title: synovial fibroblast, siHIP1a

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Inthis step, clean data (clean reads) were obtained by removing reads containing adapter, readscontaining ploy-N and low quality reads from raw data. At the same time, Q20, Q30andGCcontent the clean data were calculated. All the downstream analyses were based on thecleandata with high quality
Remove reads with adapter contamination.
Remove reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%).
Remove reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read.
Raw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality
Assembly: Hg19
Supplementary files format and content: The abundance of transcript reflects gene expression level directly. In RNA-seq experiment, we estimate gene expression level by the abundance of transcripts(count of sequencing) that mapped to genome or exon. Reads count is proportional to be proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments.(Mortazavi et al. 2008)
Supplementary files format and content: Tab-delimited text file includes fpkm for each sample

source_name: synovial fibroblast

growth_protocol: Primary FLS cell lines from patients with RA were generated as previously described (15). Briefly, freshly obtained synovial tissues were minced and incubated with a solution containing DNase (0.15mg/ml), hyaluronidase type I-S (0.15 mg/ml), and collagenase type IA (1 mg/ml) (Sigma, St.Louis, MO) in DMEM (Invitrogen, Carlsbad, CA) for 1 hour at 37°C. Cells were washed and re-suspended in complete media containing DMEM supplemented with 10% FBS (Invitrogen), glutamine (300 ng/ml), amphotericin B (500 ng/ml) (Sigma), and gentamicin (20 μg/ml) (Invitrogen). After overnight culture, non-adherent cells were removed and adherent cells kept in culture. All experiments were performed with FLS after passage four (>95% FLS purity).

treatment_protocol: Dharmacon SMARTpool siRNA targeting each gene or a non-coding control were transfected into RA FLS according to the manufacturer’s instructions. Cells were then incubated at 37°C for 24–48 hours prior to initiating any assay. Knockdown was confirmed with qPCR.

value: synovial fibroblast

value: HIP1 Knockdown


title: synovial fibroblast, siHIP1c

status: Public on Nov 21 2024

type: SRA

city: New York

first: Teresina

last: Laragione

state: NY

address: 1468 Madison Ave

department: Medicine

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNAextracted by Qiagen RNAeasy kit, and quantified by Nanodrop. 400 ng per sample was sent to Novogene (Beijing, China) for sequencing and analyses
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using randomhexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional libraryor dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, sizeselection, amplification, and purificationFor the directional library, it was ready after end repair, A-tailing, adapter ligation, sizeselection, USER enzyme digestion, amplification, and purification.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer forsize distribution detection. Quantified libraries will be pooled and sequenced on Illuminaplatforms, according to effective library concentration and data amount. The clustering of the index-coded samples was performed according to the manufacturer’sinstructions. After cluster generation, the library preparations were sequenced on an Illuminaplatform and paired-end reads were generated

tag: cell type

tag: genotype

tag: treatment


title: sgCNOT3-chase 4h_rep2_SLAM16

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
Raw data from machine were de-multiplexed and converted to fastq files using bcl2fastq.
The SLAM-seq data was processed with the slam dunk pipeline (https://github.com/t-neumann/slamdunk 0.3.3.).
The reads were aligned to the human genome GRCh38.
Assembly: Human genome assembly GRCh38
Supplementary files format and content: Processed data is in an excel sheet showing the T>C conversion ratio of each transcript in each sample at each timepoint.

molecule: polyA RNA

source_name: Human embryonic kidney

growth_protocol: HEK293T cells were cultured in Dulbeccoʹs Modified Eagleʹs Medium (DMEM) (Invitrogen) supplemented with 10% (v/v) fetal bovine serum (Sigma) and 1×Antibiotic-Antimycotic (Invitrogen).

extract_protocol:
Total RNA was isolated using TRIzol reagent(Thermofisher Scientific), accoding to the manufacturer’s instructions.
Total RNA was treated with IAA according to the SLAM-seq Kinetics Kit (Lexogen, 062.24) manufacturer’s instructions.  SLAM-seq libraries were constructed using the QuantSeq 3' mRNA-Seq V2 Library Prep Kit FWD with UDI 12 nt Set B1 (Lexogen, 192.24).
QuantSeq 3' mRNA-seq

treatment_protocol: Cells were transduced with lentiCRISPR_v2 expressing negative control guides (sgNT1 and sgNT2) or guides targeting CNOT3 (sgCNOT3-1 and sgCNOT3-2), selected in puromycin for four days, and seeded into 6-well plates coated with poly-D-lysine. 24 hours later, cells were incubated with 75 µM 4-SU for 24 hours, during which media was exchanged every 3 hours, to label newly synthesized RNA. Cells were then washed 2 times with PBS, and fresh medium containing 10 mM UTP was added to stop labelling. Cells were harvested at 0, 1, 2, 4, 8, 12 hours after UTP addition.

tag: tissue

value: Human embryonic kidney

tag: cell line


title: synovial fibroblast, siHIP1b


title: SP-Mgg500-2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Inthis step, clean data (clean reads) were obtained by removing reads containing adapter, readscontaining ploy-N and low quality reads from raw data. At the same time, Q20, Q30andGCcontent the clean data were calculated. All the downstream analyses were based on thecleandata with high quality
Remove reads with adapter contamination.
Remove reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%).
Remove reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read.
Raw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality
Assembly: mm10
Supplementary files format and content: The abundance of transcript reflects gene expression level directly. In RNA-seq experiment, we estimate gene expression level by the abundance of transcripts(count of sequencing) that mapped to genome or exon. Reads count is proportional to be proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments.(Mortazavi et al. 2008)
Supplementary files format and content: Tab-delimited text file includes fpkm for each sample

organism: Mus musculus

source_name: spleen

growth_protocol: Male C57BL/6 mice were purchased from Taconic (Rensselaer, NY). female NOD/ShiLtJ were purchased from Jackson Laboratories (Farmington, CT).  KBxN (KRN) TCR transgenic mice (gift from Dr. C. Benoist, Boston, MA) were bred and maintained at Mount Sinai. Mice were housed under specific pathogen-free conditions and all experiments conducted under a protocol approved by the Mount Sinai Institutional Animal Care and Use Committee.

treatment_protocol: KRN TCR transgenic mice were crossed with NOD (KRNxNOD F1) and the arthritogenic serum was collected from 60-day old arthritic mice. Serum from different batches was pooled and administered to male C57BL/6 mice at 100 µL IP on days 0 and 2. Mice typically develop arthritis on day 3, and were followed for 15 days and scored three times a week

value: spleen

value: regular Mg500


title: sgCNOT3-chase 4h_rep1_SLAM15


title: synovial fibroblast, siHIP1rc

value: HIP1r Knockdown


title: AS-778931-LR-60677

city: Heidelberg

first: Stephanie

last: Gehrs

address: Im Neuenheimer Feld

country: Germany

institute: DKFZ

library_source: transcriptomic single cell

data_processing:
scRNA-sew: Raw sequencing data were demultiplexed and FASTQ files were generated using bcl2fastq software (Illumina, v2.20.0.422). Using salmon, FASTQ files were mapped to the GRCm39 mouse reference genome and count matrices were constructed with the R package tximport.
Assembly: GRCm39
Supplementary files format and content: CSV files containing the count matrix (count_matrix.csv) and the Seurat object metadata (GEO_metadata.csv)

extract_protocol: Whole transcriptome scRNA-seq was performed following an adapted SMARTseq2.5 protocol.

value: Placenta

tag: age

value: Endothelial cells

value: WT


title: SP-Mgg500-1


title: sgCNOT3-chase 2h_rep2_SLAM12


title: synovial fibroblast, siHIP1rb


title: AS-778913-LR-60677


title: Chondrocytes, Col11ZS, scRNAseq

city: Suita

first: Kenji

last: Hata

state: Osaka

address: 1-8 Yamadaoka

department: Biochemistry

country: Japan

institute: Osaka University graduate school of dentistry

description: 10x Genomics

data_processing:
Sequencing data were first processed using cellranger-7.1.0 and aligned to the mouse genome (mm10).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Limbs

extract_protocol:
Limbs of Col11a2-ZsGreen mice at E15.0 were harvested and cut into small pieces with scissors and blades. Dissected tissues were then incubated with 0.25 % Collagenase Type2）in DMEM for  min at 37°C and dissociated into single cells.
Sorted single cells were applied to 10X genomics Chromium controller and Gel Beads-in-emulsion (GEMs) were generated using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Then the Gel Beads were dissolved and the cell lysate was incubated with reverse transcription (RT) reagents to produce barcoded cDNA followed by the cDNA amplification and 3’ gene expression library construction.

value: Limbs

tag: strain

value: Chondrocytes


title: sgCNOT3-chase 8h_rep2_SLAM20


title: LMNSC01 human cell line, replicate 1,scRNAseq

city: Duarte

first: Yate-Ching

last: Yuan

state: CA

address: 1500 East Duarte

institute: City of Hope

description: 10x Genomics

data_processing:
The demultiplexing, libraries were normalized based on their reads per cell. Rebalanced pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 101×11×11×101 cycles.
scRNAseq data was analyzed by Illumina Partek™ Flow™ v12.1.0 bioinformatics software (https://www.partek.com/partek-flow/).  Using two replicates for each of LMNSC01 and LMNSC02 cell lines, data were imported into Partek Flow, data were processed based on Illumina Single Cell 3' v3 protocol with estimated 13,705 cells, followed by pre-alignment QA/QC to assess the overall quality of the cells then further filtered by three quality control filters: Mitochondrial reads (>5%), the count of read between 500 - 10,000. Features where the value was <=1.0 in at least 99.9% of the cells, were excluded. PCA was made with 100 principal components, and the variance was set as the features contribute. For the UMAP the local neighborhood size was set at 30, a minimal distance of 0.3, distance metric was set as Cosine, 0 iterations, random generator seed 42, the initialize output values Random, and the number of principal components was set as 20. Normalization with the setting of log2(cpm+1) followed by differential gene expression (DGE) analysis using ANOVA to generate the statistical significant differential genes filtered by |FC|>2 and FDR < 0.001 by comparing between LMNSC01 and LNDSC02 cell lines for downstream analysis of Hierarchical clustering heatmap,  gene set enrichment and Pathway analysis. Additionally, an Qiagen Ingenuity Pathway Analysis was done to explore the interactions between the DEGs based on enrichment score calculated relative to a set of background genes relevant for this experiment.
Assembly: GRCh38
Supplementary files format and content: tab-delimited csv file include raw count matrix file

source_name: brain

growth_protocol: LMNSC01 and LMNSC02 cells were grown in T-75 flasks  in NeuroCultTM NS-A Basal Medium (Human) (Stem Cell Technologies, Cat# 05750), supplemented either with NeuroCultTM NS-A Proliferation Supplement (Human) (Stem Cell Technologies, Cat# 05751) or NeuroCultTM NS-A Differentiation Supplement (Human) (Stem Cell Technologies, Cat# 05752), basic Fibroblast Growth Factor (bFGF) at concentration 10ng/mL (Stem Cell Technologies, Cat# 78003), Epidermal Growth Factor (EGF) at concentration 10 ng/mL (Stem Cell Technologies, Cat# 78006), and heparin at 0.2x104% concentration (Stem Cell Technologies, Cat# 07980#) under physiological hypoxia conditions at at 4% O2 and 37C.

extract_protocol:
LMNSC01 and LMNSC02 cells were dissociated from T75 cell culture flasks and counted, and a targeted recovery of 15,000 cells was calculated for each sample by loading a concentration of approximately 15,000 cells.
The library constructed following the manufacturer’s protocol. Library quality control was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA)
Cells were immediately processed with the 10× Genomics Chromium Next GEM Single Cell 3’ v3.1 (Dual Index) kit (10× Genomics, Pleasanton, CA). Samples were loaded, cDNA amplified, and library constructed following the manufacturer’s protocol. Library quality control was based on Agilent Tapestation 4200 HS D1000 screentapes (Agilent Technologies, Waldbronn, Germany). Multiplexed library pool was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms (Kapa BioSystems, Boston, MA) and sequenced at shallow depths on Illumina’s iSeq 100 v2 flowcell for 28×10×10×90 cycles for estimated reads per cell. After demultiplexing, libraries were normalized based on their reads per cell. Rebalanced pool QC was based on Agilent Tapestation 4200 HS D1000 and Kapa Library Quantification Kit for Illumina platforms and high depth sequenced on Illumina’s NovaSeq 6000 S4 v1.5 flow cell for 101×11×11×101 cycles.

treatment_protocol: no treatment

value: brain

value: neural stem cells

value: wild type

value: no treatment


title: AS-778881-LR-60677


title: sgCNOT3-chase 2h_rep1_SLAM11


title: synovial fibroblast, siHIP1ra


title: AS-778879-LR-60677


title: 017_mouse_brain_IP_rep1

city: Chicago

first: Bei

last: Liu

state: IL

address: 929 EAST 57TH STREET

department: Chemistry

institute: The University of Chicago

description: two_rep_DG_clustering_mousebrain_with_seq_structure_snord115_116.csv

data_processing:
KARR-seq: Adaptors from raw reads were trimmed using cutadapt, the overlapping read pairs (2 × 150 bp) were merged into single-end reads and de-duplicated using fastp. The resulting single-end FASTQ files were then aligned to a customized reference genome containing human rDNA sequence (GenBank: KY962518.1) and snoRNA sequences (snoRNA annotation was acquired from snoDB 3) using STAR to map snoRNA-rRNA interactions. The following STAR parameters were used to recover gapped and chimeric reads based on the CRSSANT module (https://github.com/zhipenglu/CRSSANT): --runMode alignReads --outFilterMultimapNmax 20 --chimMultimapNmax 100 --alignIntronMin 1 --scoreGap 0 --scoreGapNoncan 0 --scoreGapGCAG 0 --scoreGapATAC 0 --scoreGenomicLengthLog2scale -1 --chimFilter None --chimOutType WithinBAM HardClip --chimSegmentMin 5 --chimJunctionOverhangMin 5 --chimScoreJunctionNonGTAG 0 --chimScoreDropMax 80 --chimNonchimScoreDropMin 20 --peOverlapNbasesMin 12 --peOverlapMMp 0.05 --limitOutSJcollapsed 10000000). The known snoRNA-rRNA interactions that lead to RNA modifications were obtained from snoRNA-LBME-db (https://www-snorna.biotoul.fr/), snOPY (http://snoopy.med.miyazaki-u.ac.jp/), snoDB (https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/), and snoRNA Atlas (http://snoatlas.bioinf.uni-leipzig.de/index.php#snoID_0492). The box sequences of snoRNAs were obtained from snoRNA Atlas. To map interactions between snoRNA and non-rRNA, FASTQ files were aligned to the human rDNA sequence (GenBank: KY962518.1). The unmapped reads were then used to map to the hg38 human genome. Chimeric reads were extracted from the resulting BAM file and reads containing snoRNAs were filtered out based on annotations from snoDB. The resulting chimeric reads were further de-duplicated based on the coordinates of snoRNA and their respective targets. The deduplicated coordinate pairs (snoRNA and the target) were then subjected to duplex group (DG) clustering using a spectral clustering algorithm in the CRSSANT module.   small RNA-seq: Adaptors and low-quality reads were removed from raw reads were removed using cutadapt. Duplications were removed using Clumpify (BBMap tool v.38.73). 5-mer random barcodes at reads ends were trimmed, and low-quality or short reads (less than 20 nt) were removed using cutadapt. Remaining reads were aligned to hg38 genome using HISAT2 and the expression of snoRNAs were quantified using StringTie.
Assembly: hg38/mm10
Supplementary files format and content: snoKARR-seq: csv file for snoRNA-target interactions Chr_x The chromosome name of the snoRNA Start_x The starting position of thesnoRNA in the chromosome End_x The ending position of thesnoRNA in the chromosome Strand_x The strand of thesnoRNA in the chromosome Gene Name_x The name of thesnoRNA Chr_y The chromosome name of the snoRNA target Start_y The starting position of thesnoRNA target in the chromosome End_y The ending position of thesnoRNA target in the chromosome Strand_y The strand of thesnoRNA target in the chromosome Gene Name_y The name of thesnoRNA target Gene Type_y The type of thesnoRNA target interaction_count The amount of chimeric reads in two replicates, separated by '_' dbn The predicted duplex structure in dot-bracket-notation seq_total The sequences of the predicted duplex structure energy The predicted free energy of the duplex structure   small RNA-seq: tsv file for snoRNA abundance Gene Name The name of the snoRNA Reference The name of the chromosome of the snoRNA Start The starting position of thesnoRNA in the chromosome End The ending position of thesnoRNA in the chromosome TPM_x The TPM in replicate1 TPM_y The TPM in replicate2 mean_TPM The mean TPM from replicate 1 and 2
Library strategy: KARR-seq

source_name: Brain

growth_protocol: HEK293T (ATCC, CRL11268), HepG2 (ATCC, HB8065), and MDA-MB-231 (ATCC, HTB-26) cells were cultured in DMEM (Gibco 11995), while PC3 (ATCC, CRL-1435) and A549 (ATCC, CCL-185) cells were cultured in DMEM/F-12 (Gibco 11320033). Both media were supplemented with 10% (v/v) fetal bovine serum (Gibco, A5256801), 1% penicillin-streptomycin (Gibco, 15140122). All cells were maintained at 37 °C with 5% CO2.

extract_protocol:
KARR-seq: Live cells or homogenized tissue samples were treated with N3-kethoxal, cells were then lysed and RNA inproximity is crosslinked by dendrimers. The sample was then treated with proteinase K and Dnase. RNA was extracted using phenol chloroform.  smallRNA-seq: Total RNA was extracted using TRIzol, and small RNA fraction was isolated using the mirVana™ miRNA Isolation Kit (Invitrogen, AM1561).
KARR-seq: 10-50 ng of ligated RNA was used for reverse transcription (RT) using the RT reagents in the SMARTer Stranded Total RNA-seq kit v2 – pico input mammalian (Takara, 634413). After RT, 2 µL of RNase H (NEB M0297S) was added to each sample, which was then incubated for 20 minutes at 37°C. The reaction was quenched by heating inactivation for 5 minutes at 70°C. Subsequently, cDNA was purified using the DNA Clean & Concentrator-5 kit. 10% of the cDNA was saved as an input sample, while the remaining cDNA was used for snoRNA enrichment. After streptavidin beads pulldown, the resulting cDNA was subjected to library construction using the SMARTer Stranded Total RNA-seq kit v2 – pico input mammalian (Takara, 634413).   Small RNA-seq: Small RNA fractions were isolated using the mirVana™ miRNA Isolation Kit (Invitrogen, AM1561) according to the manufacturer's protocol. The resulting small RNA fraction was subsequently used for sequencing library construction using the NEBNEB Next Small RNA Library Prep Set for Illumina (NEB E7330S) according to the manufacturer's protocol.

value: Brain


title: 017_mouse_brain_IP_rep2


title: sgCNOT3-chase 1h_rep2_SLAM8


title: AS-778935-LR-60677


title: 016_mouse_brain_input_rep2


title: sgCNOT3-chase 0h_rep2_SLAM4


title: sgCNOT3-chase 1h_rep1_SLAM7


title: 016_mouse_brain_input_rep1


title: synovial fibroblast, siCTL71a

value: sictl


title: sgCNOT3-chase 0h_rep1_SLAM3


title: synovial fibroblast, siCTL71b

value: synovial fibroblast


title: Macrophage, tumor, WT5

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Mapping and quantification using STAR and Salmon: nf-core/rnaseq pipelin (v.3.9) on mm10.
Counts were normalized for library size using TMM method from EdgeR (v.3.32.1) and voom from limma (v.3.46.0).
Assembly: mm10
Supplementary files format and content: tab separated, raw counts, TPM and normalized counts.

source_name: tumor

extract_protocol:
Tumor tissues were cut into small pieces and digested in RPMI containing collagenase IV (1mg/ml; Worthington Biochemical Corporation), DNase I (40 μg/ml; Roche), and 1% FBS for 30 min at 37 °C. Samples were mixed up and down every 10min. Tubes were centrifuged for a few seconds at 1500rpm and supernatants filtered through a 70µm cell strainer in FACS buffer to stop the reaction. Remaining tissue was further digested in RPMI with collagenase D (1 mg/ml; Roche), DNase I (40 μg/ml; Roche) and 1% of FBS for 20 min at 37 °C, with additional two cycles of repeated pipetting. The solution was filtered through a 70µm cell strainer in in FACS buffer and pool into the first collected tubes.digestion was followed by debris removal using Lympholyte®-M (CEDARLANE) according to manufacturer’s instructions. Sorting was based on common markers CD45+Lin (CD19/CD3)-Ly6G-CD11b+ with exclusion of DCs (CD11chi F4/80-), and further separated as macrophages (F4/80+Ly6C-) and monocytes (F4/80-Ly6C+). Total RNA was isolated using miRNeasy Mini Kit (Qiagen). Total RNA was quantified with a Qubit (fluorimeter from Life Technologies) and RNA integrity assessed with a Bioanalyzer (Agilent Technologies).
The SMART-Seq v4 kit from Clonetech was used for the reverse transcription and cDNA amplification according to manufacturer’s specifications, starting with 1ng (for macrophage) or 10ng (for monocyte) of total RNA as input. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina. Library molarity and quality were assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies).

value: tumor

value: macrophage

value: LEC-CH25h WT

value: CPG-B+OVA vaccination


title: AS-778877-LR-60677


title: siNUSAPc

value: NUSAP Knockdown

value: siNUSAP


title: AS-778873-LR-60677

value: Placenta

value: Endothelial cells


title: AS-778875-LR-60677

value: WT


title: RNA-seq METTL4-si Hypoxia 2

city: Taoyuang

first: Kou-Juey

last: Wu

state: Taiwan

address: No.15, Wenhua 1st Road, Gueishan Dist

department: Cancer Genome Research Center

country: Taiwan

institute: Chang Gung Memorial Hospital at Linkou

data_processing:
The RNA-seq data were was processed using the standard ENCODE pipeline (https://github.com/ENCODE-DCC/rna-seq-pipeline) with the hg38 and GENCODE v25 annotations.
We selected the RNA-Seq by Expectation-Maximization (RSEM) gene or transcript quantification tables for downstream analysis
Data from each sample was were imported using tximport, and differential gene analysis was conducted using both edgeR and limma with the cut off by p-value < 0.05 and log2FC higher or lower than 0
Assembly: hg38
Supplementary files format and content: RSEM counts files across each condition; tsv file of edgeR process tab for hypoxia vs. normoxia and METTL4-si vs scr-si under hypoxia

source_name: FADU

growth_protocol: The cell line was cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, 1 mM sodium pyruvate, and 1× Antibiotic-Antimycotic (Gibco), under the conditions of 5% CO2 at 37°C.

extract_protocol:
Cell pellets collapsed from the detached cells in the ATAC-seq procedure were washed with 1× iced cold PBS and lysed with 1 ml Trizol (Ambion) at room temperature for 5 minutes. To the lysed sample, 200 µl of chloroform was added, and it was then mixed vigorously using a vortex. The mixture was placed on ice for 10 minutes. Following this, samples were centrifuged at 12,000 g at 4°C for 15 minutes. The supernatants were carefully collected and mixed with equal volumes of ethanol. The mixture was transferred to the column and RNA was extracted followed by RNA clean & concentrator-5 (Zymo) with DNase I treatment.
The RNA-seq library was constructed using the RiboMinus with stranded RNA hyper prep kit (Zymo) with an input of 1 µg RNA. Sequencing data were generated by Illumina Nextseq 550 with 150 bp paired-end sequence.

treatment_protocol: Knockdown of METTL4 was achieved using a previously established method with lenti-virus infection. For hypoxic conditions, cells were incubated in an environment of 1% O2, 5% CO2, and 94% N2 at 37°C for 18 hours.

value: FADU

value: head and neck cancer

value: METTL4-si hypoxia


title: 6mA-ChIP-exo Hypoxia-WGA

library_source: genomic

data_processing:
Sequenced reads were processed and trimmed using Trim Galore.
To eliminate potential noise in 6mA detection, reads aligning to mycoplasma and mitochondria were filtered out.
The filtered reads were aligned to the hg38 using bowtie2.
After alignment, aligned reads were filtered based on a mapping quality (MAPQ > 30) and removed PCR duplicates by picard.
6mA border sites of various conditions, normoxia, hypoxia, and METTL4-si under hypoxia, were identified using Model based Analysis of ChIP-Exo (MACE).
Assembly: hg38
Supplementary files format and content: 6mA peaks: bed, 6mA signals: bigwig
Library strategy: 6mA-ChIP-exo

molecule: genomic DNA

extract_protocol:
DNA was extracted from cell pellets using the phenol chloroform, followed by DNA fragmentation in the range of 100-200 bp according to the manufacturer's protocol for the Bioruptor Pico with 0.65 ml microtubes.
30~100 µg of fragmented DNA was hybridized with 3 µg of the 6mA antibody (sysy-003, Synapse) overnight. The DNA:antibody mixture was crosslinked using UVC irradiation in 1× IP buffer (10 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.1% Igepal-630) and pulled down by protein A dynabeads (Invitrogen). Subsequent washes were performed with FA lysis buffer (50 mM HEPES-KOH pH 7.4, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), NaCl buffer (50 mM HEPES-KOH pH 7.4, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), LiCl buffer (100 mM Tris-HCl pH 7.9, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate), TE buffer (10 mM Tris-HCl pH 7.4, 1 mM EDTA), and Tris buffer (10 mM Tris-HCl pH 7.4) in following enzymatic steps: DNA repair with PreCR Repair mix (M0309S, NEB), A-taling with Klenow Fragment (3’-5’, exo-) (M0212S, NEB), ligase the adapter with T4 ligase (M0202S, NEB) and T4 Polynucleotide Kinase (M0201S, NEB), fill-in with phi29 DNA polymerase (M0269S, NEB), and digest with lambda exonuclease (M0262S, NEB). After a series of enzymatic reactions, DNA was eluted using an elution buffer (100 mM NaHCO3, 1% SDS) combined with RNase A. The sample was transferred to a new tube and digested with proteinase K at 56°C overnight. DNA was purified using 3× SPRI beads (Beckman) clean-up, followed by a second adapter ligation using a splint adapter. The adapter ligated sample was purified by 3× SPRI beads clean-up. Amplification was performed using 1× Phusion High-Fidelity PCR Master Mix (NEB) and Illumina library primers (P-1.3 and P-2.1) for 12-14 cycles. The product was then purified using 1× SPRI beads, resulting in a sequence library with an approximate concentration of 1~2 nM.

value: hypoxia


title: AS-778871-LR-60677


title: siNUSAPb


title: Macrophage, tumor, WT3


title: AS-778911-LR-60677


title: synovial fibroblast, siCTL71c


title: RNA-seq METTL4-si Hypoxia 1


title: Macrophage, tumor, WT2


title: AS-778869-LR-60677


title: Macrophage, tumor, WT1


title: RNA-seq Hypoxia 2


title: siCTL71b


title: siCTL71c


title: Macrophage, tumor, HE5

value: LEC-Ch25h KO


title: RNA-seq Hypoxia 1


title: AS-778909-LR-60677


title: Macrophage, tumor, HE4


title: siCTL71a


title: AS-778905-LR-60677


title: RNA-seq Normoxia 2

value: normoxia


title: Macrophage, tumor, HE3


title: MCF10A cells, delT,#3

city: Paris

first: Elodie

last: Girard

address: 11-13 rue Pierre et Marie Curie

country: France

institute: Institut Curie

data_processing:
Raw counts were generated using Star gene quantification mode (--quantMode GeneCounts) on the Gencode v19 gene database.
Raw counts were normalized using  the TMM method using EdgeR (v3.38.2) and Limma's voom function (v3.52.2).
Assembly: hg19
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample
Supplementary files format and content: Tab-delimited text file containing TPM for each sample

growth_protocol: MCF10A cells were grown in DMEM-HG/F-12 supplemented with 5% horse serum, 20 ng/ml human epidermal growth factor, 0.5 mg/ml hydrocortisone, 100 ng/ ml cholera toxin, 10 µg/ ml insulin, and 1% penicillin–streptomycin

extract_protocol:
2x106 cells were harvested and RNA isolated using the NucleoSpin Triprep kit
Stranded mRNA prep Ligation-Illumina

treatment_protocol: del5 and delT MCF10A cells were obtained using CRISPR/Cas9- or TALEN gene editing , clones  from these and MCF10A parental controls were selected, confirmed by Sanger sequencing and expanded  prior to RNA extraction

value: non-malignant breast epithelial cell line

value: delT


title: RNA-seq Normoxia 1


title: Macrophage, tumor, WT4

value: tumor


title: AS-778903-LR-60677


title: H3K27Ac Hypoxia

data_processing:
Sequenced reads were processed and trimmed using Trim Galore.
To eliminate potential noise in 6mA detection, reads aligning to mycoplasma and mitochondria were filtered out.
The filtered reads were aligned to the hg38 using bowtie2.
After alignment, aligned reads were filtered based on a mapping quality (MAPQ > 30) and removed PCR duplicates by picard.
Peaks were called by MACS2.
Assembly: hg38
Supplementary files format and content: ChIP peaks: bed, ChIP signals: bigwig

extract_protocol:
Approximately 1 × 10^7 cells were harvested by scraping the plates and transferring them into a 15 ml tube. Cells were centrifuged at 2,000 g at 4°C for 5 minutes. The supernatant was discarded, and cells were lysed in 10 ml ice-cold cell lysis buffer (20 mM Tris-HCl pH 8.0, 85 mM KCl and 0.5% NP-40) containing 1× proteinase inhibitor (PI). The lysed cell suspension was rotated at 8 r.p.m. at 4°C for 15 minutes using a hula mixer. Nuclei were counted, and approximately 3 × 10^7 nuclei were pelleted by centrifugation at 2,000 g at 4°C for 5 minutes. The pelleted nuclei were resuspended in 2 ml nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, and 1% SDS) containing 1× PI. Sonication was performed in a 15 ml tube with sonication beads with Bioruptor pico, alternating 30 seconds "on" and 30 seconds "off" for a total of 30 cycles at 4°C. The quality and size range of the sheared DNA were assessed using gel electrophoresis to confirm the desired fragmentation.For chromatin fraction quality assessment, 10 µl of the fraction was treated with proteinase K and purified using a PCR clean-up kit, followed by gel electrophoresis. 40 µl of protein A dynabeads were blocked in 500 µl of RIPA-150 (50 mM Tris-HCl pH 8.0, 0.15 M NaCl, 1 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate) containing 3% BSA at 8 r.p.m. at 4°C for 1 hour in a 1.5 ml tube using a hula mixer. 2 µg of antibody (H3K4me1, H3K4me3, H3K27Ac) was pre-bound to the protein A dynabeads in 500 µl of RIPA-150 at 8 r.p.m. at 4°C for 2 hours in a 1.5 ml tube using a hula mixer. 700 µl of chromatin fraction was diluted with 6.4 ml of ChIP dilution buffer (50 mM Tris-HCl pH 8.0, 0.167 M NaCl, 1.1% Triton X-100, 0.11% sodium deoxycholate) and 2 ml of RIPA-150. The pre-bound dynabeads were mixed with the diluted chromatin fraction. The mixture was then incubated at 8 r.p.m. at 4°C overnight in a 15 ml tube using a hula mixer. The beads were washed sequentially with 500 µl of RIPA-150, RIPA-500 (50 mM Tris-HCl pH 8.0, 0.5 M NaCl, 1 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100 and 0.1% sodium deoxycholate), RIPA-LiCl (50 mM Tris-HCl pH 8.0, 0.5 M NaCl, 1 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100 and 0.1% sodium deoxycholate) and TE buffer. Between each wash, the beads were transferred to a new tube to minimize non-specific binding. DNA was eluted in elution buffer containing RNase A. The eluted sample was transferred to a new tube and digested with proteinase K at 56°C overnight. Purified DNA followed by DNA concentrator-5 (Zymo).
Library construction was carried out using KAPA HyperPrep Kits.


title: Macrophage, tumor, HE2

value: macrophage


title: MCF10A cells, delT,#2


title: MCF10A cells, delT,#1


title: H3K27Ac Normoxia


title: Macrophage, tumor, HE1


title: AS-778901-LR-60677


title: siNUSAPa

value: synovial fibroblast


title: AS-778867-LR-60677


title: AS-778899-LR-60677


title: MCF10A cells, del5,#3


title: MCF10A cells, del5,#2


title: H3K4me3 Hypoxia


title: AS-778897-LR-60677


title: H3K4me3 Normoxia


title: Monocyte, tumor, WT4

value: monocyte

value: LEC-CH25h WT

value: CPG-B+OVA vaccination


title: Monocyte, tumor, WT5


title: AS-778907-LR-60677

value: Placenta


title: H3K4me1 Hypoxia


title: Monocyte, tumor, WT3


title: MCF10A cells, del5,#1


title: MCF10A cells, Ctrl,#3


title: AS-778895-LR-60677

value: Endothelial cells


title: AS-778893-LR-60677

value: WT


title: Monocyte, tumor, WT2


title: Monocyte, tumor, WT1


title: ATAC-seq METTL4-si Hypoxia 2

data_processing:
ATAC-seq was processed followed by standard ENCODE pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) with the hg38 and GENCODE v25 annotations
Tag aligned bed files which did not contain mitochondria reads were selected for downstream analysis.
Peaks were identified using MACS2 with the parameters “-f BED -g --shift -75 --extsize 150 --nomode --call-summits --keep-dup all -p 0.01”, targeting chromatin accessible regions
To identify conserved accessible regions across biological replicates for each condition, we called peaks from the merged tag-aligned files for each condition.
Only peaks conserved across all replicates were selected for downstream analysis.
Assembly: hg38
Supplementary files format and content: ATAC peaks: bed, ATAC signals: bigwig, csv file of diffbind process tab for hypoxia vs. normoxia and METTL4-si vs scr-si under hypoxia

extract_protocol:
Cells were detached from the plates using trypsin, and 5 × 104 detached cells were collected into a 1.5 ml tube. Cells were centrifuged at 500 g, 4°C for 5 minutes and washed twice with 1× iced cold PBS.  Cell pellets were resuspended in 50 µl ATAC resuspend buffer (ATAC-RSB) (10 mM Trizma pH 7.8, 10 mM NaCl and 3 mM MgCl2), supplemented with 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin. The mixture was gently pipetted and incubated on ice for 3 minutes. To quench the lysis, 1 ml ATAC-RSB supplemented with 0.1% Tween-20 was added. The samples were centrifuged at 500 g, 4°C for 5 minutes to pellet the nuclei. The nuclei were subjected to a transposase mix (2.5 µl TDE1, 25 µl 2X TD buffer, 16.5 µl 1× PBS, 0.5 µl 10% Tween-20, 0.5 µl 1% digitonin and 5 µl ultra pure water) and reaction was performed at 37°C with shaking at 1,000 r.p.m. on a ThermoMixer for 30 minutes. After transposition, DNA was purified using the DNA Clean & Concentrator-5 kit (Zymo), following the manufacturer's protocol.
PCR was performed using the NEBNext High-Fidelity 1× PCR Master Mix, supplemented with primers containing the sequence of Illumina adapters and indexes, to generate sequencing libraries.

value: FADU


title: Monocyte, tumor, HE5


title: ATAC-seq METTL4-si Hypoxia 1

value: head and neck cancer


title: ATAC-seq Hypoxia 2


title: Monocyte, tumor, HE4


title: Negative control at 5 day (replicate 2 of 3)

city: Tuscaloosa

first: Daryl

last: Lam

state: Alabama

department: Biological Sciences

institute: University of Alabama

data_processing:
Reads were cleaned using TRIMGALORE v 0.4.2 using the default settings
Cleaned reads were mapped to GRCh38.110 genome using STAR version 2.5.3a using the default settings
BAM files were assessed by featureCounts in the Subread package v 2.0.1 using the default settings
Differential expression was analyzed in DeSeq2 v 1.34.0
Supplementary files format and content: comma separated values files contains the raw counts for the 2 day experiments
Supplementary files format and content: comma separated values files contains the raw counts for the 5 day experiments
Assembly: none; clean reads were mapped to annotated human genome (GRch38.110)

source_name: derived brain-like endothelial cell

growth_protocol: iBEC cells were grown on Endothelial Cell (EC) media (human endothelial cell serum free medium (Gibco; 11111-044) containing 1% B27 (Gibco; 17504044), 20 ng/mL basic fibroblast growth factor (bFGF) (Peprotech; 100-18B) and 10 µM retinioic acid (RA) (Sigma; 2625)

extract_protocol:
Total RNA was extracted using a NucleoSpin RNA kit (Machery Nagel 740955)
Total RNA was poly-A tail enriched
2 x 150 base paired end  libraries; RNA seq

treatment_protocol: iBEC cells were infected with cocksackievirus B3 (in DMSO) for either 2 days or 5 days before RNA was extracted

value: derived brain-like endothelial cell

tag: time

value: 5 days

value: no infection


title: Negative control at 5 day (replicate 1 of 3)


title: Monocyte, tumor, HE3

value: LEC-Ch25h KO


title: Negative control at 2 day (replicate 3 of 3)

value: 2 days


title: Monocyte, tumor, HE2


title: AS-778883-LR-60677


title: Negative control at 2 day (replicate 2 of 3)


title: AS-778887-LR-60677


title: AS-778885-LR-60677


title: H3K4me1 Normoxia

value: normoxia


title: AS-778865-LR-60677


title: MCF10A cells, Ctrl,#2

value: non-malignant breast epithelial cell line


title: Monocyte, tumor, HE1

value: tumor


title: AS-778891-LR-60677


title: ATAC-seq Normoxia 2


title: ATAC-seq Normoxia 1


title: AS-778833-LR-60677


title: 6mA-ChIP-exo METTL4-si hypoxia 2

value: METTL4-si hypoxia


title: Negative control at 5 day (replicate 3 of 3)


title: AS-778889-LR-60677


title: Coxsackievirus infection at 5 day (replicate 2 of 3)

value: virus infected


title: 6mA-ChIP-exo METTL4-si hypoxia 1


title: ATAC-seq Hypoxia 1

value: hypoxia


title: 6mA-ChIP-exo hypoxia 3


title: AS-778829-LR-60677


title: AS-778827-LR-60677


title: Coxsackievirus infection at 2 day (replicate 3 of 3)


title: Coxsackievirus infection at 5 day (replicate 1 of 3)


title: Coxsackievirus infection at 2 day (replicate 2 of 3)


title: 6mA-ChIP-exo hypoxia 2


title: AS-778825-LR-60677


title: AS-778831-LR-60677


title: 6mA-ChIP-exo hypoxia 1


title: Negative control at 2 day (replicate 1 of 3)


title: 6mA-ChIP-exo normoxia 3


title: 6mA-ChIP-exo METTL4-si hypoxia 3


title: Coxsackievirus infection at 2 day (replicate 1 of 3)


title: AS-778821-LR-60677


title: 6mA-ChIP-exo normoxia 2


title: Coxsackievirus infection at 5 day (replicate 3 of 3)


title: AS-778823-LR-60677


title: AS-778863-LR-60677


title: AS-778861-LR-60677


title: cpc400_mir181_day7

city: Durham

first: Austin

last: Bell-Hensley

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

description: CPCs were seeded in T75 flasks at a density of 2.4 x 106 cells/flask and transduced with lentivirus over-expressing either pre-miR-138, pre-miR-181a/b-1 or a non-silencing control RNA (NS). Transduced CPCs were trypsinized and high cell density pellet cultures were formed with 3 x 105 cells/pellet. Chondrogenic differentiation was then induced by addition of an serum-free induction medium (DMEM-high glucose, 1% Penicillin/streptomycin, 1% ITS+, 100 nM dexamethasone, 50 µg/mL ascorbic acid, 40 µg/mL L-proline, and 10 ng/mL rhTGF-β3) in a hypoxic incubator (5% CO2, 5% O2, 37°C). At Day 7 of chondrogenic induction, RNA was harvested.

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32.
Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04.
Assembly: Ensembl release 101
Supplementary files format and content: Gene counts in tab-delimited text MS Excel format
Supplementary files format and content: Isoform counts in tab-delimited text MS Excel format

source_name: knee osteoarthritic articular cartilage

growth_protocol: Human osteoarthritic cartilage was digested in DMEM/F12 contaiing 10% FBS, 0.025% collagenase, and 0.025% pronase solution. The resulting cell suspension was plated on a fibronectin-coated tissue culture flask. Adherent cells were cultured up to passage 6-7 in DMEM/F12 medium containing 10% FBS to obtain a cartilage progeintor cell (CPC) population with low heterogeneity.

extract_protocol:
At Day 7 of chondrogenic induction, 8 to 10 CPC Pellets were pooled, rinsed with DPBS, and submerged in a lysis buffer from Norgen BioTek’s Total RNA Purification kit for 5 minutes. Pellets were then flash frozen in liquid nitrogen and dissociated using a handheld motorized pellet pestle. The flash freeze and pellet pestle process was repeated 3 to 5 times, or until the pellets were effectively homogenized. RNA was extracted from the dissociated pellets using Norgen BioTek’s Total RNA Purification kit according to the manufacturer’s instructions. Isolated total RNA was quantified using a NanoDrop 2000 Spectrophotometer. Total RNA integrity was determined using Agilent Bioanalyzer.
Library preparation was performed with 500 ng to 1 µg of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94°C for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

treatment_protocol:
Passage 6-7 CPCs were seeded in T75 flasks at a density of 2.4 x 10^6 cells/flask and transduced with lentivirus over-expressing either pre-miR-138, pre-miR-181a/b-1 or a non-silencing control RNA (NS).
Transduced CPCs were dissociated using 0.05% Trypsin-EDTA and pellet cultures were formed by aliquoting 3 x 105 cells into 15 mL conical tubes and centrifuging (300 x g) for 5 minutes. Chondrogenic differentiation was then induced by addition of an serum-free induction medium (DMEM-high glucose, 1% Penicillin/streptomycin, 1% ITS+, 100 nM dexamethasone, 50 µg/mL ascorbic acid, 40 µg/mL L-proline, and 10 ng/mL rhTGF-β3) in a hypoxic incubator (5% CO2, 5% O2, 37°C).

value: knee osteoarthritic articular cartilage

value: cartilage progenitor cells passage 6-7

value: miR-181a/b-1 over-expression

value: chondrogenic differentiation


title: cpc339_mir181_day7


title: cpc362_mir181_day7


title: AS-778859-LR-60677

value: Placenta

value: Endothelial cells

value: WT


title: cpc316_mir181_day7


title: Ramos cells wild type, input

city: Milano

first: Ettore

last: Zapparoli

address: via Olgettina 60

country: Italy

institute: Ospedale San Raffaele

data_processing:
Raw reads were aligned to the human reference genome (hg38) with Bowtie 2 version 2.2.9 (Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359).
Peaks were called after duplicate filtering, by macs2 2.1.2 (Zhang et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol (2008) vol. 9 (9) pp. R137) with default parameters.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Ramos

growth_protocol: Ramos cells were grown in Roswell Park Memorial Institute (RPMI 1640, Invitrogen), supplemented with 10% FBS (PAA), sodium pyruvate 1 mM (Euroclone), non-essential aminoacids (Euroclone).

extract_protocol:
Ramos cells were crosslinked in 1% formaldehyde at room temperature for 10 minutes, followed by lysis in SDS lysis buffer. Precipitation for all samples was performed with ChIP grade protein G sepharose beads. After the overnight incubation, washing steps were performed, followed by the elution in fresh elution buffer.
Libraries were prepared following the manufacturer protocols for Chipseq sequencing with Illumina NextSeq 550DX sequencer (ILLUMINA).

treatment_protocol: Sp140 knock-out Ramos cell lines were generated by targeted introduction of indels in the coding region of the gene by the CRISPR/Cas9 system. Four different sgRNAs designed to maximize the on-target activity were evaluated for their ability to introduce indels in an easy-to-transfect cell line. Finally, the most active guide RNAs were used to target the Sp140 gene in the Ramos cells

value: Ramos

value: B lymphocyte

value: Ramos wild type

tag: chip antibody


title: cpc400_mir138_day7

value: miR-138 over-expression


title: AS-778857-LR-60677


title: Ramos cells Sp140 KO, MBD3

value: Ramos SP140 KO

value: Rabbit MBD3 monoclonal  (ab157464)


title: cpc362_mir138_day7


title: Ramos cells wild type, MBD3


title: AS-778819-LR-60677


title: AS-778853-LR-60677


title: AS-778851-LR-60677


title: cpc316_mir138_day7


title: 6mA-ChIP-exo normoxia 1

value: FADU

value: head and neck cancer

value: normoxia


title: cpc339_mir138_day7


title: cpc400_ns_control_day7

value: control


title: Whole sac-fry, Medium choline, Family B, Sire 2, 0-days post-hatch BS

city: Birmingham

first: Peggy

last: Biga

address: 902 14th Street South

department: Biology

institute: University of Alabama at Birmingham

data_processing:
Trimmed sequence reads were mapped to GCF_013265735.2_USDA_OmykA_1.1/GCF_013265735.2_USDA_OmykA_1.1_rna.fna.gz using Bismark (v0.19.0) (default parameters for paired end)
Read count extraction and normalization were performed using methylKit.
Genes from RRBS and RNA-seq analyses were investigated for overlapping genes.
Assembly: OmykA_1.1
Supplementary files format and content: Excel worksheet file includes differentially methylated bases, annotated features, and overlapping genes from previous RNA-seq analysis for each sample at different comparisons used in the manuscript.

organism: Oncorhynchus mykiss

source_name: Whole organism

extract_protocol:
DNA was harvested using DNeasy Minikit (Qiagen).
DNA libraries were prepared using Ovation RRBS Methyl-Seq Core Kit  following manufacturer's instructions.

value: Whole organism

value: NCCCWA breeding program

value: ARS-Fp/Fc-R

value: Medium Choline

value: 0-days post-hatch


title: AS-778847-LR-60677

value: Placenta

value: Endothelial cells


title: Ramos cells Sp140 KO, input

value: Ramos


title: Whole sac-fry, High choline, Family A, Sire 2, 0-days post-hatch BS

value: High Choline


title: AS-778849-LR-60677

value: WT


title: Whole sac-fry, Low choline, Family E, Sire 2, 0-days post-hatch BS

value: Low Choline


title: Whole sac-fry, Medium choline, Family A, Sire 2, 0-days post-hatch BS


title: AS-778845-LR-60677


title: Whole sac-fry, Low choline, Family A, Sire 2, 0-days post-hatch BS


title: 020_MDA_smallRNA_rep2

data_processing:
KARR-seq: Adaptors from raw reads were trimmed using cutadapt, the overlapping read pairs (2 × 150 bp) were merged into single-end reads and de-duplicated using fastp. The resulting single-end FASTQ files were then aligned to a customized reference genome containing human rDNA sequence (GenBank: KY962518.1) and snoRNA sequences (snoRNA annotation was acquired from snoDB 3) using STAR to map snoRNA-rRNA interactions. The following STAR parameters were used to recover gapped and chimeric reads based on the CRSSANT module (https://github.com/zhipenglu/CRSSANT): --runMode alignReads --outFilterMultimapNmax 20 --chimMultimapNmax 100 --alignIntronMin 1 --scoreGap 0 --scoreGapNoncan 0 --scoreGapGCAG 0 --scoreGapATAC 0 --scoreGenomicLengthLog2scale -1 --chimFilter None --chimOutType WithinBAM HardClip --chimSegmentMin 5 --chimJunctionOverhangMin 5 --chimScoreJunctionNonGTAG 0 --chimScoreDropMax 80 --chimNonchimScoreDropMin 20 --peOverlapNbasesMin 12 --peOverlapMMp 0.05 --limitOutSJcollapsed 10000000). The known snoRNA-rRNA interactions that lead to RNA modifications were obtained from snoRNA-LBME-db (https://www-snorna.biotoul.fr/), snOPY (http://snoopy.med.miyazaki-u.ac.jp/), snoDB (https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/), and snoRNA Atlas (http://snoatlas.bioinf.uni-leipzig.de/index.php#snoID_0492). The box sequences of snoRNAs were obtained from snoRNA Atlas. To map interactions between snoRNA and non-rRNA, FASTQ files were aligned to the human rDNA sequence (GenBank: KY962518.1). The unmapped reads were then used to map to the hg38 human genome. Chimeric reads were extracted from the resulting BAM file and reads containing snoRNAs were filtered out based on annotations from snoDB. The resulting chimeric reads were further de-duplicated based on the coordinates of snoRNA and their respective targets. The deduplicated coordinate pairs (snoRNA and the target) were then subjected to duplex group (DG) clustering using a spectral clustering algorithm in the CRSSANT module.   small RNA-seq: Adaptors and low-quality reads were removed from raw reads were removed using cutadapt. Duplications were removed using Clumpify (BBMap tool v.38.73). 5-mer random barcodes at reads ends were trimmed, and low-quality or short reads (less than 20 nt) were removed using cutadapt. Remaining reads were aligned to hg38 genome using HISAT2 and the expression of snoRNAs were quantified using StringTie.
Assembly: hg38/mm10
Supplementary files format and content: snoKARR-seq: csv file for snoRNA-target interactions Chr_x The chromosome name of the snoRNA Start_x The starting position of thesnoRNA in the chromosome End_x The ending position of thesnoRNA in the chromosome Strand_x The strand of thesnoRNA in the chromosome Gene Name_x The name of thesnoRNA Chr_y The chromosome name of the snoRNA target Start_y The starting position of thesnoRNA target in the chromosome End_y The ending position of thesnoRNA target in the chromosome Strand_y The strand of thesnoRNA target in the chromosome Gene Name_y The name of thesnoRNA target Gene Type_y The type of thesnoRNA target interaction_count The amount of chimeric reads in two replicates, separated by '_' dbn The predicted duplex structure in dot-bracket-notation seq_total The sequences of the predicted duplex structure energy The predicted free energy of the duplex structure   small RNA-seq: tsv file for snoRNA abundance Gene Name The name of the snoRNA Reference The name of the chromosome of the snoRNA Start The starting position of thesnoRNA in the chromosome End The ending position of thesnoRNA in the chromosome TPM_x The TPM in replicate1 TPM_y The TPM in replicate2 mean_TPM The mean TPM from replicate 1 and 2


title: cpc316_ns_control_day7

value: knee osteoarthritic articular cartilage

value: cartilage progenitor cells passage 6-7

value: chondrogenic differentiation


title: cpc362_ns_control_day7


title: AS-778855-LR-60677


title: Whole sac-fry, High choline, Family E, Sire 2, 0-days post-hatch BS


title: AS-778843-LR-60677


title: AS-778841-LR-60677


title: Whole sac-fry, Medium choline, Family E, Sire 1, 0-days post-hatch BS


title: 020_MDA_smallRNA_rep1


title: AS-778839-LR-60677


title: 019_A549_smallRNA_rep2


title: Whole sac-fry, Medium choline, Family E, Sire 2, 0-days post-hatch BS


title: Whole sac-fry, Low choline, Family E, Sire 1, 0-days post-hatch BS


title: AS-778837-LR-60677


title: cpc339_ns_control_day7


title: 019_A549_smallRNA_rep1


title: Whole sac-fry, High choline, Family B, Sire 2, 0-days post-hatch BS


title: AS-778835-LR-60677


title: AS-778817-LR-60677


title: 018_PC3_smallRNA_rep2


title: 018_PC3_smallRNA_rep1


title: Whole sac-fry, Low choline, Family B, Sire 1, 0-days post-hatch BS


title: AS-778785-LR-60677


title: AS-778783-LR-60677


title: 015_MDA_50ASO_rep1

description: two_rep_DG_clustering_MDA_with_seq_structure.csv


title: Whole sac-fry, Medium choline, Family B, Sire 1, 0-days post-hatch BS


title: 015_MDA_50ASO_rep2


title: Whole sac-fry, High choline, Family E, Sire 1, 0-days post-hatch BS


title: AS-778779-LR-60677


title: 014_MDA_input_rep1


title: 014_MDA_input_rep2


title: Whole sac-fry, High choline, Family A, Sire 1, 0-days post-hatch BS


title: AS-778777-LR-60677


title: AS-778781-LR-60677


title: Whole sac-fry, Low choline, Family A, Sire 1, 0-days post-hatch BS


title: Whole sac-fry, Medium choline, Family A, Sire 1, 0-days post-hatch BS


title: 013_A549_50ASO_rep2

description: two_rep_DG_clustering_A549_with_seq_structure.csv


title: Whole sac-fry, High choline, Family B, Sire 1, 0-days post-hatch BS


title: AS-778775-LR-60677


title: Input-2

library_source: other

data_processing:
Raw data from machine are de-multiplexed and adapter was trimmed using custom scripts
Reads were converted to fastq files using bcl2fastq.
Reads that mapped to noncoding RNA were discarded.
Reads were mapped to human reference genome using HISAT2.1.0
Uniquely mapped reads between 28 and 35nt were kept.
Assembly: Human genome assembly GRCh38.
Supplementary files format and content: Processed data is in an excel sheet containing information of all ribosomal footprints.

molecule: other

extract_protocol:
Ribosome protected fragments (ribosomal footprints) were isolated as described in McGlincy and Ingolia, Methods, 2017.
Ribosome profiling libraries were prepared as described in Ingolia et al., Nature Protocols, 2012, and McGlincy and Ingolia, Methods, 2017.

treatment_protocol: HEK293T cell lysate was treated with RNase I to collapse polysomes to monosomes. Monosomes were isolated by sucrose density gradient ultracentrifugation and fractionation. CNOT3-bound monosomes were purified by CNOT3 immunoprecipitation.

value: Human embryonic kidney


title: 013_A549_50ASO_rep1


title: AS-778773-LR-60677


title: 012_A549_input_rep2


title: Input-1


title: AS-778815-LR-60677


title: 012_A549_input_rep1


title: CNOT3-IP-2


title: AS-778813-LR-60677


title: CNOT3-IP-1


title: AS-778811-LR-60677


title: AS-778807-LR-60677


title: 010_PC3_input_rep2

description: two_rep_DG_clustering_PC3_with_seq_structure.csv


title: AS-778809-LR-60677


title: Ki-U2AF1-WT-2, bulk RNA-seq

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
For scRNA-seq, read alignment and expression matrice generation were done via cellranger. For bulk RNA-seq, read alignment were done using STAR.
Seurat was used to analyze the single cell datasets. DESeq2 was used to analyze the bulk RNA-seq data.
Assembly: hg38
Supplementary files format and content: raw expression counts

source_name: primary cells

growth_protocol: BMMNCs were enriched in CD34+ cells using magnetic separation with the CD34 Microbead Kit (Miltenyi Biotec), and Enriched CD34+ cells were precultured in stem cell expansion medium (StemSpan SFEM II, StemCell Technologies) supplemented with 1% penicillin/streptomycin-glutamine (Gibco) and hematopoietic cytokines (100 ng/ml SCF, 100 ng/ml FLT3L, and 100 ng/ml TPO; Peprotech) at 37°C in a 5% CO2 incubator for 24 hours prior transduction. The pRCDCMEGP-CMV-U2AF1S34-EF1-TagGFP2-2A-Puro or the pRCDCMEGP-CMV-U2AF1wild-type-EF1-TagGFP2-2A-Puro vectors, expressing the U2AF1S34 or the U2AF1wild-type allele, respectively.

extract_protocol:
live GFP+ CD34+ cells were sorted by flow cytometry and submitted for sequening
For single cell RNA 3’ sequencing, Sorted transduced CD34+ cell concentration and viability were evaluated using a Countess II FL Automated Cell Counter (ThermoFisher Scientific). Samples were normalized for input onto the Chromium Single Cell A Chip Kit (catalog number #PN120236, 10x Genomics), and single cells were lysed and barcoded for reverse transcription, as previously described.9 Briefly, libraries were sequenced using the NovaSeq6000 SP 100-cycle flow cell (Illumina). Sequencing analysis was performed using the 10x Genomics’ Cell Ranger software.   For single cell 5’ sequencing, Sorted CD34+ cells from NIH-39 were processed for 5’ scRNA-seq library preparation using Chromium Next GEM Single Cell 5’ kit v2 (10x Genomics, catalog number #PN-1000265). Libraries were sequenced on the Illumina NovaSeq 6000 system. Single cell expression measurements (digital counts) were obtained from raw sequence data (FASTQ) with the 10x Genomics Cell Ranger pipeline v4.0.0 (default settings, the GRCh38 reference).  For bulk RNA sequencing, Total RNA from sorted U2AF1S34 or U2AF1wild-type transduced CD34+ cells was purified using the PicoPure RNA Isolation Kit (catalog number #KIT0204, ThermoFisher Scientific). Quality checks and quantifications were performed with the 2100 Expert Bioanalyzer (Agilent). Illumina low input total RNA libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (catalog number #634412; Takara Bio), as previously described.15 Libraries were combined and sequenced on the Illumina NextSeq500 sequencer using the High Output 150 cycle flow cell with the 100nt PE format.

tag: disease

value: No

value: TERT mutation

value: BM CD34+

value: primary cells

tag: conditions

value: overexpressed U2AF1 WT

value: No treatment


title: 010_PC3_input_rep1


title: AS-778805-LR-60677

data_processing:
scRNA-sew: Raw sequencing data were demultiplexed and FASTQ files were generated using bcl2fastq software (Illumina, v2.20.0.422). Using salmon, FASTQ files were mapped to the GRCm39 mouse reference genome and count matrices were constructed with the R package tximport.
Assembly: GRCm39
Supplementary files format and content: CSV files containing the count matrix (count_matrix.csv) and the Seurat object metadata (GEO_metadata.csv)


title: AS-778771-LR-60677


title: Ramos, Input, KO

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Nextseq output.
Raw reads were processed with BBDUK to remove low quality and adapter sequences from both ends.
The resulting trimmed reads were aligned by BWA-mem version 0.7.15 with a human reference genome (hg38) and duplicate reads were removed with GATK PicardTools MarkDuplicates.
BigWig profiles were generated to visually inspect genomic enrichments.
Peaks were detected for each sample using MACS2 (ref2) version 2.1.1.
Assembly: hg38
Supplementary files format and content: bigWig, broadPeak

extract_protocol: SDS buffer (100mM NaCl, tris HCl pH 8 50mM,0,5% SDS)

value: SP140 knockout

value: B lymphocyte


title: 009_HEK193T_190ASO_rep2

description: two_rep_DG_clustering_HEK293T_with_seq_structure.csv


title: Ki-U2AF1-WT-1, bulk RNA-seq


title: 008_HEK293T_100ASO_rep2


title: AS-778801-LR-60677

extract_protocol: Whole transcriptome scRNA-seq was performed following an adapted SMARTseq2.5 protocol.

value: Placenta

value: Endothelial cells


title: 008_HEK293T_100ASO_rep1


title: Ki-U2AF1-S34F-2, bulk RNA-seq

value: overexpressed U2AF1 S34F


title: Ramos, Input, WT

value: Ramos

value: wild type


title: Ki-U2AF1-S34F-1, bulk RNA-seq


title: AS-778803-LR-60677

value: WT


title: 011_PC3_50ASO_rep2


title: 007_HEK293T_50ASO_rep1


title: 007_HEK293T_50ASO_rep2


title: AS-778795-LR-60677


title: AS-778797-LR-60677


title: 011_PC3_50ASO_rep1


title: AS-778799-LR-60677


title: Daudi, Input, WT

source_name: Daudi

value: Daudi


title: 006_HEK293T_input_rep2


title: Sp140, Daudi, replicate 1


title: 009_HEK193T_190ASO_rep1


title: AS-778791-LR-60677


title: AS-778793-LR-60677


title: H3K27ME3, SP140 ko, replicate 2

extract_protocol:
Daudi and Ramos cells were harvested and washed twice with PBS. Then, cells were crosslinked by formaldehyde 1% for 10 min at room temperature under rotation. Crosslinking reaction was quenched by adding Glycine (0.125 M final) to the solution. Crosslinked cells were then washed twice with PBS and lysed with SDS buffer (100 mM NaCl, 50 mM Tris-HCl pH8, 5 mM EDTA, 0.5% SDS). Cells were incubated on dry ice for 10 min and then pellet at 1200 rpm for 6 min. Cells were resuspended in ice cold IP Buffer (IP Buffer: 1 volume of SDS Buffer: 0.5 volume of Triton dilution Buffer (100 mM Tris HCl pH8.6, 100 mM NaCl, 5 mM EDTA, 5% Triton). Fixed cells were then sonicated to an average length of 200-500 bp by Branson Sonifier 250 (settings: output control 1, duty cycle 30) for 6 times on ice with 2-3 min rest in between. The quality of DNA sharing was assessed by loading samples on agarose gel (2%) and using Agilent Bioanalyzer instrument. Then, sonicated chromatin was centrifuged at 20000g for 30 min at 4oC. Sonicated chromatin was quantified by Bradford and used to immunoprecipitate Sp140, H3K27Me3 and MBD3 overnight at 4oC. IgG were used as negative control while input (1%, was saved as total control to normalize the signal). 40 μL of G-Sepharose beads were added and incubated for 4 hours. Then, beads were washed 3 times with washing buffer 1 (1% Triton, 0.1% SDS, 150 mM NaCl, 2 mM EDTA pH8, 20 mM Tris-HCl pH8) and once with washing buffer 2 (1% Triton, 0.1% SDS, 500 mM NaCl, 2 mM EDTA pH8, 20 mM Tris-HCl pH 8). Samples were decrosslinked by adding the decrosslinking solution (1% SDS, 0.1M NaHCO3) and incubated overnight at 65oC.
Libraries were constructed using the ChIP TruSeq Chip Kit (Illumina) sequencing library preparation kit. Sequencing was performed on Illumina NextSeq 500, in the following mode: 75nt paired-end in order to obtain 30M clusters of fragments for Sp140 ChIP-Seq libraries and 60M clusters of fragments for H3K27me3 ChIP-Seq libraries.
Each size selected library was diluted according to the final concentration of 11 pM and clonally amplified using the Ion Proton™ Hi‑Q™Template Kit (Thermo Fisher Scientific/Life Technologies) with IonOneTouch 2 instrument (Thermo Fisher Scientific/Life Technologies). After emulsion PCR, DNA positive ISPs were recovered and enriched according to standard protocols with the IonOneTouch ES Instrument (Thermo Fisher Scientific/Life Technologies). A sequencing primer was annealed to DNA positive ISPs and the sequencing polymerase bound, prior to loading of ISPs into Ion P1 sequencing chips. Sequencing of the samples was conducted according to the Ion Proton™ Hi-Q Sequencing Kit Protocol. One P1 sequencing chips with the 3 libraries were loaded and run on an Ion Proton sequencer to generate reads with an average length of 150-200.

value: mAb #9736  Cell signaling


title: 006_HEK293T_input_rep1


title: 005_HepG2_ribo_100ASO_rep2

description: two_rep_DG_clustering_HepG2_with_seq_structure.csv


title: AS-778789-LR-60677


title: 005_HepG2_ribo_100ASO_rep1


title: H3K27ME3, wt, replicate 2

value: mAb #9734  Cell signaling


title: AS-778787-LR-60677


title: H3K27ME3, wt, replicate 1

value: mAb #9733 Cell signaling


title: H3K27ME3, SP140 ko, replicate 1

value: mAb #9735  Cell signaling


title: Sp140, wt, replicate 2


title: AS-778769-LR-60677


title: Sp140, wt, replicate 1


title: Sp140, Daudi, replicate 2


title: 004_HepG2_ribo_50ASO_rep1


title: 003_HepG2_ribo_Input_rep2


title: AS-778737-LR-60677


title: AS-778735-LR-60677


title: 003_HepG2_ribo_Input_rep1


title: AS-778733-LR-60677


title: WT, IRI35min, K6

city: Kurashiki

first: HAJIME

last: NAGASU

state: Okayama

address: 577 Matsushima

department: Nephrology and Hypertension

institute: Kawasaki Medical School

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Clean data (clean reads) were obtained by removing reads containing adapter,reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30　and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10｜Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

source_name: kidney

extract_protocol:
Total RNA extraction was performed, as previously described(Satoh M, Lab Invest 2011).  Briefly, total RNA was isolated from the kidneys using TRIzol (Invitrogen; Thermo Fisher Scientific Inc., Waltham, MA, USA), followed by digestion with DNase (Sigma-Aldrich).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: kidney

value: severe ischemia-reperfusion injury


title: 002_HepG2_no_ribo_50ASO_rep2

data_processing:
KARR-seq: Adaptors from raw reads were trimmed using cutadapt, the overlapping read pairs (2 × 150 bp) were merged into single-end reads and de-duplicated using fastp. The resulting single-end FASTQ files were then aligned to a customized reference genome containing human rDNA sequence (GenBank: KY962518.1) and snoRNA sequences (snoRNA annotation was acquired from snoDB 3) using STAR to map snoRNA-rRNA interactions. The following STAR parameters were used to recover gapped and chimeric reads based on the CRSSANT module (https://github.com/zhipenglu/CRSSANT): --runMode alignReads --outFilterMultimapNmax 20 --chimMultimapNmax 100 --alignIntronMin 1 --scoreGap 0 --scoreGapNoncan 0 --scoreGapGCAG 0 --scoreGapATAC 0 --scoreGenomicLengthLog2scale -1 --chimFilter None --chimOutType WithinBAM HardClip --chimSegmentMin 5 --chimJunctionOverhangMin 5 --chimScoreJunctionNonGTAG 0 --chimScoreDropMax 80 --chimNonchimScoreDropMin 20 --peOverlapNbasesMin 12 --peOverlapMMp 0.05 --limitOutSJcollapsed 10000000). The known snoRNA-rRNA interactions that lead to RNA modifications were obtained from snoRNA-LBME-db (https://www-snorna.biotoul.fr/), snOPY (http://snoopy.med.miyazaki-u.ac.jp/), snoDB (https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/), and snoRNA Atlas (http://snoatlas.bioinf.uni-leipzig.de/index.php#snoID_0492). The box sequences of snoRNAs were obtained from snoRNA Atlas. To map interactions between snoRNA and non-rRNA, FASTQ files were aligned to the human rDNA sequence (GenBank: KY962518.1). The unmapped reads were then used to map to the hg38 human genome. Chimeric reads were extracted from the resulting BAM file and reads containing snoRNAs were filtered out based on annotations from snoDB. The resulting chimeric reads were further de-duplicated based on the coordinates of snoRNA and their respective targets. The deduplicated coordinate pairs (snoRNA and the target) were then subjected to duplex group (DG) clustering using a spectral clustering algorithm in the CRSSANT module.   small RNA-seq: Adaptors and low-quality reads were removed from raw reads were removed using cutadapt. Duplications were removed using Clumpify (BBMap tool v.38.73). 5-mer random barcodes at reads ends were trimmed, and low-quality or short reads (less than 20 nt) were removed using cutadapt. Remaining reads were aligned to hg38 genome using HISAT2 and the expression of snoRNAs were quantified using StringTie.
Assembly: hg38/mm10
Supplementary files format and content: snoKARR-seq: csv file for snoRNA-target interactions Chr_x The chromosome name of the snoRNA Start_x The starting position of thesnoRNA in the chromosome End_x The ending position of thesnoRNA in the chromosome Strand_x The strand of thesnoRNA in the chromosome Gene Name_x The name of thesnoRNA Chr_y The chromosome name of the snoRNA target Start_y The starting position of thesnoRNA target in the chromosome End_y The ending position of thesnoRNA target in the chromosome Strand_y The strand of thesnoRNA target in the chromosome Gene Name_y The name of thesnoRNA target Gene Type_y The type of thesnoRNA target interaction_count The amount of chimeric reads in two replicates, separated by '_' dbn The predicted duplex structure in dot-bracket-notation seq_total The sequences of the predicted duplex structure energy The predicted free energy of the duplex structure   small RNA-seq: tsv file for snoRNA abundance Gene Name The name of the snoRNA Reference The name of the chromosome of the snoRNA Start The starting position of thesnoRNA in the chromosome End The ending position of thesnoRNA in the chromosome TPM_x The TPM in replicate1 TPM_y The TPM in replicate2 mean_TPM The mean TPM from replicate 1 and 2
Library strategy: KARR-seq

extract_protocol:
KARR-seq: Live cells or homogenized tissue samples were treated with N3-kethoxal, cells were then lysed and RNA inproximity is crosslinked by dendrimers. The sample was then treated with proteinase K and Dnase. RNA was extracted using phenol chloroform.  smallRNA-seq: Total RNA was extracted using TRIzol, and small RNA fraction was isolated using the mirVana™ miRNA Isolation Kit (Invitrogen, AM1561).
KARR-seq: 10-50 ng of ligated RNA was used for reverse transcription (RT) using the RT reagents in the SMARTer Stranded Total RNA-seq kit v2 – pico input mammalian (Takara, 634413). After RT, 2 µL of RNase H (NEB M0297S) was added to each sample, which was then incubated for 20 minutes at 37°C. The reaction was quenched by heating inactivation for 5 minutes at 70°C. Subsequently, cDNA was purified using the DNA Clean & Concentrator-5 kit. 10% of the cDNA was saved as an input sample, while the remaining cDNA was used for snoRNA enrichment. After streptavidin beads pulldown, the resulting cDNA was subjected to library construction using the SMARTer Stranded Total RNA-seq kit v2 – pico input mammalian (Takara, 634413).   Small RNA-seq: Small RNA fractions were isolated using the mirVana™ miRNA Isolation Kit (Invitrogen, AM1561) according to the manufacturer's protocol. The resulting small RNA fraction was subsequently used for sequencing library construction using the NEBNEB Next Small RNA Library Prep Set for Illumina (NEB E7330S) according to the manufacturer's protocol.


title: AS-778731-LR-60677


title: WT, IRI35min, K5


title: AS-778729-LR-60677


title: 002_HepG2_no_ribo_50ASO_rep1


title: 001_HepG2_no_ribo_Input_rep2


title: 001_HepG2_no_ribo_Input_rep1


title: AS-778727-LR-60677


title: WT, IRI20min, K3

value: mild ischemia-reperfusion injury


title: WT, IRI20min, K1


title: AS-778725-LR-60677


title: WT, IRI20min, K2


title: AS-778767-LR-60677


title: 004_HepG2_ribo_50ASO_rep2


title: MSC_ATAC

data_processing:
Quality control and preprocessing of ATAC-seq reads were performed using fastp.
ATAC-seq Reads were mapped to the mm10 reference sequence using Bowtie2 (ver. 2.4.4).
Duplicate reads were removed with Picard (ver. 2.20.7) and samtools (ver. 1.9). Peak calling was performed using MACS2 (ver. 2.2.4) with default parameters.
Assembly: mm10
Supplementary files format and content: narrowPeak

source_name: Bone Marrow

extract_protocol:
approximately 50,000 cells were lysed and transposition reaction was performed with the Tn5 Transposase (Illumina Catalog #FC121-1030) at 37°C for 30 minutes. The reaction liquid was purified with Qiagen MinElute PCR Purification Kit. Then 5 cycles of PCR with custom Nextera PCR primers (from Wu and Buenrostro 2013) were conducted using NEBNext Q5 Hot Start HiFi PCR Master Mix (New England Biolabs). Additional number of PCR cycles was determined by qPCR of the partly amplified products, following Wu and Buenrostro 2013. The PCR products were purified with Agencourt AMPure XP beads (Beckman Coulter: A63881), using double size selection (left ratio: 1.4x, right ratio: 0.5x) according to the manufacturer’sprotocol.
sequencing libraries were prepared using TruSeq ChIP Sample Prep Kit (Illumina) according to the manufacturer’s protocol.

value: Bone Marrow

value: Mesenchymal Stem cells


title: iSLK/Bac16_57KO_Bu/DOX_D3

city: Frederick

first: Zhi-Ming

last: Zheng

state: Maryland

department: Center for Cancer Research

institute: National Cancer Institute

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CutAdapt v1.18 (parameters: --pair-filter=any nextseq-trim=2 --trim-n -n 5 -O 5 -q 10,10 -m 35:35)
Trimmed reads were mapped to hg38/KSHV (HQ404500) sequences using STAR 2.7.0f aligner
Read count extraction was performed using RSEM v1.3.0
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes RSEM counts for each sample

source_name: iSLK

growth_protocol: Both wt and 57KO iSLK/Bac16 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% defined fetal bovine serum and 1× penicillin-streptomycin-glutamine in humidified atmosphere with 5% CO2 at 37C. The cell medium was supplanted  with 150 μg/ml of hygromycin B, 1 μg/ml puromycin, and 250 μg/ml G418 for iSLK/Bac16 cells to maintain the virus genome.

extract_protocol:
Total RNA was extracted with TriPure Isolation Reagent (SigmaAldrich) followed by 15 min on column DNase treatment using  Qiagen Rneasy Mini Kit (Qiagen).
Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

treatment_protocol: To induce KSHV lytic replication, the cells were treated a combination of 1mM sodium butyrate (Bu) and 1 ug/ml of doxycycline (DOX) for 48 hours. The untreated (UN) cells with KSHV latent infection were used as negative control.

value: iSLK

value: Clear cell renal cell carcinoma

value: Bu/DOX


title: AS-778765-LR-60677

value: Placenta

value: Endothelial cells


title: iSLK/Bac16_57KO_Bu/DOX_D4


title: WT, IRI35min, K4


title: Tumor 4

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

description: mRNA

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Assembly: GRCm38.80
Supplementary files format and content: Raw counts measurements

extract_protocol:
Tumor and lymph nodes were excised, digested and lymphatic endothelial cells were FACS-sorted based on CD45negCD31+gp38+. They were collected in RNAprotect Cell Reagent (Qiagen). RNA was isolated using RNeasy Plus Micro kit (Qiagen)
cDNA libraries were constructed by the Genomic platform of the University of Geneva as followed: the SMARTer™ Ultra Low RNA kit from Clontech was used for the reverse transcription and cDNA amplification according to manufacturer’s specifications, starting with 1 ng of total RNA. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina.Pools of 10 libraries were loaded for clustering on a Single-read Illumina Flow cell. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 sequencer.

tag: group

value: tumor

value: 10 weeks


title: Tumor 5

description: mRNA


title: iSLK/Bac16_57KO_Bu/DOX_D1


title: AS-778761-LR-60677

value: WT


title: iSLK/Bac16_57KO_uninduced_C4


title: Tumor 2

description: mRNA


title: AS-778759-LR-60677


title: iSLK/Bac16_57KO_uninduced_C3


title: Tumor 1

description: mRNA


title: AS-778723-LR-60677


title: iSLK/Bac16_57KO_uninduced_C2


title: TdLN 5

description: mRNA

source_name: draining LN

value: draining LN


title: AS-778757-LR-60677


title: TdLN 4

description: mRNA


title: iSLK/Bac16_57KO_uninduced_C1


title: TdLN 3

description: mRNA


title: AS-778753-LR-60677


title: iSLK/Bac16_WT_Bu/DOX_B4


title: iSLK/Bac16_WT_Bu/DOX_B3


title: AS-778755-LR-60677


title: iSLK/Bac16_57KO_Bu/DOX_D2


title: AS-778751-LR-60677


title: Tumor 3

description: mRNA


title: iSLK/Bac16_WT_Bu/DOX_B2


title: TdLN 1

description: mRNA


title: AS-778749-LR-60677


title: TdLN 2

description: mRNA


title: AS-778763-LR-60677


title: AS-778747-LR-60677


title: iSLK/Bac16_WT_Bu/DOX_B1


title: NdLN 5

description: mRNA

source_name: non-draining LN

value: non-draining LN


title: AS-778745-LR-60677


title: NdLN 4

description: mRNA


title: iSLK/Bac16_WT_uninduced_A4


title: NdLN 3

description: mRNA


title: AS-778743-LR-60677


title: iSLK/Bac16_WT_uninduced_A2


title: AS-778741-LR-60677


title: NdLN 2

description: mRNA


title: NdLN 1

description: mRNA


title: iSLK/Bac16_WT_uninduced_A1


title: AS-778739-LR-60677


title: Sample oxa3 technical replicate d

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

description:
2020_006d
Blood vessels of sciatic nerves with oxaliplatine injection, sample oxa3, technical replicate d

data_processing:
Illumina bcl2fastq 2.18.0.12 software used for basecalling.
The analyses were performed using the Eoulsan pipeline version 2.4. Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Rattus norvegicus genome (GRCm38 from Ensembl version 88) using the STAR mapper (version 2.7.2d, with –outSAMunmapped Within parameter). Alignments from reads matching more than once on the reference genome were removed. To compute gene expression, Mus musculus GTF genome annotation version 88 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted and aggregated by genes using HTSeq-count 0.5.3.
Assembly: GRCm38 from Ensembl 88
Supplementary files format and content: tab-delimited text files include transcripts counting for each Sample

source_name: Blood vessels of sciatic nerves

extract_protocol:
Total mRNAs were extracted and purified using the NucleoSpin RNA XS kit
Messenger (polyA+) RNAs were purified from 300 ng of total RNA using oligo(dT). Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina).

value: Blood vessels of sciatic nerves

value: Oxaliplatine injection


title: AS-778689-LR-60677


title: AS-778721-LR-60677


title: Sample oxa3 technical replicate c

description:
2020_006c
Blood vessels of sciatic nerves with oxaliplatine injection, sample oxa3, technical replicate c


title: H820, Vehicle, 24 h, rep1

city: Columbia

first: Donald

last: Burke-Agüero

state: Missouri

address: 1201 Rollins St

department: molecular microbiology and immunology

institute: University of Missouri

data_processing:
Trimmed fastq files were mapped to the reference genome GRCh38.p12 using hisat2
Cufflink was used to calculate the FPKM
Cuffdiff was used to identify the differentially expressed genes
Assembly: hg38
Supplementary files format and content: comma-seperated text files include FPKM values for each Sample

growth_protocol: RPMI (H1975, H820, H3255) or DMEM (A549) supplemented  10% (maintence) or 1% (treatment) Fetal Bovine Serum, 1 mM sodium pyruvate, 2 mM L-glutamine, and 1X NEAAs.

extract_protocol:
RNA was extracted using Monarch Total RNA Miniprep Kit (NEB) according to manfacuters protocol. RNA concentration and purity was assessed using a NanoDrop (ThermoFisher). RNA was stored at -80C until submission for NGS.
Libraries were constructed using the Illumina Stranded mRNA Prep following the manufactures protocol. This is a poly-A enrichment approach. Unique dual-indexes were used to barcode libraries.
RNA-Seq; Sequences were generated on a NovaSeq 6000 using a paired end, 100 base read length run. Files were provided in FASTQ format.

treatment_protocol: Aptamers were folded at 10X in 1X DPBS + 5mM MgCl2. Aptamers were diluted to 1X in media and added to cells for 24 h before RNA extraction.

value: NSCLC cell line

value: EGFR Ex19del/T790M

value: Vehicle, 24 h


title: H820, Vehicle, 24 h, rep2


title: Sample oxa3 technical replicate b

description:
2020_006b
Blood vessels of sciatic nerves with oxaliplatine injection, sample oxa3, technical replicate b


title: AS-778687-LR-60677

city: Heidelberg

first: Stephanie

last: Gehrs

institute: DKFZ


title: H820, MinE07, 24 h, rep3

value: MinE07, 24 h


title: Sample oxa2 technical replicate d

description:
2020_005d
Blood vessels of sciatic nerves with oxaliplatine injection, sample oxa2, technical replicate d


title: H820, MinE07, 24 h, rep2


title: iSLK/Bac16_WT_uninduced_A3


title: H820, MinE07, 24 h, rep1


title: Sample oxa2 technical replicate c

description:
2020_005c
Blood vessels of sciatic nerves with oxaliplatine injection, sample oxa2, technical replicate c


title: Sample oxa3 technical replicate a

description:
2020_006a
Blood vessels of sciatic nerves with oxaliplatine injection, sample oxa3, technical replicate a


title: AS-778685-LR-60677


title: Setaria, 18 days after sowing, replicate 4

city: Canberra

first: Florence

middle: R

last: Danila

state: ACT

address: Building 134 Linneaus Way, Acton

country: Australia

institute: Australian National University

description: sequenced thru BGI HongKong using DNBseq platform

data_processing:
Raw reads were trimmed for adapter sequences, unknown bases, and low-quality base-calls, before being mapped to the corresponding reference genomes (IRGSP-1.0-Oryza_sativa; Setaria viridis v2) using Bowtie2 (Langmead and Salzberg 2012).
Expression quantification was performed using RSEM (Li and Dewey, 2011) on transcripts defined in the corresponding reference annotations (Oryza_sativa.IRGSP-1.0.51.gff3, Setaria_viridis_v2.0.51.gff3). Genes detected at CPM > 1 in at least four samples were retained for analysis.
Fold-changes in expression were estimated with DEseq2 (Li and Dewey 2011; Love et al. 2014).
Assembly: IRGSP-1.0-Oryza_sativa; Setaria viridis v2
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes log2fold change and gene details for each sample

organism: Setaria viridis

source_name: Leaf

growth_protocol: Seeds from homozygous ZmPDLP1-YFP rice and setaria lines were surface sterilized and sown in Murashige and Skoog medium supplemented with 30 g sucrose/L in magenta boxes. Both species were grown in a controlled growth cabinet maintained at 14-h photoperiod, 28°C/24°C day/night temperatures, 60% relative humidity, and ambient CO2 concentration.

extract_protocol:
Total RNA was extracted using the Plant RNeasy kit (Qiagen) as per the manufacturer's instructions.
Poly(A)-enriched RNA sequencing (mRNA sequencing) libraries were constructed and sequenced (100 bp paired-end with 30M clean reads per sample) on a DNBSEQ (DNBSEQ Technology, MGI Co. Ltd.) platform by BGI Genomics (Hong Kong).

treatment_protocol: Leaf tissue samples taken at 1, 3, 5, 7, 9 and 18 days after sowing (DAS) from 30 individual plants for each of the 3-4 biological replicates were flash frozen in liquid nitrogen and stored at -80°C for RNA isolation.

value: Leaf

tag: ecotype

tag: developmental stage

value: 18 days after sowing


title: AS-778683-LR-60677


title: Sample oxa2 technical replicate b

description:
2020_005b
Blood vessels of sciatic nerves with oxaliplatine injection, sample oxa2, technical replicate b


title: H820, C36, 24 h, rep3


title: Setaria, 18 days after sowing, replicate 3


title: AS-778679-LR-60677


title: H820, C36, 24 h, rep2


title: AS-778681-LR-60677


title: Setaria, 18 days after sowing, replicate 2


title: Sample oxa2 technical replicate a

description:
2020_005a
Blood vessels of sciatic nerves with oxaliplatine injection, sample oxa2, technical replicate a


title: H820, Vehicle, 24 h, rep3


title: AS-778677-LR-60677


title: H820, C36, 24 h, rep1


title: Sample oxa1 technical replicate d

description:
2020_004d
Blood vessels of sciatic nerves with oxaliplatine injection, sample oxa1, technical replicate d


title: Setaria, 18 days after sowing, replicate 1


title: H3255, Vehicle, 24 h, rep3

value: EGFR L858R


title: AS-778717-LR-60677


title: AS-778719-LR-60677


title: Sample oxa1 technical replicate b

description:
2020_004b
Blood vessels of sciatic nerves with oxaliplatine injection, sample oxa1, technical replicate b


title: H3255, Vehicle, 24 h, rep2


title: Setaria, 9 days after sowing, replicate 3

value: 9 days after sowing


title: H3255, Vehicle, 24 h, rep1


title: Sample oxa1 technical replicate c

description:
2020_004c
Blood vessels of sciatic nerves with oxaliplatine injection, sample oxa1, technical replicate c


title: Sample sham3 technical replicate d

description:
2020_003d
Blood vessels of sciatic nerves with control solution injection, sample sham3, technical replicate d

value: Control solution injection


title: AS-778713-LR-60677

value: Placenta

value: Endothelial cells


title: AS-778711-LR-60677


title: Setaria, 9 days after sowing, replicate 2


title: Sample oxa1 technical replicate a

description:
2020_004a
Blood vessels of sciatic nerves with oxaliplatine injection, sample oxa1, technical replicate a


title: H3255, MinE07, 24 h, rep3


title: Setaria, 9 days after sowing, replicate 1


title: H3255, MinE07, 24 h, rep2


title: AS-778675-LR-60677


title: Setaria, 7 days after sowing, replicate 4

value: 7 days after sowing


title: Sample sham3 technical replicate c

description:
2020_003c
Blood vessels of sciatic nerves with control solution injection, sample sham3, technical replicate c


title: Setaria, 7 days after sowing, replicate 3


title: Sample sham3 technical replicate b

description:
2020_003b
Blood vessels of sciatic nerves with control solution injection, sample sham3, technical replicate b


title: H3255, MinE07, 24 h, rep1


title: AS-778709-LR-60677

value: WT


title: Sample sham3 technical replicate a

description:
2020_003a
Blood vessels of sciatic nerves with control solution injection, sample sham3, technical replicate a


title: Setaria, 9 days after sowing, replicate 4


title: H3255, C36, 24 h, rep3


title: AS-778707-LR-60677


title: AS-778715-LR-60677


title: H3255, C36, 24 h, rep2


title: Sample sham2 technical replicate d

description:
2020_002d
Blood vessels of sciatic nerves with control solution injection, sample sham2, technical replicate d


title: Setaria, 7 days after sowing, replicate 1


title: AS-778705-LR-60677


title: Sample sham2 technical replicate c

description:
2020_002c
Blood vessels of sciatic nerves with control solution injection, sample sham2, technical replicate c


title: H3255, C36, 24 h, rep1


title: Setaria, 5 days after sowing, replicate 3

value: 5 days after sowing


title: AS-778703-LR-60677


title: H1975, Vehicle, 24 h, rep2

value: EGFR L858R/T790M


title: H1975, Vehicle, 24 h, rep3


title: Setaria, 5 days after sowing, replicate 2


title: AS-778701-LR-60677


title: Sample sham2 technical replicate b

description:
2020_002b
Blood vessels of sciatic nerves with control solution injection, sample sham2, technical replicate b

value: Blood vessels of sciatic nerves


title: Sample sham2 technical replicate a

description:
2020_002a
Blood vessels of sciatic nerves with control solution injection, sample sham2, technical replicate a


title: Setaria, 5 days after sowing, replicate 1


title: Setaria, 3 days after sowing, replicate 2

value: 3 days after sowing


title: H1975, Vehicle, 24 h, rep1

value: NSCLC cell line


title: Setaria, 3 days after sowing, replicate 3


title: AS-778697-LR-60677


title: AS-778699-LR-60677


title: Sample sham1 technical replicate d

description:
2020_001d
Blood vessels of sciatic nerves with control solution injection, sample sham1, technical replicate d


title: H1975, MinE07, 24 h, rep2


title: Setaria, 3 days after sowing, replicate 1


title: Sample sham1 technical replicate b

description:
2020_001b
Blood vessels of sciatic nerves with control solution injection, sample sham1, technical replicate b


title: H1975, MinE07, 24 h, rep3


title: Setaria, 7 days after sowing, replicate 2

description: sequenced thru BGI HongKong using DNBseq platform


title: AS-778695-LR-60677


title: AS-778691-LR-60677


title: Rice, 18 days after sowing, replicate 4

organism: Oryza sativa

value: Kitaake


title: H1975, MinE07, 24 h, rep1


title: AS-778693-LR-60677


title: H1975, C36, 24 h, rep2


title: Sample sham1 technical replicate a

description:
2020_001a
Blood vessels of sciatic nerves with control solution injection, sample sham1, technical replicate a


title: AS-778673-LR-60677


title: RNAseq-KO-1

data_processing:
Bulk RNA-seq: Prior to analysis, gene count matrix was filtered to include genes with a minimum total 5 raw counts across samples. Differential gene expression analysis was performed using the DESeq2 package.
Assembly: GRCm39
Supplementary files format and content: tab-delimited txt file containing the raw counts for the RNAseq experiment; excel file containing the DESeq2 analysis.

source_name: placenta

extract_protocol:
For bulk RNA-seq, RNA was isolated using the Arcturus PicoPure RNA Isolation Kit (Thermo Fisher Scientific) according to manufacturer instructions.
For the bulk RNA-seq library preparation, the SMARTer Ultra-low RNA kit (Takara) was used.

value: placenta

value: endothelial cells


title: Rice, 9 days after sowing, replicate 4

value: Leaf


title: H1975, C36, 24 h, rep1


title: Rice, 18 days after sowing, replicate 2

value: 18 days after sowing


title: Rice, 18 days after sowing, replicate 3


title: RNAseq-KO-2


title: A549, Vehicle, 24 h, rep2

value: WT EGFR

value: Vehicle, 24 h


title: RNAseq-WT-3


title: Sample sham1 technical replicate c

description:
2020_001c
Blood vessels of sciatic nerves with control solution injection, sample sham1, technical replicate c

value: Control solution injection


title: Rice, 9 days after sowing, replicate 2

value: 9 days after sowing


title: RNAseq-KO-3


title: A549, MinE07, 24 h, rep3

value: MinE07, 24 h


title: RNAseq-WT-1


title: Rice, 9 days after sowing, replicate 1


title: Rice, 7 days after sowing, replicate 4

value: 7 days after sowing


title: H1975, C36, 24 h, rep3


title: A549, MinE07, 24 h, rep2


title: A549, MinE07, 24 h, rep1


title: A549, C36, 24 h, rep3


title: iFTn-R4_2

city: tinajin

first: qiqi

last: liu

state: other

address: nankai university

country: China

institute: nankai university

data_processing:
The raw data was filtered with SOAPnuke (v1.4.0) by 1) Removing readscontaining adapters (adapter contamination); 2) Removing reads whose unknown base('N' base) ratio is more than 5%; 3) Removing reads whose low-quality base ratio(Base quality less than or equal to 15) is more than 20%, afterwards clean reads wereobtained and stored in FASTQ format.
The clean data were mapped to the reference genome by HISAT (v2.1.0).
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5).
The expression level of genes was calculated by RSEM (v1.2.8).
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: heart

extract_protocol:
The heart was removed and frozen in liquid nitrogen.The tissue sample were homogenized the lysated using a rotor-stator homogenizer in Trizol. After DNA removal by AllPrep DNA spin column,the RNA were collected using a RNeasy spin column. After two washes, the RNA was dissolved in RNase-free water.
After QC step, a certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. Then the RNAs were fragmented and cDNA were synthesized . Double-stranded cDNA fragments were subjected to end-repair, add A and adaptor ligation.The PCR reaction system and program are configured and set up to amplify the product. After Library QC step, single-stranded PCR products are produced via denaturation. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: heart

value: ischemia-reperfusion and iFTn-R4


title: Rice, 18 days after sowing, replicate 1


title: A549, Vehicle, 24 h, rep3


title: Rice, 7 days after sowing, replicate 2


title: RNAseq-WT-2

address: Im Neuenheimer Feld


title: iFTn-R4_1


title: Rice, 7 days after sowing, replicate 1


title: Rice, 9 days after sowing, replicate 3


title: Rice, 5 days after sowing, replicate 4

value: 5 days after sowing


title: SHUNCD34, scRNA-seq

value: No

value: TERC mutation

value: BM CD34+

value: primary cells

value: No treatment


title: iFTn-M4_2

value: ischemia-reperfusion and iFTn-M4


title: A549, Vehicle, 24 h, rep1

value: NSCLC cell line


title: iFTn-MR4_1

value: ischemia-reperfusion and iFTn-MR4


title: A549, C36, 24 h, rep2

value: WT EGFR


title: Rice, 5 days after sowing, replicate 3

value: Leaf

value: Kitaake


title: iFTn-M4_1


title: MU2AF1-WT, scRNA-seq

value: overexpressed U2AF1 WT


title: PBS_2

value: ischemia-reperfusion and PBS


title: Rice, 5 days after sowing, replicate 2


title: iFTn-MR4_2


title: Rice, 7 days after sowing, replicate 3

value: 7 days after sowing


title: PBS_1

value: heart