_100729]

source_name: superior temporal sulcus

value: superior temporal sulcus


title: HepG2 spheroid, control, day 2, replicate 2


title: HepG2 spheroid, control, day 1, replicate 1


title: MIA PaCa-2, CEBPD, 48h, 2

city: Amsterdam

first: C.

middle: Arnold

last: Spek

address: Meibergdreef 9

department: CEMM

country: Netherlands

institute: Amsterdam UMC

data_processing:
Reads were trimmed using Trimmomatic version 0.36.
Read alignment done by Hisat2 version 2.3.4.3.
Count data were generated by means of the HTSeq method.
Assembly: GRCh38 (Ensembl 84)
Supplementary files format and content: counts

source_name: MIA PaCa-2

growth_protocol: MIA PaCa-2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 2mM L-glutamine and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA extraction kit (Macherey-Nagel). RNA quality was assessed by bioanalysis (Agilent) and samples with RNA integrity number > 7 were included for RNA sequencing using > 200 ng of total RNA.
RNA libraries for RNA-seq were prepared using KAPA RNA HyperPrep Kit with RiboErase (Roche) following manufacturer's protocols.

treatment_protocol: CTRL cells and CEBPD-inducible cells were treated with 2 ug/ml doxycycline hycalte (Sigma) for transgene induction in complete medium for 0, 8, 24 or 48 hours.

value: MIA PaCa-2

value: pancreatic ductal adenocarcinoma

value: tet-on CEBPD

value: doxycycline 2ug/ml

value: 48 hours


title: vmPFC from 60T [LID_100728]

source_name: ventromedial prefrontal cortex

value: ventromedial prefrontal cortex

value: male

value: low


title: V1 from 60T [LID_100726]

source_name: primary visual cortex

value: primary visual cortex


title: vmPFC from 7L7 [LID_100727]


title: CA3 from 3L5 [LID_100731]

source_name: cornu ammonis 3


title: MIA PaCa-2, CEBPD, 48h, 1


title: MIA PaCa-2, CTRL, 48h, 2

value: tet-on CTRL


title: shPON3

city: Suwon-si

first: Hyeong min

last: Lee

address: 304, Sinwon-ro

department: Reasearch

institute: Glaceum

data_processing:
RNA quality was assessed using an Agilent Bioanalyzer, and the samples had average RNA Integrity Number (RIN) value of 8.1 ± 0.7 and 7.3 ± 0.9, respectively
Alignment to human reference genome using HISAT2 program for read mapping
Transcript assembly was performed with StringTie program. DESeq2 was used to identify differentially expressed genes
Assembly: StringTie
Supplementary files format and content: tab-delimited text files include FPKM for each Sample

growth_protocol: L02 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 100 U/mL of penicillin and streptomycin at 37°C in a 5% CO2 incubator

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
The libraries were prepared with the Illumina TruSeq Stranded mRNA kit and sequenced using the high output on NovaSeq 6000 platform yielding 101bp paired end reads

value: immortalized normal liver cell

value: PON2 Knockdown


title: shPON2


title: MIA PaCa-2, CTRL, 48h, 3


title: MIA PaCa-2, CEBPD, 48h, 3


title: shCOM_3

value: WT


title: shPON1


title: vmPFC from 3L5 [LID_100724]


title: N1

value: normal healing fracture site


title: shCOM_2


title: vmPFC from 94S [LID_100725]

value: female


title: MIA PaCa-2, CTRL, 48h, 1


title: vmPFC from 4J0 [LID_100722]

value: mid


title: V1 from 94S [LID_100723]


title: MIA PaCa-2, CEBPD, 24h, 2

value: 24 hours


title: shCOM_1


title: MIA PaCa-2, CEBPD, 24h, 3

value: MIA PaCa-2


title: MIA PaCa-2, CEBPD, 24h, 1

value: pancreatic ductal adenocarcinoma


title: vmPFC from 4N7 [LID_100721]

value: high


title: Erythroid media Scramble replicate  4

first: Findlay

last: Bewicke-Copley

address: John Vane Science Centre, Barts Cancer Institute

institute: Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London

data_processing:
FASTQC was used to assess the quality of the FASTQ files prior to use
FASTQ files were aligned to GRCh38.p10 using hisat2 v2.1.0
Feature Counting was carried out using htseq-count 0.13.5
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: Counts text files

source_name: Primary HSPC isolated from umbilical cord blood

extract_protocol:
Total RNA was extracted from cells using an RNeasy Mini Kit (Qiagen Germany) and reverse-transcribed using a High-Capacity cDNA Reverse Transcription Kit (ThermoFisher, MA, USA)
Library preparation and mRNA sequencing was performed by Novogene (China) at 40 million reads per sample using an Illumina PE150 instrument. Paired end, 150 bp reads.

tag: culture condition

value: Erythroid media

value: HSPC

tag: batch

tag: genotype/variation

value: scramble


title: V1 from 65Z [LID_100720]

tag: individual id


title: Erythroid media Knockdown replicate  3

value: knockdown


title: Erythroid media Knockdown replicate  4


title: MIA PaCa-2, CTRL, 24h, 3

value: doxycycline 2ug/ml


title: Erythroid media Scramble replicate  3


title: Granulocytic media Knockdown replicate  2

value: Granulocytic media


title: Granulocytic media Scramble replicate  2


title: MIA PaCa-2, CEBPD, 8h, 3

value: tet-on CEBPD

value: 8 hours


title: vmPFC from 8L6 [LID_100716]

tag: tissue

value: ventromedial prefrontal cortex

value: male

value: low


title: vmPFC from 3A6 [LID_100717]

tag: age


title: vmPFC from 9C6 [LID_100718]

tag: Sex


title: vmPFC from 4J3 [LID_100719]

value: female

tag: dominance rank


title: MIA PaCa-2, CEBPD, 8h, 2

tag: cell line


title: vmPFC from 5B6 [LID_100715]


title: MIA PaCa-2, CTRL, 8h, 3

tag: cell type

value: tet-on CTRL


title: MIA PaCa-2, CTRL, 8h, 2

tag: genotype


title: MIA PaCa-2, CEBPD, 8h, 1

tag: treatment


title: vmPFC from 49Z [LID_100714]


title: DG from 5B6 [LID_100755]

source_name: dentate gyrus

value: dentate gyrus


title: Expansion MEM-a media Knockdown replicate  1

source_name: Primary MSC isolated from bone marrow

value: Expansion MEM-a media

value: MSC


title: MIA PaCa-2, CTRL, 8h, 1

value: MIA PaCa-2

value: pancreatic ductal adenocarcinoma

tag: time


title: Granulocytic media Knockdown replicate  1

value: HSPC


title: Expansion MEM-a media Knockdown replicate  2


title: Expansion MEM-a media Scramble replicate  2

value: scramble


title: Granulocytic media Scramble replicate  1


title: vmPFC from 3A9 [LID_100713]


title: MIA PaCa-2, CTRL, 24h, 2

value: 24 hours


title: vmPFC from 65Z [LID_100711]


title: MIA PaCa-2, CEBPD, t0, 3

value: doxycycline 2ug/ml


title: Expansion MEM-a media Scramble replicate  1


title: Adipogenic media Knockdown replicate  2

value: Adipogenic media

value: knockdown


title: vmPFC from 4N8 [LID_100710]

value: mid


title: MIA PaCa-2, CEBPD, t0, 2

value: tet-on CEBPD


title: MIA PaCa-2, CTRL, t0, 3


title: vmPFC from 9N0 [LID_100712]

value: ventromedial prefrontal cortex

value: high


title: Adipogenic media Knockdown replicate  1


title: MIA PaCa-2, CEBPD, t0, 1


title: Adipogenic media Scramble replicate  1


title: MIA PaCa-2, CTRL, t0, 2


title: Adipogenic media Patient 2

source_name: Patient Bone Marrow


title: Adipogenic media Scramble replicate  2


title: MIA PaCa-2, CTRL, 24h, 1


title: Adipogenic media Patient 1


title: Osteogenic media Knockdown replicate  2

value: Osteogenic media


title: Osteogenic media Knockdown replicate  1


title: Osteogenic media Patient 2


title: Osteogenic media Scramble replicate  1


title: vmPFC from 1B7 [LID_100707]

value: male


title: vmPFC from 5N1 [LID_100706]

value: female


title: vmPFC from 7L0 [LID_100709]

value: low


title: vmPFC from 2E9 [LID_100708]


title: Osteogenic media Patient 1

value: MSC


title: Osteogenic media Scramble replicate  2


title: MIA PaCa-2, CTRL, t0, 1

value: MIA PaCa-2

value: tet-on CTRL


title: Erythroid media Knockdown replicate  2

value: Erythroid media

value: HSPC


title: STS from 7L7 [LID_100698]

value: superior temporal sulcus


title: STS from 1B7 [LID_100697]


title: STS from 49Z [LID_100702]


title: STS from 94S [LID_100700]


title: STS from 3L5 [LID_100701]


title: STS from 9I7 [LID_100699]


title: STS from 6I4 [LID_100703]


title: STS from 65Z [LID_100704]


title: Erythroid media Knockdown replicate  1


title: Erythroid media Scramble replicate  2

value: scramble


title: STS from 60T [LID_100694]


title: Erythroid media Patient 2


title: STS from 5N1 [LID_100696]


title: Erythroid media Scramble replicate  1


title: STS from 5B6 [LID_100693]


title: STS from 8L6 [LID_100692]


title: Erythroid media Patient 1


title: blood, P121, NEC

city: Pittsburgh

first: David

last: Peters

state: PA

address: 204 Craft Avenue

institute: Magee-Womens Research Institute

library_source: genomic

data_processing:
DNA sequence reads were quality trimmed and adaptor sequences were removed using Trim-Galore.
The reads were aligned to the human reference sequence using Bismark Bisulfite Read Mapper in paired-end, bowtie2 mode. Any unmapped reads were aligned in single-end, bowtie2 mode.
Read duplicates were removed using Bismark.
Methylation was called on paired-end and single-end files and then merged to determine the methylation status for each CpG site.
Assembly: GRCh38
Supplementary files format and content: Bismark Coverage output merged from PE and SE methylation extractor outputs. <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

molecule: genomic DNA

source_name: blood

extract_protocol:
Blood genomic DNA was extracted then was quantified using the KAPA hgDNA Quantification and QC Kit.
DNA was sheared with Covaris to a size of ~175bp. Libraries were prepared using the KAPA HyperPrep Kit. Libraries were bisulfite converted post-ligation using the EZ DNA Methylation-Direct Kit and amplified 10 cycles. Bisulfite-converted DNA libraries underwent targeted capture using the SeqCap Epi CPGiant Enrichment Kit and amplified 10 cycles. Samples were sequenced on a HiSeqX with 150 bp paired-end reads to a mean targeted read depth of ~56x.

value: blood

tag: disease state

value: NEC


title: blood, P143, NEC


title: blood, P119, NEC


title: blood, P139, NEC


title: blood, P140, NEC


title: blood, P137, NEC


title: blood, P113, NEC


title: blood, P108, NEC


title: blood, P101, NEC


title: blood, P51c, control

value: control


title: blood, P52c, control


title: CN from 94S [LID_100691]

source_name: caudate nucleus

value: caudate nucleus


title: CN from 4J3 [LID_100690]

value: mid


title: dsRNA-seq_NSUN2-KO_IP_3

city: Chicago

first: Li-Sheng

last: Zhang

state: IL

address: 929 E 57th St Rm E313

department: Department of Chemistry

institute: The University of Chicago

data_processing:
The sequencing data was all trimmed with cutadapt tool to remove adapters and low-quality reads (length shorter than 20). Reads were processed with BBMap tool (https://sourceforge.net/projects/bbmap/) to remove PCR duplicates, and then further trimmed the random barcode using cutadapt tool and remove low-quality reads again. Reads were then aligned to the relevant genome (human-hg38) using Tophat2 (version 2.1.1) and bowtie2 (version 2.3.5.1) with at most 2 mismatches. The generated .bam files were sorted using Samtools. Cufflinks and Cuffdiff were used to make inferential tests where differentially expressed genes were identified at FDR < 0.05 cut-off. Gene ontology analysis was performed using the online analysis software DAVID v6.8 (https://david.ncifcrf.gov) and REViGO tool (http://revigo.irb.hr).
Genome_build: hg38
Supplementary_files_format_and_content: xlsx (excel)

source_name: cell

growth_protocol: A549 cell line was purchased from the American Type Culture Collection (ATCC). A549 cells were grown in ATCC-formulated F-12K Medium (Catalog No. 30-2004) supplemented with 10% v/v FBS and 1% penicillin/streptomycin (GIBCO). Cells were cultured at 37 °C with 5.0% CO2 in a Heracell™ VIOS 160i incubator (Thermo Scientific).

extract_protocol:
NSUN2 knockout and wild-type A549 cells were prepared as described (3 replicates each, four 15-cm plates per replicate). For each sample, 250 µL of Protein G Dynabeads (Invitrogen™, 10004D) was washed twice and resuspended in 1 mL of IP wash buffer (50 mM HEPES, pH 7.5, 150 mM NaCl, 1 mM MgCl2, 0.5% NP-40). 25 µg of anti-dsRNA mAb (J2) was added to the beads and incubated for 1 hour at room temperature, followed by another 1-2 hours at 4 °C. Cultured cells were washed once with cold DPBS. Each plate of cells was soaked in 5 mL cold DPBS and collected by cell lifters, combining 5 plates for each sample. The cell suspension was spun at 300 g at 4 °C for 2 mins. Cells were resuspended in 1 mL NP-40 lysis buffer (10mL solution: 50 mM HEPES pH 7.5, 150 mM NaCl, 2 mM EDTA, 10 mM MgCl2, 0.5% NP-40, plus 50 µL TURBO™ DNase (2 U/µL, AM2238, Invitrogen), 500 µL SUPERase•In™ RNase Inhibitor (20 U/µL, AM2694, Invitrogen), Pierce™ EDTA-free Protease Inhibitor Tablet) and incubated at 4 °C for 30 mins. The lysate was spun at 16,000 g at 4 °C for 5 mins. The supernatant was transferred to a new Eppendorf tube and 10 µL of that was kept as the “input”. The lysate was diluted to 4.75 mL with IP wash buffer. 250 µL of J2-Dynabeads was added to the lysate and incubated at 4 °C for 2 hours. The magnetic beads were washed once with 1 mL IP wash buffer and transferred to a new Eppendorf tube. The beads were further washed twice by 1 mL of IP wash buffer. Input RNA and J2-bound dsRNA were extracted using TRIzol, with small RNA (< 200 nt) removal by RNA Clean & Concentrator (Zymo Research).
The "purified dsRNA" and "input" was subjected to library construction with SMARTer® Stranded Total RNA-Seq Kit v2.
RNA-Seq. All libraries were sequenced on Illumina NovaSeq 6000 with paired-end 50 bp read length.

treatment_protocol: CRISPR-Cas9 was used to knock out the NSUN2 gene in A549 cells. Three single guide RNAs (sgRNAs) specific for exon 4 of the NSUN2 gene and one control sgRNA (5’-GTACGTCGGTATAACTCCTC-3’) were designed and cloned into the lentiviral vector plentiCRISPR v2. 293T cells (2.5×106) were transfected with the lentiviral vector expressing both the sgRNA and Cas9 (5 mg), the packaging plasmid (5 mg), and the VSV-G envelope expression plasmid (2.5mg) to generate lentiviral particles that were used to transduce A549 cells (2×105). After puromycin (2 mg/ml) selection, the transduced cells were single cell cloned. The knockout of NSUN2 expression in A549 cells was con firmed by Western blotting. Genome editing of the targeted region was also confirmed by PCR of exon 4 of NSUN2 from genomic DNA followed by sequencing.


title: dsRNA-seq_NSUN2-KO_IP_2


title: blood, P48c, control


title: blood, P39c, control


title: blood, P49c, control


title: dsRNA-seq_NSUN2-KO_Input_3


title: dsRNA-seq_NSUN2-KO_IP_1


title: blood, P24c, control


title: blood, P47c, control


title: dsRNA-seq_NSUN2-KO_Input_2


title: blood, P136, NEC


title: CN from 5N1 [LID_100687]


title: CN from 4N8 [LID_100689]


title: CN from 60T [LID_100688]


title: CN from 9N0 [LID_100686]

value: high


title: blood, P124, NEC


title: blood, P117, NEC


title: CN from 2E9 [LID_100685]


title: CN from 4N7 [LID_100684]


title: CN from 1B7 [LID_100683]


title: MCF10A cells, MAP3K9, 18 hours Dox rep 1

city: Baltimore

first: Amy

middle: Fukumoto

last: Peterson

state: MD

address: 735 N Wolfe St. PCTB 502

department: MBG

institute: Johns Hopkins University

data_processing:
Genewiz Standard RNA-sequencing library preparation
Poly(A) selection
Trimmed sequence reads were mapped to GRCh38 using STAR
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: MCF10A cells were plated in DMEM-F12 supplemented with 5% horse serum, 10 ng/mL EGF, 0.5 mg/mL Hydrocortisone, 100 ng/mL cholera toxin, 10 μg/ml Insulin and antibiotics in humidified atmosphere with 5% CO2 at 37C. Then starved overnight in DMEM-F12 supplemented with 0.5% horse serum and antibiotics and maintained in this starvation medium during doxycycline treatment.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).> 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Genewiz  following manufacturer's protocols.

treatment_protocol: Serum-starved MCF10a cells were 2 μg/ml doxycycline for 18 hours to induce expression of specified MAP3Ks

value: mammary epithelial cells

value: Doxycycline


title: MCF10A cells, MAP3K7, 18 hours Dox rep 2


title: MCF10A cells, RAF1, 18 hours Dox rep 2


title: MCF10A cells, MAP3K2, 18 hours Dox rep 2


title: MCF10A cells, ARAF, 18 hours Dox rep 1


title: MCF10A cells, MAP3K14, 18 hours Dox rep 1


title: MCF10A cells, MAP3K7, 18 hours Dox rep 1


title: MCF10A cells, MAP3K11, 18 hours Dox rep 2


title: MCF10A cells, BRAF, 18 hours Dox rep 2


title: MCF10A cells, ZAK, 18 hours Dox rep 1


title: MCF10A cells, ZAK, 18 hours Dox rep 2


title: MCF10A cells, MAP3K5, 18 hours Dox rep 2


title: MCF10A cells, MAP3K11, 18 hours Dox rep 1


title: MCF10A cells, MAP3K9, 18 hours Dox rep 2


title: MCF10A cells, BRAF, 18 hours Dox rep 1


title: MCF10A cells, MAP3K15, 18 hours Dox rep 1


title: MCF10A cells, MAP3K2, 18 hours Dox rep 1


title: MCF10A cells, ARAF, 18 hours Dox rep 2


title: MCF10A cells, RAF1, 18 hours Dox rep 1


title: MCF10A cells, MAP3K5, 18 hours Dox rep 1


title: MCF10A cells, MAP3K14, 18 hours Dox rep 2


title: MCF10A cells, MAP3K3, 18 hours Dox rep 2


title: CN from 8L6 [LID_100682]

value: male


title: dsRNA-seq_NSUN2-KO_Input_1


title: dsRNA-seq_WT_IP_2


title: dsRNA-seq_WT_IP_3


title: dsRNA-seq_WT_IP_1


title: dsRNA-seq_WT_Input_3


title: blood, P102, NEC


title: blood, P85, NEC


title: MCF10A cells, MAP3K3, 18 hours Dox rep 1


title: blood, P80, NEC


title: blood, P45c, control


title: blood, P54c, control


title: blood, P46c, control


title: blood, P55c, control


title: RIG-I_RIP_NSUN2-KO_RSV-infected_IP_2

extract_protocol:
After 12-hour RIG-I overexpression, cells were lysed in 200 uL lysis buffer and save 10 uL as "input". The remaining lysate was subjected to FLAG-beads pulldown. After washing, the purified RIG-I bound RNA was eluted from beads by TRIzol reagent.
Both the "input" and "RIG-I bound RNA" were directly subjected to SMARTer® Stranded Total RNA-Seq Kit v2.
RNA-Seq. All libraries were sequenced on Illumina NovaSeq 6000 with single-end 100 bp read length.

treatment_protocol: CRISPR-Cas9 was used to knock out the NSUN2 gene in A549 cells. Three single guide RNAs (sgRNAs) specific for exon 4 of the NSUN2 gene and one control sgRNA (5’-GTACGTCGGTATAACTCCTC-3’) were designed and cloned into the lentiviral vector plentiCRISPR v2. 293T cells (2.5×106) were transfected with the lentiviral vector expressing both the sgRNA and Cas9 (5 mg), the packaging plasmid (5 mg), and the VSV-G envelope expression plasmid (2.5mg) to generate lentiviral particles that were used to transduce A549 cells (2×105). After puromycin (2 mg/ml) selection, the transduced cells were single cell cloned. The knockout of NSUN2 expression in A549 cells was con firmed by Western blotting. Genome editing of the targeted region was also confirmed by PCR of exon 4 of NSUN2 from genomic DNA followed by sequencing. Both wild-type and NSUN2-knockout cells were infected with RSV or VSV virus. A 12-hour transfection of FLAG-tagged RIG-I plasmid was conducted to overexpress RIG-I protein.


title: MCF10A cells, MAP3K1, 18 hours Dox rep 2


title: dsRNA-seq_WT_Input_1


title: RIG-I_RIP_NSUN2-KO_VSV-infected_IP_1


title: RIG-I_RIP_NSUN2-KO_VSV-infected_IP_2


title: dsRNA-seq_WT_Input_2


title: MCF10A cells, MAP3K8, 18 hours Dox rep 2


title: MCF10A cells, Control, 18 hours Dox rep 2

value: WT


title: MCF10A cells, Control, 18 hours Dox rep 1


title: MCF10A cells, MAP3K8, 18 hours Dox rep 1


title: MCF10A cells, MAP3K1, 18 hours Dox rep 1


title: RIG-I_RIP_WT_RSV-infected_IP_2


title: AMY from 4J0 [LID_100675]

source_name: amygdala

value: amygdala


title: blood, P37c, control


title: AMY from 3L5 [LID_100676]


title: CN from 3L5 [LID_100681]


title: AMY from 5N1 [LID_100677]

value: female


title: AMY from 65Z [LID_100679]

value: low


title: AMY from 49Z [LID_100678]


title: CN from 7L7 [LID_100680]


title: AMY from 4N8 [LID_100674]


title: blood, P38c, control


title: PAM2

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description:
10x 3' v2 scRNA-seq
raw data will be submitted to dbGap

data_processing:
Read alignment and gene-expression quantification of human single-cell RNA-seq (scRNA-seq) were performed using Cell Ranger version 2.1.1 and 2.0.0 pipeline (10x Genomics).
For scRNA-seq alignment and quantification, Cell Ranger pre-built human (hg19) reference package was used.
Assembly: hg19
Supplementary files format and content: Raw Feature Barcode Matrix and 10x Cell Ranger filtered Feature Barcode Matirx in HDF5 format

source_name: CD45+ PAM lung

extract_protocol:
Single-cell suspensions were processed through the 10X Chromium to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA was prepared for sequencing using a modified Nextera XT protocol
single-cell RNA-seq

value: lung

value: PAM


title: Cre_Ex_miRNA

city: Guangzhou

first: chunxiao

last: yin

state: Guangdong

address: Xingke Road

department: Agriculture and Biotechnology Research Center

institute: South China Botanical Garden, Chinese Academy of Sciences

description: Small RNA

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: ftp://miRBase.org/pub/miRBase/CURRENT/; http://citrus.hzau.edu.cn/data/Genome_info/JZ.v1.0/JZ.v1.0.genome.fa
Supplementary files format and content: excel,expression profiles

organism: Citrus reticulata

source_name: exosomes

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: exosomes


title: D071

source_name: Normal Donor lung 24 years old

value: Control


title: RIG-I_RIP_WT_RSV-infected_IP_1


title: AMY from 4N7 [LID_100673]

first: Kenneth

last: Chiou

address: 427 E Tyler Mall

institute: Arizona State University

data_processing:
Gene expression counts were quantified from RNA-seq reads using the pseudoalignment method implemented in kallisto.
Estimated counts and transcripts-per-million (TPM) values were then imported into R v4.0.2 and summarized to genes using the tximport package.
Genome_build: rhesus macaque reference genome (Mmul_10)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with transcripts per million (TPM) values for every gene and every sample

extract_protocol:
Total RNA was extracted using a TRIzol-chloroform gradient followed by column isolation of RNA using the Quick-RNA Microprep kit (Zymo Research). Briefly, 1 ml of TRIzol (Invitrogen) was added to each 2-ml sample tube, along with a sterile 5-mm stainless steel grinding bead (QIAGEN cat. no. 69989). Samples were then homogenized using the Tissuelyser II system (QIAGEN) at 20 Hz in two sets of 2 minutes each, with rotation in between, and the lysate transferred to a new tube. 200 µl of chloroform were added to each sample, which was then vortexed at full speed for 15 seconds and incubated at room temperature for 2 minutes. The sample was then centrifuged at 12,000 × g for 15 minutes at 4°C. After centrifugation, the aqueous layer was transferred to a new tube and mixed with 600 µl of 70% ethanol to precipitate RNA. The resulting solution was transferred to Quick-RNA Microprep columns (Zymo Research). The remainder of the protocol followed manufacturer instructions for the Quick-RNA Microprep kit. Total RNA was eluted in 60 µl of RNase-free water.
We prepared bulk RNA-seq libraries using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) with an initial mRNA isolation step using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). We followed manufacturer instructions and guidelines for library preparation using these kits. We used 200 ng of starting RNA and set the enzymatic fragmentation time (10 minutes), first-strand synthesis incubation time (50 minutes at 42°C), and bead cleanup volume ratios for a target insert size of 400 bp. Libraries were amplified using 10 cycles of PCR and eluted in a final volume of 20 µl of RNase-free water. Libraries were quantified by Qubit 3 using the Qubit DNA HS Assay kit (Invitrogen) and library quality was assessed using the Fragment Analyzer HS NGS kit (AATI/Agilent). Libraries were pooled in equimolar quantities prior to sequencing.


title: RIG-I_RIP_WT_VSV-infected_IP_2


title: RIG-I_RIP_WT_VSV-infected_IP_1


title: AMY from 3A9 [LID_100672]


title: RIG-I_RIP_NSUN2-KO_RSV-infected_Input_2


title: PAM1

source_name: CD45- PAM lung


title: RIG-I_RIP_NSUN2-KO_RSV-infected_Input_1


title: AMY from 9C6 [LID_100671]


title: AMY from 4J3 [LID_100670]


title: CD4 cells from patient 3 cultured without CLL

first: Fleur

institute: Amsterdam UMC (AMC)

description:
NEBNext RNA library prep
Paired-end on NovaSeq6000

data_processing:
Quality of the sequencing data was assessed using FastQC. Raw FastQ files were aligned to the GRCh38 human genome using STAR v2.7.9a and the .transcriptome.out.bam files were used as input for RSEM’s calculate expression (v1.3.3) to generate expected counts
Genome_build: GRCh38
Supplementary_files_format_and_content: Expected counts (output RSEM)

source_name: CD4 T cells

extract_protocol:
Total RNA was extracted with the Qiagen Mini kit
NEBNext Ultra II Directional RNA library prep kit for Illumina

value: CD4 T cells

value: Isolated


title: neuron 6C, replicate 1, read 1

city: Merced

first: Michael

last: Cleary

state: CA

address: 5200 N. Lake Rd.

department: School of Natural Sciences

institute: University of California, Merced

description:
nsyb_6C_1_est_counts
nsyb_PC_processed.txt

data_processing:
Sequence data were trimmed using Trimmomatic prior to mapping to the Drosophila melanogaster cDNA transcriptome (BDGP6) using kallisto.
Assembly: BDGP6
Supplementary files format and content: insc_PC_processed.txt provides raw counts per transcript for neuroblast_targeted experiments, first column is transcript identifier, subsequent columns are counts for each pulse_chase timepoint
Supplementary files format and content: nsyb_PC_processed.txt provides raw counts per transcript for neuron_targeted experiments, first column is transcript identifier, subsequent columns are counts for each pulse_chase timepoint

organism: Drosophila melanogaster

source_name: brain

growth_protocol: larvae were cultured on standard growth medium at 25C.

extract_protocol:
Total RNA was extracted using Trizol.  RNA biotinylation and purification was performed using the Click IT Nascent RNA Capture Kit (ThermoFisher)
NuGen Ovation Universal RNA-Seq with AnyDeplete ribosomal RNA removal

treatment_protocol: 5EC and untagged uridine feeding was performed in standard media.

value: brain

tag: developmental stage


title: neuron 12C, replicate 2, read 1

description:
nsyb_12C_2_est_counts
nsyb_PC_processed.txt


title: neuron 6C, replicate 2, read 1

description:
nsyb_6C_2_est_counts
nsyb_PC_processed.txt


title: CD4 cells from patient 4 cultured without CLL


title: RIG-I_RIP_NSUN2-KO_VSV-infected_Input_2


title: CD4 cells from patient 2 cultured without CLL


title: AMY from 7L7 [LID_100668]

city: Tempe


title: AMY from 94S [LID_100669]


title: RIG-I_RIP_NSUN2-KO_RSV-infected_IP_1


title: CD4 cells from patient 1 cultured without CLL


title: MCF10A cells, MAP3K15, 18 hours Dox rep 2


title: neuron 3C, replicate 1, read 1

description:
nsyb_3C_1_est_counts
nsyb_PC_processed.txt


title: CD4 cells from patient 4 cultured with CLL

value: CLL


title: neuron 12P, replicate 2, read 1

description:
nsyb_12P_2_est_counts
nsyb_PC_processed.txt


title: RIG-I_RIP_NSUN2-KO_VSV-infected_Input_1


title: neuron 12C, replicate 1, read 1

description:
nsyb_12C_1_est_counts
nsyb_PC_processed.txt


title: RIG-I_RIP_WT_RSV-infected_Input_2


title: AMY from 8L6 [LID_100666]


title: RIG-I_RIP_WT_RSV-infected_Input_1


title: AMY from 5B6 [LID_100667]


title: neuron 3C, replicate 2, read 1

description:
nsyb_3C_2_est_counts
nsyb_PC_processed.txt


title: neuron 12P, replicate 1

description:
nsyb_12P_1_est_counts
nsyb_PC_processed.txt


title: CD4 cells from patient 2 cultured with CLL


title: AMY from 3A6 [LID_100665]


title: AMY from 7L0 [LID_100663]


title: neuroblast 12C, replicate 2

description:
insc_12C_2.est_counts
insc_PC_processed.txt


title: RIG-I_RIP_WT_VSV-infected_Input_1


title: neuroblast 12C, replicate 1

description:
insc_12C_1.est_counts
insc_PC_processed.txt


title: CD4 cells from patient 1 cultured with CLL


title: Simvastatin1_rep1_ChIPSeq

city: Palo Alto

first: Yu

address: 1215 Welch Road

department: CVI

institute: Stanford University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore
Trimmed data was mapped to hg19 whole genome using bowtie2
Peaks were called against sequenced input chromatin using MACS2
Differences in peaks between conditions were detected by using Manorm2
Genome_build: hg19
Supplementary_files_format_and_content: Peaks in bigWig format
Supplementary_files_format_and_content: Raw read counts in TXT format

source_name: hiPSC-ECs

extract_protocol:
hiPSC-ECs RNA was harvested using Trizol reagent. ATAC-seq DNA was extracted as described in previous protocol (Buenrostro J et al. Nat Methods 10: 1213-1218). Genomic DNA was clarified from sonicated nuclei and YAP-DNA complexes were isolated with antibody.
RNA Libraries prepared from 10ng RNA, Sequencing data was un-stranded, ERCC spike-in (Ambion) used for data normalization.  ATAC-seq libraries were prepared for sequencing using TruSeq Library Prep Kit (Illumina). ChIP-seq libaries were prepared following Zymo Spin-ChIP kit protocol from Zymo Research.

value: hiPSC-ECs

value: simvastatin

tag: antibody

value: YAP, Novus Biologicals, NB110-583582


title: Simvastatin1_rep2_ChIPSeq


title: m5C_NSUN2-KO_Total-RNA_VSV-infected_BS-treated_2

data_processing:
The sequencing data was all trimmed with cutadapt tool to remove adapters and low-quality reads. PCR duplicates were removed with BBMap tool (https://sourceforge.net/projects/bbmap/), 5-mer random barcodes at reads ends were trimmed, and low-quality or short reads (less than 30 nt) were removed using cutadapt tool. Remaining reads were aligned to the converted human genome (hg38, C->T or G->A converted, by Bismark-0.22.3 tool, https://github.com/FelixKrueger/Bismark/releases) using Tophat2 (version 2.1.1) and bowtie2 (version 2.3.5.1) allowing at most three mismatches. The generated .bam files were split into positive and negative strands and sorted using Samtools (http://samtools.sourceforge.net/). Sequence variants were identified by measuring the base composition at each position using fine-tuned bam-readcount (https://github.com/genome/bam-readcount). The generated bam-readcount results were parsed and analyzed by in-house scripts. T to C mutation ratio at each m5C candidate site were calculated by data output from bam-readcount pipeline and confirmed by direct visualization through IGV software (https://software.broadinstitute.org/software/igv/).
Genome_build: hg38
Supplementary_files_format_and_content: xlsx (excel)

extract_protocol:
For virus-infected or uninfected A549 wild-type and NSUN2 knockout cells, cellular total RNA was isolated with TRIzol reagent (Invitrogen) following manufacturer’s protocol by isopropanol precipitation.   When extracting rRNA-depleted total RNA for sequencing m5C in RNA, RiboMinus™ Eukaryote System v2 (Invitrogen™) was further used for rRNA removal. When extracting polyA+ RNA for sequencing m5C in RNA, Dynabeads™ mRNA DIRECT™ Purification Kit (Invitrogen™) was used for polyA+ RNA enrichment.
RSV-infected or VSV-infected NSUN2 knockout and wild-type A549 cells were prepared as described (2 replicates each, one 10-cm plate per replicate). After extracting the rRNA-depleted total RNA, ~200 ng RNA was fragmented into 50-70 nt length using Na2CO3/NaHCO3 buffer (pH 9.2) and heated at 95 °C for 3 min, followed by purification with Oligo Clean & Concentrator (Zymo Research). ~50 ng was saved as “input” and the remainder was subjected to EZ RNA Methylation Kit (Zymo Research) for bisulfite treatment. 3’- and 5’-end repair was conducted for “input” and bisulfite-treated RNA by T4 Polynucleotide Kinase (EK0032, Thermo Fisher Scientific). RNA was mixed with 5 µL of 10X T4 Polynucleotide Kinase Reaction Buffer (B0201S, NEB) and 5 µL of T4 PNK, diluted to a final volume of 50 µL, and incubated at 37 °C for 1 hour; then 2 µL of T4 PNK and 5 µL 10 mM ATP were added for another incubation 37 °C for 30 min, followed by Oligo Clean & Concentrator purification. To perform 3’-adaptor ligation, ~6 µL repaired RNA fragments were incubated with 1.0 µL 3’-Adaptor (5’App-NNNNN ATCACGAGATCGGAAGAGCACACGTCT-3SpC3) at 70 °C for 2 mins and immediately placed on ice. 10 µL 3´ Ligation Reaction Buffer (2X) (NEB) and 3 µL 3´ Ligation Enzyme Mix (NEB) were added to the RNA-adapter mixture. The reaction was incubated at 25 °C for 2 hours followed by 16 °C for 10 hrs. Then 1.0 µL SR RT Primer for Illumina (NEB) was added to the mixture, followed by 5 minutes at 75°C, 15 minutes at 37°C, 15 minutes at 25°C, and then on ice. The denatured 1.0 µL 5’-Adaptor (5’-GUUCAGAGUUCUACAGUCCGACGAUCNNNNN-3’) was added into the mixture, together with 1.0 µL 5´ Ligation Reaction Buffer (10X) (NEB) and 2.5 µL 5´ Ligation Enzyme Mix (NEB). The reaction was incubated at 25 °C for 4 hours, followed by RNA Clean & Concentrator purification  The purified RNA was mixed with 4 µL 5X SSIV Buffer (Thermo Scientific), 2 µL of 10 mM dNTP Solution Mix (NEB), 1 µL 100 mM DTT, 1 µL of RNaseOUT Recombinant Ribonuclease Inhibitor (Thermo Scientific), and 1 µL of SuperScript IV Reverse Transcriptase (Thermo Scientific). The reaction was diluted to 20 uL and incubated at 50 °C for 30 mins. 1.0 µL of RNase H (NEB, M0297L) was then added and the reaction was incubated at 37 °C for 20 mins. The cDNAs were purified by Oligo Clean & Concentrator (Zymo Research). The libraries were amplified using the SR Primer for Illumina (NEB) and indexed primers (from NEBNext Multiplex Oligos for Illumina).
RNA-Seq. All libraries were sequenced on Illumina NovaSeq 6000 with single-end 100 bp read length.

treatment_protocol: CRISPR-Cas9 was used to knock out the NSUN2 gene in A549 cells. Three single guide RNAs (sgRNAs) specific for exon 4 of the NSUN2 gene and one control sgRNA (5’-GTACGTCGGTATAACTCCTC-3’) were designed and cloned into the lentiviral vector plentiCRISPR v2. 293T cells (2.5×106) were transfected with the lentiviral vector expressing both the sgRNA and Cas9 (5 mg), the packaging plasmid (5 mg), and the VSV-G envelope expression plasmid (2.5mg) to generate lentiviral particles that were used to transduce A549 cells (2×105). After puromycin (2 mg/ml) selection, the transduced cells were single cell cloned. The knockout of NSUN2 expression in A549 cells was con firmed by Western blotting. Genome editing of the targeted region was also confirmed by PCR of exon 4 of NSUN2 from genomic DNA followed by sequencing. Both wild-type and NSUN2-knockout cells were infected with RSV or VSV virus.


title: neuroblast 6C, replicate 2

description:
insc_6C_2.est_counts
insc_PC_processed.txt


title: neuroblast 6C, replicate 1

description:
insc_6C_1.est_counts
insc_PC_processed.txt


title: AMY from 60T [LID_100661]


title: neuroblast 3C, replicate 2

description:
insc_3C_2.est_counts
insc_PC_processed.txt


title: AMY from 1B7 [LID_100662]

value: high


title: CD4 cells from patient 3 cultured with CLL


title: m5C_NSUN2-KO_Total-RNA_VSV-infected_BS-treated_1


title: STS from 0K1 [LID_100658]

source_name: superior temporal sulcus

value: superior temporal sulcus

value: male


title: GGTI1_rep1_ChIPSeq


title: GGTI1_rep2_ChIPSeq


title: AMY from 2E9 [LID_100660]

value: amygdala


title: dlPFC single-nucleus transcriptomes from I1755R

data_processing:
Single-nucleus RNA sequencing reads were processed following the methods described by Cao et al. (PMID: 30787437, series accession: GSE119945) to produce a matrix of unique molecular index (UMI) counts, where rows correspond to genes and columns correspond to unique index combinations, which mainly delineate transcripts from single nuclei but also include a small fraction of multiplets. Our pipeline was modified for the most recent rhesus macaque reference genome (Mmul_10) and annotation, obtained from Ensembl (version 101). Haplotype sequences were removed from the genome FASTA in order to avoid mapping inefficiencies due to multi-mapping and the 3' UTR annotations of genes and transcripts were extended in the reference transcriptome (GTF file) in order to avoid misclassifying genic reads as intergenic. The remainder of the Cao et al. sci-RNA-seq3 pipeline for demultiplexing, mapping, deduplication, and count matrix generation proceeded using the 3' UTR extended GTF file as input. We used monocle 3 to generate a cell dataset (cds) object.
Genome_build: rhesus macaque reference genome (Mmul_10)
Supplementary_files_format_and_content: Text file in MatrixMarket coordinate format with raw gene counts for every gene and every unique sci-RNA-seq3 index
Supplementary_files_format_and_content: Text file with gene annotations (rows) for count matrix
Supplementary_files_format_and_content: Text file with cell annotations (columns) for count matrix

source_name: dorsolateral prefrontal cortex

extract_protocol:
We generated nuclei suspensions from frozen tissue biopsies following methods described by Cao et al. 2019 (PMID: 30787437, series accession: GSE119945), with the following modifications. We first homogenized samples by thoroughly grinding samples with a pre-chilled disposable pestle (Fisher Scientific cat. no. 12-141-364) in 50 µl of cell lysis buffer on ice. We brought the volume to 1 ml with ice-cold cell lysis buffer and filtered the mixture using a 70 µm cell strainer (pluriSelect cat. no. 43-10070-70). The nuclei were then fixed in 4% paraformaldehyde (6 ml reaction volume) for 15 minutes with gentle mixing, washed once in 1 ml of ice-cold nuclei wash buffer, then resuspended in 200 µl of nuclei wash buffer. After counting a small aliquot with a 1:1 trypan blue stain using the Countess II system, nuclei were allocated in 1-million-nucleus aliquots and flash frozen in liquid nitrogen.
Methods for sci-RNA-seq3 library preparation and sequencing followed those described by Cao et al. (PMID: 30787437, series accession: GSE119945). Briefly, nuclei were thawed in a 37°C water bath for 5 minutes, spun down at 500 × g for 5 minutes, and incubated in 400 µl of permeabilization buffer (nuclei wash buffer supplemented with 0.2% Triton X-100) for 3 minutes. Nuclei were washed, sonicated for 12 sec on low power mode (Diagenode), washed, and resuspended in 100 µl of nuclei wash buffer. The sci-RNA-seq3 prep follows the Cao et al. methods for paraformaldehyde-fixed nuclei with the following modifications: samples were counted with the ImageExpress Pico System (Molecular Devices), 2 µl of oligo-dT primers were added to each well with 80,000 nuclei for reverse transcription, Quick Ligation kit (New England Biolabs) was used in place of T4 ligase, and tagmentation was performed using 1/40th µl per well of i7 loaded TDE1 enzyme, prepared at the University of Washington following Hennig et al. 2018 (PMID: PMID: 29118030).

treatment_protocol: Following veterinary euthanasia, a necropsy was immediately performed during which the brain was perfused by transcardial perfusion with sterile saline. The brain was then removed from the cranium and sagittally sectioned into left and right hemispheres. The left hemisphere was fixed in 10% formalin and not used for this study. The right hemisphere was further sectioned prior to cryopreservation. First, the cerebellum was separated from the cerebrum. The cerebrum was then placed on a custom mold and sectioned coronally into 11 ~0.5 cm-thick slices. All 12 slices (including the cerebellar hemisphere) were individually stored in Whirl-pak bags and flash frozen in a dry-ice/ethanol bath immediately before storage in ultralow (-80°C) freezers. The dorsolateral prefrontal cortex was dissected in sterile, RNase-free conditions on dry ice to minimize RNA degradation. Six 2-mm tissue biopsies were then collected by biopsy punch.

value: dorsolateral prefrontal cortex

value: female


title: Control1_rep1_ChIPSeq

value: DMSO


title: m5C_NSUN2-KO_Total-RNA_VSV-infected_Input_2


title: neuroblast 12P, replicate 2

description:
insc_12P_2.est_counts
insc_PC_processed.txt


title: RIG-I_RIP_WT_VSV-infected_Input_2


title: neuroblast 3C, replicate 1

description:
insc_3C_1.est_counts
insc_PC_processed.txt


title: STS from 4N7 [LID_100659]


title: m5C_WT_Total-RNA_VSV-infected_BS-treated_1


title: m5C_WT_Total-RNA_VSV-infected_BS-treated_2


title: neuroblast 12P, replicate 1

description:
insc_12P_1.est_counts
insc_PC_processed.txt


title: dlPFC single-nucleus transcriptomes from 44V


title: Control1_rep2_ChIPSeq


title: Simvastatin3_rep4_ATACseq


title: meRIP_Mettl3null_brain_2

data_processing:
Sequence data were trimmed using Trimmomatic prior to mapping to the Drosophila melanogaster cDNA transcriptome (BDGP6) using kallisto.
Assembly: BDGP6
Supplementary files format and content: meRIP_Processed_Data.txt provides raw counts per gene for all experiments, first column is gene identifier, followed by counts for each sample in a separate column
Library strategy: meRIP-seq

extract_protocol:
anti_m6A RNA immunoprecipitation
NuGen Ovation Universal RNA-Seq with AnyDeplete ribosomal RNA removal

treatment_protocol: brain lobe dissection

value: Mettl3 null


title: dlPFC single-nucleus transcriptomes from 0V5


title: m5C_WT_Total-RNA_VSV-infected_Input_1


title: dlPFC single-nucleus transcriptomes from 8I9


title: meRIP_Mettl3null_brain_1


title: Simvastatin3_rep3_ATACseq


title: m5C_NSUN2-KO_Total-RNA_RSV-infected_BS-treated_1

description: A549_Host-RNA_m5C_sites.xlsx, RSV_Viral-RNA_Antisense-genome_m5C_sites.xlsx


title: meRIP_neuroblast_biased_brain_1


title: Simvastatin3_rep2_ATACseq


title: m5C_NSUN2-KO_Total-RNA_RSV-infected_BS-treated_2


title: Simvastatin3_rep1_ATACseq


title: Simvastatin2_rep4_ATACseq


title: meRIP_neuroblast_biased_brain_2


title: dlPFC single-nucleus transcriptomes from 2R9


title: dlPFC single-nucleus transcriptomes from 3F5


title: dlPFC single-nucleus transcriptomes from 2E9


title: Simvastatin2_rep3_ATACseq


title: meRIP_neuron_biased_brain_1


title: m5C_NSUN2-KO_Total-RNA_VSV-infected_Input_1


title: Simvastatin2_rep2_ATACseq


title: m5C_WT_Total-RNA_RSV-infected_BS-treated_1


title: dlPFC single-nucleus transcriptomes from 60R


title: m5C_WT_Total-RNA_VSV-infected_Input_2


title: meRIP_neuron_biased_brain_2


title: m5C_WT_Total-RNA_RSV-infected_BS-treated_2


title: Input_Mettl3null_brain_2


title: dlPFC single-nucleus transcriptomes from 20S


title: Simvastatin2_rep1_ATACseq


title: m5C_NSUN2-KO_Total-RNA_RSV-infected_Input_2


title: Input_Mettl3null_brain_1


title: m5C_NSUN2-KO_Total-RNA_RSV-infected_Input_1


title: dlPFC single-nucleus transcriptomes from 4L8


title: Simvastatin1_rep4_ATACseq


title: m5C_WT_Total-RNA_RSV-infected_Input_2


title: dlPFC single-nucleus transcriptomes from 65Z


title: Input_neuroblast_biased_brain_2


title: m5C_WT_Total-RNA_RSV-infected_Input_1


title: Simvastatin1_rep1_ATACseq


title: Simvastatin1_rep3_ATACseq


title: Input_neuroblast_biased_brain_1


title: IN03

city: Hefei

first: Cheng

last: Sun

state: Anhui

address: 17, Lujiang Road

department: the First Affiliated Hospital of USTC

institute: University of Science and Technology of China

description:
Sample 13
Liver
Bulk RNA-seq
gene_count.txt

data_processing:
Sample1-9: Raw FASTQ files were processed with CellRanger software (v2.1), which performs alignment, filtering, barcode counting and UMI counting.
Sample1-9: Downstream analysis of the data was applied with Seurat (v3.0.2).
Sample10-13: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Sample10-13: FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Sample10-13: Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.6.
Genome_build: GRch38
Supplementary_files_format_and_content: Sample1-9: barcodes.tsv (barcodes), features.tsv (genes), matrix.mtx (expression matrix).
Supplementary_files_format_and_content: Sample10-13: gene_count.txt: Tab-delimited matrix table with raw gene counts for every gene and every sample.

source_name: CD150- ILC2s

extract_protocol:
Fresh liver tissue was minced into pieces. Tissue homogenates were treated with 1mg/ml Liberase and 10 U/ml DNase (Sigma-Aldrich) for up to 1h as needed. The digested tissue homogenates were then filtered through a 70-µm filter. Then tumor infiltrating lymphocytes were isolated by Percoll-Paque density centrifugation and the RBC is removed by the RBC lysate. The PBMC were isolated by Ficoll-Paque density centrifugation. Cells which we need were sorted on a cell sorter from BD.
Sample1-9: We used the 10x Genomics Chromium single-cell kit and protocol to prepare the libraries.
Sample10-13: Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

value: HCC tumor

value: SLAMF1- ILC2s

value: Untreated


title: Simvastatin1_rep2_ATACseq


title: dlPFC single-nucleus transcriptomes from 1C5


title: Input_neuron_biased_brain_2


title: Input_neuron_biased_brain_1


title: TAC_1376M

first: Bernhard

last: Kuhn

state: Pennsylvania

address: 4401 Penn Ave

institute: Children's Hospital of Pittsburgh

data_processing:
Quality controlled FASTQ files were aligned to the Ensembl Mus musculus genome (GRCm38) using STAR aligner (version 2.5.1). Reads that mapped to the coding genes were quantified using featureCounts(Liao et al., 2014), and genes with count values of zero were filtered out before the downstream analysis.
Differential gene expression analysis between the different conditions was done using DESeq2(Love et al., 2014) using a model based on the negative binomial distribution. The resulting p-values were then adjusted using the Benjamini and Hochberg approach for controlling the false discovery rate, and differentially expressed genes were determined at the 5% threshold.
Gene set enrichment analysis was used to assess the statistical enrichment of gene ontologies, and pathways(Subramanian et al., 2005), and visualization of the significant functional enrichment results was facilitated by clusterProfiler (Yu et al., 2012).
Genome_build: GRCm38
Supplementary_files_format_and_content: counts

extract_protocol:
Cardiac tissue was removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
The transcriptome profiling of ventricular myocardium from mouse hearts were sequenced in triplicate. The libraries were sequenced by the sequencing core facility at Children’s Hospital of Pittsburgh. An average of 25 ± 3 millions reads were produced for each sample, in accordance to the standard requirements for RNA-seq analysis.

treatment_protocol: TAC was performed on Tnnt2-Cre Lmnb2Flox/Flox (Lmnb2 KO) and Tnnt2-Cre (Control) mice at the age of 10 weeks – 12 weeks. The mice were anesthetized in a chamber with 4% isoflurane. A midline incision was made in the anterior neck exposing the suprasternal notch. From there, the sternum was cut open to the 2nd intercoastal rib space to reach the aortic arch by separating the thymus and connective tissues. An 8.0 silk suture was passed under the aortic arch and tied over a blunt 271⁄2 gauge needle. The chest wall was then closed with 6.0 Nylon suture. Bupivacaine (8 μg/g body weight) was administered through subcutaneous injection. The mice were recovered from anesthesia. Bupivacaine was administered subcutaneously for the following 3 days post injury.

value: WT

value: ventricular myocardium

value: Sham surgery


title: Control3_rep4_ATACseq

value: hiPSC-ECs


title: IP18

description:
Sample 11
Liver
Bulk RNA-seq
gene_count.txt

source_name: CD150+ ILC2s

value: SLAMF1+ ILC2s


title: dlPFC single-nucleus transcriptomes from 93O


title: Control3_rep3_ATACseq


title: Control3_rep2_ATACseq


title: TAC_1126F

value: Lmnb2 KO

value: TAC surgery


title: PBMC

description:
Sample 9
Blood
Single-cell RNA-seq

source_name: innate lymphoid cells

value: peripheral blood


title: dlPFC single-nucleus transcriptomes from V80


title: dlPFC single-nucleus transcriptomes from 22H


title: TAC_1138M


title: dlPFC single-nucleus transcriptomes from I192F2


title: IT

description:
Sample 8
Liver
Single-cell RNA-seq


title: IN30

description:
Sample 12
Liver
Bulk RNA-seq
gene_count.txt


title: Control3_rep1_ATACseq


title: IP03

description:
Sample 10
Liver
Bulk RNA-seq
gene_count.txt


title: TAC_1117M

value: Lmnb2 WT


title: dlPFC single-nucleus transcriptomes from 4S0


title: TAC_1101M


title: Control2_rep4_ATACseq


title: dlPFC single-nucleus transcriptomes from 51V


title: TAC_1137M


title: HD3

description:
Sample 6
Liver
Single-cell RNA-seq

value: Healthy liver


title: dlPFC single-nucleus transcriptomes from 5P6

value: dorsolateral prefrontal cortex


title: Control2_rep3_ATACseq


title: TAC_1331M


title: TAC_1119F


title: HD1

description:
Sample 4
Liver
Single-cell RNA-seq


title: Control2_rep1_ATACseq


title: dlPFC single-nucleus transcriptomes from 36O

value: female


title: Control2_rep2_ATACseq

value: DMSO


title: dlPFC single-nucleus transcriptomes from 76J


title: HCC3

description:
Sample 3
Liver
Single-cell RNA-seq


title: PT

description:
Sample 7
Liver
Single-cell RNA-seq

value: HCC tumor-adjacent normal liver tissue


title: dlPFC single-nucleus transcriptomes from 94S


title: Control1_rep3_ATACseq


title: Control1_rep2_ATACseq


title: TAC_1301M


title: HCC2

description:
Sample 2
Liver
Single-cell RNA-seq

value: HCC tumor


title: HCC1

description:
Sample 1
Liver
Single-cell RNA-seq


title: HD2

description:
Sample 5
Liver
Single-cell RNA-seq


title: TAC_1375M


title: Control1_rep1_ATACseq


title: Pit_Cre_Deg

data_processing:
Raw sequencing reads were obtained using Illumina’s software to remove adaptors and low quality reads.
The extracted sequencing reads were then used to identify potentially cleaved targets by the CleaveLand pipeline.
The degradome reads were matched to transcriptome to generate the degradome density file. In addition, the targeted mRNA sequences of the miRNAs were predicted using TargetFinder software (http://targetfinder.org/). The overlapped mRNAs of the predicted target mRNAs and the mRNAs in degradome density file were considered as the target genes of the miRNAs.
Assembly: ftp://mirbase.org/pub/mirbase/CURRENT/；https://www.ncbi.nlm.nih.gov/genome/13236?genome_assembly_id=383744；https://www.ncbi.nlm.nih.gov/genome/34360?genome_assembly_id=315890
Supplementary files format and content: excel,expression profiles

organism: Penicillium italicum

source_name: spores

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Poly(A) RNA is purified from plant total RNA(20ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Because of the 3′ cleavage product of the mRNA contains a 5′-monophosphate，the 5' adapters were ligated to the 5' end of the 3′ cleavage product of the mRNA by the RNA ligase. The next step is reverse transcription to make the first strand of cDNA with a 3′-adapter random primer. and size selection was performed with AMPureXP beads.Then the cDNA were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 15cycles 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 200-400 bp. At last, we performed the 50bp single-end sequencing on an Illumina Hiseq 2500 (LC Bio, China) following the vendor's recommended protocol.
Degradome sequencing

value: spores

value: incubated with Citrus reticulata exosomes or PBS


title: Control1_rep4_ATACseq


title: dlPFC single-nucleus transcriptomes from 6H6


title: Test_set_52 [204776820110_R08C01]

status: Public on Sep 25 2022

type: genomic

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

institute: Ludwig Maximilians University Hospital Munich

hyb_protocol: Bisulphite converted (using the EpiTect Bisulfite Kit (Qiagen)) DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing:
Statistical analysis was performed using the minfi package running on RStudio version 1.3.1093 based on the statistical language R version 3.5.1
Average beta-Values after normalization using the Noob method

label: Cy5 and Cy3

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction was performed on the Maxwell RSC Instrument using the Maxwell RSC FFPE Plus DNA Purification Kit (Custom, AX4920; Promega), according to the manufacturer’s instructions.

tag: gender

value: Male

tag: predicted class

value: LECA

tag: conventional class

tag: molecular workup

tag: initial diagnosis

value: Lymphoepithelial carcinoma

tag: localization

value: Nasal cavity, nasopharynx

tag: tissue source

value: Pathology, LMU Munich


title: Test_set_51 [205724780126_R08C01]

tag: age

value: ALV RMS

value: Alveolar rhabdomyosarcoma

value: Nasal cavity, paranasal sinus


title: dlPFC single-nucleus transcriptomes from 4M9

tag: individual id

tag: tissue

tag: Sex


title: Test_set_48 [205724780126_R01C01]

value: MCC

value: Merkel-cell carcinoma

value: Ridge of nose, dorsum nasi, orbit


title: Test_set_47 [205107400166_R08C01]

value: CPH

value: Craniopharyngiom

value: Base of skull

value: Neuropathology, Charité


title: Test_set_46 [203163300085_R04C01]

value: ONB

value: Olfactory neuroblastoma


title: Test_set_50 [205724780126_R07C01]

value: Male

value: Nasal cavity, base of skull


title: Test_set_45 [201876940067_R06C01]

value: PIT AD

value: Pituitary adenoma

value: Sellar region


title: BS2-2

city: Zhanjiang

first: Wei

last: Feng

address: 236 Yuanzhu Road

institute: Central People's Hospital of Zhanjiang

data_processing:
Raw data (raw reads) of fastq format were processed with Fastp (v 0.23.0), an ultra-fast FASTQ preprocessor with useful quality.
The clean reads were mapped to the mus musculus genome (mm10) using the HISAT2 software (v 2.1.0).
Reads Per Kilobase of exon per Megabase of library size (RPKM) 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.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene counts for each Sample

source_name: Interparietal bone

extract_protocol:
The mouse brain and skull tissue contains ischemic and peri-ischemic regions were harvested for RNA sequencing. Total RNA was extracted using TRIzol Reagent (Thermo Fisher Scientific Inc.) and further treated with DNase to remove genomic DNA contamination. The mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA), and was then used for RNA-sequencing library preparation with the NEBNext Ultra II mRNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA). The library was performed using Illumina sequencing with the paired-end 2 x 150 sequencing mode.
NA libraries were prepared for sequencing using standard Illumina protocols

value: Interparietal bone

tag: cell line

value: skull cell

value: 2 day of ischemic injury in brain


title: SB2-1

source_name: brain cortex

value: brain cortex

value: brain cell

tag: treatment

value: 2 day of ischemic injury in skull


title: BS2-3


title: Test_set_49 [205724780126_R05C01]

value: Female

value: EMB RMS

value: Embryonal rhabdomyosarcoma

value: Nasal cavity, paranasal sinus, orbit

value: Pathology, LMU Munich


title: BS2-1


title: SB2-2


title: SB4-2

value: 4 day of ischemic injury in skull


title: SB4-3


title: BS6-2

value: 6 day of ischemic injury in brain


title: BS6-3


title: SB2-3


title: BS6-1


title: SB4-1


title: TAC_1308F

tag: genotype

value: Lmnb2 KO

value: ventricular myocardium

value: Sham surgery


title: Test_set_40 [203982200038_R02C01]

value: PIT AD

value: Pituitary adenoma

value: Sellar region

value: Neuropathology, Charité


title: Test_set_38 [205724780127_R05C01]

value: NUT

value: SCC

value: NUT IHC positive, EBER ISH negative

value: Squamous cell carcinoma

value: Nasal cavity, paranasal sinus, base of skull, orbit


title: Test_set_42 [203821710002_R05C01]

value: Male


title: Test_set_44 [203013210156_R04C01]

value: Female

value: Unknown


title: Test_set_43 [203867050020_R08C01]


title: Test_set_41 [203821710034_R06C01]


title: Test_set_37 [205724780127_R03C01]

value: EWS

value: Ewing's sarcoma

value: Nasal cavity

value: Pathology, LMU Munich


title: Test_set_35 [205751550069_R04C01]

value: ACC

value: Adenoid cystic carcinoma


title: Test_set_36 [205724780127_R02C01]

value: ONB

value: Olfactory neuroblastoma


title: Test_set_34 [205751550069_R02C01]

value: ADC

value: Adenocarcinoma


title: Test_set_32 [205041760069_R05C01]

value: NUT

value: NUT midline carcinoma

value: Nasal cavity, paranasal sinus


title: Test_set_33 [205751550069_R01C01]


title: Test_set_30 [205617070152_R08C01]

value: LECA

value: SCC

value: NUT IHC negative, EBER ISH positive

value: Squamous cell carcinoma

value: Nasal cavity, nasopharynx


title: Test_set_31 [205041760041_R04C01]

value: Male

value: PIT AD

value: Pituitary adenoma

value: Sellar region


title: Test_set_39 [205041750127_R07C01]

value: Female

value: Neuropathology, Charité


title: Test_set_29 [205617070152_R07C01]

value: ACC

value: Adenoid cystic carcinoma

value: Nasal cavity

value: Pathology, LMU Munich


title: GPC7

tag: methylation class

value: GPC

value: Sinunasal glomangioperizytoma

value: female


title: GPC6

value: male


title: Test_set_14 [204792780042_R06C01]

value: Unknown

value: SCC

value: NUT IHC negative, EBER ISH negative


title: Test_set_23 [205751540075_R02C01]

value: Male

value: ADC

value: Adenocarcinoma


title: Test_set_24 [205617070122_R07C01]

value: Squamous cell carcinoma


title: Test_set_21 [205724780075_R08C01]

value: Female

value: ONB

value: Olfactory neuroblastoma


title: Test_set_19 [205724780075_R06C01]

value: MCC

value: Merkel-cell carcinoma

value: Dorsum nasi, nasal cavity


title: Test_set_22 [205751530163_R08C01]

value: ACC

value: Adenoid cystic carcinoma

value: Nasal cavity

value: Pathology, LMU Munich


title: Test_set_16 [205724780075_R03C01]

value: NEC-like IDH2

value: SNUC

value: IDH2 R172G mutation

value: Nasal cavity, paranasal sinus


title: Test_set_28 [205617070152_R06C01]

value: SCC

value: NUT IHC negative, EBER ISH negative


title: Test_set_20 [205724780075_R07C01]

value: Male


title: Test_set_18 [205724780075_R05C01]

value: Female

value: Ridge of nose, nasal cavity


title: Test_set_13 [205537620101_R07C01]


title: Test_set_17 [205724780075_R04C01]


title: Test_set_26 [205617070152_R03C01]

value: Unknown

value: EWS

value: Ewing's sarcoma


title: Test_set_25 [205617070152_R01C01]

value: Nasal cavity, paranasal sinus, orbit


title: Test_set_27 [205617070152_R04C01]

value: ONB

value: Olfactory neuroblastoma


title: GPC4

value: GPC

value: Sinunasal glomangioperizytoma

value: male

value: Nasal cavity


title: GPC5

value: Pathology, LMU Munich


title: GPC3


title: ACC18

value: ACC

value: Adenoid cystic carcinoma

value: Pathology, UKGM Marburg


title: Test_set_6 [205624890080_R06C01]

value: Nasal cavity, base of skull


title: Test_set_7 [205624890080_R07C01]

value: Female

value: MELA

value: Mucosal melanoma


title: Test_set_8 [205624890080_R08C01]

value: Male

value: Unknown

value: EMB RMS

value: Embryonal rhabdomyosarcoma

value: Nasal cavity, orbit


title: Test_set_5 [205624890080_R05C01]

value: NEC-like IDH2

value: SNUC

value: IDH2 R172S mutation

value: Nasal cavity, paranasal sinus


title: Test_set_12 [205537620171_R07C01]

value: NEC-like SMARCA4 ARID1A

value: SMARCA4 p.Q611* mutation, ARID1A wild type

value: Nasal cavity

value: Pathology, LMU Munich


title: Test_set_10 [204958100140_R05C01]

value: SCC

value: NUT IHC negativ, EBER ISH negative

value: Squamous cell carcinoma


title: Test_set_4 [205624890080_R04C01]

value: IDH2 R172T mutation


title: Test_set_11 [204958100140_R06C01]

value: Female


title: GPC2

value: GPC

value: Sinunasal glomangioperizytoma

value: male


title: SNUC91

value: female

value: Pathology, UKGM Marburg


title: Test_set_9 [205310760146_R01C01]

value: Male

value: ONB

value: Olfactory neuroblastoma


title: EMB_RMS9

value: EMB RMS

value: Embryonal rhabdomyosarcoma

value: Others  Koelsche, Nature Comm 2021


title: ONB82


title: SNUC89

description:
Not included in analysis
Noise point

value: SNUC

value: Nasal cavity, base of skull

tag: excluded

value: Not included in analysis

tag: rationale for exclusion

value: Noise point


title: EMB_RMS4

tag: gender


title: EMB_RMS6


title: EMB_RMS8


title: EMB_RMS7


title: EMB_RMS5


title: ADC46

value: ADC

value: Adenocarcinoma

value: University of Oviedo


title: EMB_RMS10


title: SNUC88

value: NEC-like SMARCA4 ARID1A

value: Base of skull

value: Neuropathology, Charite Berlin


title: SNUC90

description:
Not included in analysis
Low tumor cell content

value: male

value: Nasal cavity

value: Pathology, UKGM Marburg

value: Low tumor cell content


title: ADC47


title: ADC45

value: NEC-like IDH2

value: female


title: PDCA7

value: PDCA

value: Poorly differentiated carcinoma

value: Pathology, UCL London


title: ADC44


title: ADC43


title: ADC42


title: ADC41


title: ADC35


title: ADC33


title: ADC40


title: ADC34


title: ADC38


title: Test_set_1 [205624890096_R03C01]

value: Male

tag: predicted class

value: ONB

value: Olfactory neuroblastoma

value: Pathology, LMU Munich


title: Test_set_3 [205624890080_R01C01]

tag: conventional class

value: SNUC

value: IDH2 R172S mutation


title: ADC39

value: ADC

value: Adenocarcinoma

value: University of Oviedo


title: ADC37

value: male


title: Test_set_2 [205624890096_R05C01]

value: Female

value: MELA

tag: molecular workup

value: Mucosal melanoma

value: Nasal cavity


title: ADC36

tag: initial diagnosis


title: ADC31


title: ADC28


title: ADC32


title: ADC29


title: ADC27


title: ADC26


title: ADC30


title: ADC25


title: ADC23


title: ADC20

value: NEC-like SMARCA4 ARID1A

tag: localization


title: ADC22

tag: tissue source


title: ADC21

tag: age


title: Test_set_15 [205724780075_R01C01]

value: ACC

value: Adenoid cystic carcinoma


title: LECA18

value: LECA

value: Lymphoepithelial carcinoma

value: Pathology, Charite Berlin


title: LECA19


title: LECA17


title: ADC19


title: CTRL3

value: CTRL

value: Normal sinunasal tissue

value: Paranasal sinus


title: ADC24

value: ADC


title: CTRL8


title: NEC21

value: NEC

value: Neuroendocrine carcinoma


title: CTRL2

value: male


title: CTRL4

value: female


title: NUT5

value: NUT

value: NUT midline carcinoma

value: Pathology, University Stanford


title: NUT6

description:
Not included in analysis
Bad overall quality

value: Not included in analysis

value: Bad overall quality


title: CTRL6


title: SCC40

value: SCC

value: Squamous cell carcinoma

value: Nasal cavity


title: SNUC87

value: NEC-like SMARCA4 ARID1A

value: SNUC


title: CTRL7

value: CTRL

value: Normal sinunasal tissue

value: Pathology, Charite Berlin


title: SNUC82

description:
Not included in analysis
Noise point

value: Neuropathology, UKSH Luebeck

value: Noise point


title: SNUC84

value: ACC


title: SNUC86

value: male


title: SNUC81

value: Nasal cavity, base of skull, orbit

value: Neuropathology, WWU Muenster


title: SNUC78

value: female

value: Nasal cavity, paranasal sinus

value: Pathology, University Stanford


title: SNUC80

value: Pathology, MSKCC New York

tag: related publication

value: Dogan, Mod Pathol 2019

value: Not included in analysis

value: Bad overall quality


title: SNUC79

value: SNUC

value: Paranasal sinus


title: NUT7

value: NUT

value: NUT midline carcinoma


title: CTRL1

value: CTRL

value: Normal sinunasal tissue

value: Pathology, USB Basel


title: SNUC85

value: male

value: Nasal cavity

value: Pathology, Charite Berlin


title: SNUC83


title: PDCA6

value: ACC

value: PDCA

value: Poorly differentiated carcinoma


title: SNUC77

value: Pathology, MSKCC New York


title: SNUC76

value: Dogan, Mod Pathol 2019


title: SNUC75

value: Neuropathology, WWU Muenster


title: SNUC73


title: SNUC72


title: SNUC74

value: female


title: SNUC68

value: SNUC

value: Neuropathology, UKSH Luebeck


title: CTRL5

value: Paranasal sinus


title: SNUC69

value: Nasal cavity, base of skull, orbit

value: Neuropathology, Charite Berlin


title: SNUC70

value: Others


title: SNUC71


title: SNUC63

value: NEC-like IDH2


title: SNUC62

value: male


title: SNUC66

value: Pathology, USB Basel


title: SNUC65

value: Not included in analysis

value: Low tumor cell content


title: SNUC64


title: SNUC59


title: PDCA4

value: NEC-like SMARCA4 ARID1A

value: PDCA


title: SNUC58

value: Pathology, MSKCC New York


title: SNUC61

value: Dogan, Mod Pathol 2019


title: SNUC57


title: SNUC60


title: SNUC56


title: ONB81

value: ONB

value: Olfactory neuroblastoma

value: Nase of skull

value: Neuropathology, UKE Hamburg


title: NEC20

description:
Not included in analysis
Noise point

value: NEC

value: Neuroendocrine carcinoma

value: Nasal cavity, Paranasal sinus, orbit

value: Neuropathology, University Heidelberg

value: Noise point


title: ONB80

value: NEC-like IDH2

value: male

value: Nasal cavity, base of skull

value: Neuropathology, UKM Muenster


title: PDCA5

value: NEC-like SMARCA4 ARID1A

value: Poorly differentiated carcinoma

value: female


title: SNUC67

value: SNUC

value: Nasal cavity, paranasal sinus

value: Pathology, Charite Berlin


title: SNUC54


title: PDCA3

value: PDCA

value: Pathology, MSKCC New York

value: Dogan, Mod Pathol 2019


title: SNUC55

value: Base of skull

value: Neuropathology, Charite Berlin


title: SNUC53

value: Neuropathology, UKGM Giessen/Marburg


title: SNUC52

value: Neuropathology, WWU Muenster

value: Not included in analysis

value: Bad overall quality


title: SNUC50

description:
Not included in analysis
Noise point

value: Nasal cavity, paranasal sinus, orbit

value: Noise point


title: SNUC47

description:
Not included in analysis
Noise point


title: PDCA2

value: ACC

value: male


title: SNUC48


title: SNUC46

value: Paranasal sinus, base of skull

value: Neuropathology, UKM Muenster


title: SNUC51

value: SNUC


title: SNUC44

value: NEC-like SMARCA4 ARID1A


title: SNUC40

value: Brain metastasis


title: SNUC41

value: Nasal cavity


title: SNUC42

value: Neuropathology, UKSH Luebeck

value: Low tumor cell content


title: PDCA1

value: PDCA

value: Poorly differentiated carcinoma

value: Pathology, MSKCC New York

value: Dogan, Mod Pathol 2019


title: SNUC43

value: NEC-like IDH2

value: Neuropathology, Charite Berlin


title: ADC17

value: ADC

value: Adenocarcinoma

value: female

value: Paranasal sinus


title: ONB79

value: ONB

value: Olfactory neuroblastoma


title: SNUC39

description:
Not included in analysis
Noise point

value: SNUC

value: male

value: Neuropathology, University Frankfurt am Main

value: Not included in analysis

value: Noise point


title: SNUC45


title: SNUC37

value: ACC

value: Pathology, Charite Berlin


title: SNUC38

description:
Not included in analysis
Noise point


title: SNUC36

description:
Not included in analysis
Noise point

value: Pathology, USB Basel


title: SCC38

value: SCC

value: Squamous cell carcinoma

value: Nasal cavity

value: Neuropathology, UKSH Luebeck


title: SCC39


title: SNUC35

value: NEC-like IDH2

value: Neuropathology, UKGM Giessen/Marburg


title: SNUC30

value: Pathology, University Stanford


title: SNUC34

description:
Not included in analysis
Noise point

value: Pathology, MSKCC New York

value: Dogan, Mod Pathol 2019


title: SNUC31

value: SNUC


title: ONB78

value: ONB

value: Olfactory neuroblastoma

value: female

value: Bad overall quality


title: SCC37


title: SNUC28

value: male


title: SNUC29


title: SNUC27

value: High grade carcinoma consistent with SNUC


title: SNUC25

value: ACC


title: ADC18

value: ADC

value: Adenocarcinoma

value: Nasal cavity, paranasal sinus

value: Pathology, Charite Berlin


title: SNUC26

value: NEC-like IDH2


title: SNUC24


title: SNUC33


title: SNUC49

value: Nasal cavity

value: Neuropathology, Charite Berlin


title: SNUC32

value: Pathology, University Stanford

value: Not included in analysis


title: SNUC21

value: NEC-like SMARCA4 ARID1A

value: SNUC


title: SNUC22


title: SNUC19


title: SNUC20


title: ADC16

value: Intermediate-grade adenocarcinoma

value: Paranasal sinus


title: SNUC18

description:
Not included in analysis
Noise point

value: Noise point


title: ACC17

value: Adenoid cystic carcinoma

value: male


title: SNUC16

value: female


title: SCC33

value: SCC

value: Squamous cell carcinoma


title: SCC36


title: SNUC17

value: Bad overall quality


title: SCC34

value: Pathology, Charite Berlin


title: SCC32


title: SCC31


title: SNUC23

value: NEC-like IDH2


title: SCC30

value: Nasal cavity


title: SCC29


title: SCC27


title: SCC22


title: SCC25


title: SCC24


title: SCC28


title: SCC23


title: SCC21


title: SNUC15

value: Neuropathology, University Frankfurt am Main


title: SCC20


title: ACC16

value: ACC


title: SCC18

value: Squamous cell carcinoma, HPV-related


title: SCC26


title: SNUC14

value: NEC-like SMARCA4 ARID1A


title: ONB77

value: ONB

value: Olfactory neuroblastoma


title: SCC15