title: BABAgraft_1

data_processing:
Trimmomatic (Bolger et al., 2014) was used to remove adapters and discard low-quality reads.
The cleaned reads were aligned to the tomato genome (ITAG4.0) using Shortstack (version 3.8.5) (Axtell, 2013).
Clusters were identified as 20-24 nt in size using the mobileRNA package (https://doi.org/doi:10.18129/B9.bioc.mobileRNA). For each replicate the consensus cluster size was identified and non-dicer-derived clusters were excluded from the analysis. Differentially expressed clusters were identified amng conditions using the DEseq2 method.
Differentially expressed clusters were identified amng conditions using the DEseq2 method (Anders and Huber, 2010) and default parameters. sRNA clusters with a significance p-value below 0.05 after Benjamini and Hochberg correction were considered to be differentially expressed.
Assembly: ITAG4.0
Supplementary files format and content: For each sample, the list of sRNA clusters and their coverage calculated by mobileRNA is provided (https://doi.org/doi:10.18129/B9.bioc.mobileRNA).

source_name: scion leaves

extract_protocol:
Total RNA was isolated from 100 mg of scion leaves samples using  TRIzol (Thermo Fisher; catalogue number 15596026) following manufacturer's specifications.
sRNA sequencing analysis was conducted on RNA extracted from scion leaf tissue from BG, HG and MG plants 6 weeks post grafting. Library preparation and sequencing was conducted by Novogene using NovaSeq SE50. 20 million paired reads were generated per sample.

treatment_protocol: two-week old Micro Tom plants were treated to a final concentration of 0.5 mM BABA via soil drench treatment or with water. 3 days after soil treatments, grafting was conducted on seedlings using the cleft method (Lee, 1994). The following graft combinations were used with a minimum of 4 biological replicates per treatment: BABA graft (BG) =  BABA treated root stock + BABA treated scion; Hetero graft (HG) = BABA treated root stock + water treated scion; and Mock graft (MG) = water treated root stock + water treated scion.

value: scion leaves

tag: treatment scion

value: BABA treated

tag: treatment rootstock


title: Control/Normoxia 2

status: Public on Nov 17 2024

type: SRA

city: Chiba

first: Takeshi

last: Kawasaki

address: 1-8-1, Inohana, Chuoku

department: Respirology

country: Japan

institute: Chiba University

library_source: transcriptomic

data_processing:
Removal of poly A tail and adapter sequences were performed using BBDuk (BBMap version 38.96) with the following settings (k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20).
Trimmed reads were mapped to hg38 using STAR version 2.7.6a with the following settings (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000).
Read counts for each gene were obtained using HTSeq-count version 1.99.2 with the following settings (-m intersection-nonempty -s yes).
Assembly: hg38
Supplementary files format and content: xlsx files include raw conts for each sample
Supplementary files format and content: xlsx files include RPM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: human lung fibroblasts

growth_protocol: HLFs were obtained from Lonza (Basel, Switzerland) and cultured in Dulbecco’s Modified Eagle’s Medium with high glucose supplemented with 15% fetal bovine serum.

extract_protocol:
Total RNA was isolated from HLFs and stored in Isogen (Nippon Gene, Tokyo, Japan).
Purified total RNA (200 ng) with an RNA integrity value of > 9 was used for RNA library preparation according to the instructions of the QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria). Libraries were amplified via 13 cycles of polymerase chain reaction. RNA libraries were sequenced using the Illumina (San Diego, California, USA) NextSeq 500 system (75 cycles).

treatment_protocol: For siRNA transfection, DPP4-siRNA (Cat# 4392421, siRNA ID:s4255) and negative control siRNA (Cat# 4390843, Silencer™ Select Negative Control No.1 siRNA) were purchased from Thermo Fisher Scientific. Using the Lipofectamin™ RNAiMAX Transfection Reagent (Thermo Fisher Scientific), HLFs were transfected with siRNA for 72 h according to the manufacture’s protocol. After siRNA treatment, cells were ex-posed to normoxia or hypoxia. Cells in the normoxic groups were maintained at 37℃ in 21% O₂ and 5% CO₂. Cells in the hypoxia groups were separately cultured in 1% O₂ and 5% CO₂ for 48 h, using AnaeroPack-Kenki 5% (Mitsubishi Gas Chemical, Tokyo, Japan) and an oxygen indicator. Cells were used at passages 6–8 in all experiments.

tag: cell type

value: human lung fibroblasts


title: Mockgraft_3

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

organism: Solanum lycopersicum

growth_protocol: Seeds of tomato cv Micro Tom were placed in Petri dishes containing wetted tissue paper and maintained at 28°C in the dark for 3-6 days to stimulate homogeneous germination. Germinated seeds were planted in individual pot propagators containing Scott’s M3 compost and cultivated under standard tomato growth conditions (16h/8h day/night cycle; 144 25°C/20°C).

tag: tissue

tag: ecotype

value: Micro Tom

value: Water


title: W1M_T1_leaf_Water_Mock_1

data_processing:
Trimmomatic (Bolger et al., 2014) was used to remove adapters and discard low-quality reads.
The cleaned reads were aligned to the tomato genome (ITAG4.0) using Hisat2 (version 2.2.1) (Kim et al., 2019)
Samtools (version 1.12) (Li et al., 2009) was used to sort and index Sam files into Bam format.
Read counts were generated using Htseq (version190 0.13.5) (Anders et al., 2015), and the raw count per gene was used to determine differentially expressed genes using DESeq (Anders and Huber, 2010) and default parameters. Genes with a significance p-value below 0.05 after Benjamini and Hochberg correction were considered to be differentially expressed.
Assembly: ITAG4.0
Supplementary files format and content: For each genotype, the rawcount file is provided, generated with htseq-count (Anders et al., 2015).

source_name: leaves

extract_protocol:
One-week after each respective BABA treatment, two leaves from four individual plants were collected and stored in liquid nitrogen. Plants were left to grow and produce red fruit. The first three fruit on all plants were marked and collected. Total RNA was isolated from 100 mg of leaves or fruits samples using  TRIzol (Thermo Fisher; catalogue number 15596026) following manufacturer's specifications.
Libraries for RNA expression analysis were prepared by Novogene following their standard protocol. After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichmen

treatment_protocol: At two-weeks, 1/3 of plants were soil drenched with 5 mM BABA (catalogue number A4420-148 7, Sigma Aldrich) to provide a final concentration of 0.5 mM in the soil. All other plants were treated with the same volume of water. One week after BABA treatment, seedlings were removed from soil, roots were gently washed, and seedlings were replanted in new compost. At twelve weeks, 1/3 of plants were soil treated to a final concentration of 0.5 mM BABA. The remaining 1/3 of plants were left as water controls. Infections of leaves with Botrytis cinerea (R16) were performed entirely as previously described (Luna et al., 2016). Infection of fruit was performed  as described in Wilkinson et al., 2018.

value: leaves

tag: treatment 1

tag: treatment 2

value: mock


title: 5637KO1_NSG9

city: la jolla

first: Xue

last: Wang

state: CA

address: 10010 N Torry Pines Rd

department: MCBL-H

country: USA

institute: Salk Institute

data_processing:
The Fastq files of the RNA-seq data were processed to read quality control by running "FastQC" (Galaxy version 0.72) in Galaxy  (usegalaxy.org) and then to remove the adapters by running ‘Trim Galore!’ (Galaxy version 0.4.3.1). The trimmed reads were mapped to human genome 38 by ‘HISAT2’ (Galaxy version 2.1.0+galaxy 4) and the mapped reads were then counted with ‘featureCounts’ (Galaxy version 1.6.3+galaxy 2). The counts were processed to differentially expressed gene analysis with R package‘DESeq2’(Version 1.14.1).
Assembly: hg19
Supplementary files format and content: counts.txt
Supplementary files format and content: Counts of all RNA-seq files including replicates

growth_protocol: T24 cells with different PIN1 expression levels were cultured in McCoy’s 5A complete medium. 5637  with different PIN1 expression levels cells were maintained in RPMI-1640 complete medium.

extract_protocol: Total RNA was extracted according to the manufacturer’s instructions from the NucleSpin RNA purification kit (Macherey-Nagel, 740955.50) and processed to library construction with TruSeq RNA library Prep Kit (illumine).

tag: cell line

value: human bladder cancer cell line

tag: genotype

value: PIN1 knockout


title: 5637C2_NSG8

value: Control


title: N2a_total RNA

city: Nanning

first: yunfeng

last: zou

address: Shuangyong road

country: China

institute: Guangxi Medical University

data_processing:
Illumina HiSeqTM 4000 software used for basecalling.
Reads obtained from the sequencing machines included raw reads containing adapters or low  quality bases which would affect the following assembly and analysis. Thus, to get high  quality clean reads, reads were further filtered by fastp(version 0.18.0). hort reads alignment tool Bowtie2 [2] (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database.
Transcripts abundances were quantified by software StringTie in a reference-based approach. For  each transcription region, a FPKM (fragment per kilobase of transcript per million mapped  reads) value was calculated to quantify its expression abundance and variations, using  StringTie software.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include count and normalized (fpkm,rpm, tpm).

organism: Mus musculus

source_name: Mouse neuroblastoma cells

extract_protocol:
RNA was harvested using Trizol reagent.  Illumina HiSeqTM 4000 was used with 1 ug of total RNA (ribosomal RNA removed) for the construction of sequencing
C_S19_L005_R1_001.fastq and T_S18_L005_R1_001.fastq files were prepared with small RNAs.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: N2a cells were cultured in  MEM medium containing 300 μM manganese for 48 hours

value: Mouse-derived neural  cells

tag: strain


title: Mockgraft_4


title: Mockgraft_2


title: Control/Normoxia 1


title: 5637C1_NSG7


title: B3M_T1_leaf_BABA_Mock_3

value: BABA 2 wpg


title: T24RE2_NSG6

value: PIN1 re-expression


title: Heterograft_3


title: Heterograft_4


title: T24RE1_NSG5


title: KO_input rep1

city: Shenzhen

first: yuan

last: meng

address: College avenue 1066#

department: Department of Medicine

institute: Shenzhen University

data_processing:
Illumina Casava (1.8) software used for basecalling.
Data were aligned to the mm10 mouse genome assembly using Bowtie (v2.2.5) with the settings ‘--very-sensitive’.
Low quality mapped reads were removed using SAMtools (v1.3.1) with the settings ‘-q 30’.
Use the RNAcentral database to filter known rRNA sequences.
Peaks were called using MACS2 (v2.1.0) with the settings ‘--keep-dup 1 -q 0.05’, and further annotated by HOMER (v4.10)
Assembly: mm10
Supplementary files format and content: bigwig files were generated using deepTools (v 3.3.0)

source_name: colon

extract_protocol:
Colons were removed from the sacrificed mice and cut open longitudinally. Feces were removed and mucus was lightly scraped off. Then, the colon tissues were washed with cold PBS three times, cut into small pieces and incubated with PBS supplemented with 5 mM EDTA, 1 mM DTT and 10 μM ROCK inhibitor (Y-27632; MedChemExpress, Monmouth Junction, NJ, USA) at 37℃ for 25 min with gentle shaking. Cell supernatant containing isolated epithelial cells was then centrifuged (500 × g, 5 min), and the pellet was used for total RNA isolation.
Methylated RNA immunoprecipitation(MeRIP) with specific m6A antibody and RNA libraries were prepared for sequencing using standard Illumina protocols
Libraries were sequenced on an Illumina HiSeq™ 2500 platform with 6G base PE150 reads.

value: colon

value: colon epithelial cell

value: Ythdf1 KO


title: Heterograft_2


title: T24KO2_NSG4


title: Heterograft_1


title: BABAgraft_4


title: BABAgraft_2


title: KO_input rep2


title: WT_input rep2

value: WT


title: T24C2_NSG2


title: Sample D1: Ri rep1

city: Guangzhou

first: Xiaohui

last: Mo

address: 483 WUSHAN ROAD, TIANHE DISTRICT.

institute: South China Agricultural University

data_processing:
Oligo (dT) magnetic beads were used to select mRNA with polyA tail.
Remove reads with adaptors; Remove reads in which unknown bases were more than 10%;Remove low quality reads (the percentage of low quality bases was over 50% inaread,we define the low quality base to be the base whose sequencing quality is no more than 5).
Bowtie2 were used to map clean reads to reference gene and use HISAT to reference genome.
The quantification tool was RSEM and the expression level were calculated by FPKM method.
The DEGs was screened using NOISeq.
Genome_build: Glycine max Wm82.a2.v1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

organism: Glycine max

source_name: Root

extract_protocol:
Total root RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA, USA)
BGI RNA-Seq kit

tag: genotype/variation

value: suppression of GmHAD1-2 transgenic soybean (Ri)

value: Root


title: T24C1_NSG1


title: C126 miRNA

city: Shanghai

first: Yu

last: Zhang

address: 639 Zhizaoju Road, Shanghai, PR China

institute: Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine

description: All.miRNA.mature.Counts.exp.txt

data_processing:
(mRNA and lncRNA) We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 10% base quality <15 b) 13% base quality <20.
(mRNA and lncRNA) Hisat2 2.0.4 mapping to reference genome
(mRNA and lncRNA) count counting
(circRNA) Circular RNA was predicted based on the sequencing data with ACFS circRNA prediction pipeline. Unmapped Reads was collected utilizing BWA-mem(bwa mem -t 1 -k 16 -T 20) for circRNA identification: head-to-tail junction was identified and highest splicing strength score was calculated by MaxEntScan33 with a filtering criterion greater than or equal to 10. Base on the re-alignment of the unmapped reads on the circular RNA candidates, Reads that mapped to the circular RNA back splicing junction(with an overhang of at least 6 nt) were counted for each circRNA.
(circRNA) count counting
(miRNA) We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) a) 10% base quality <15 b) 13% base quality <20 c) 15bp < read length < 30bp.
(miRNA) Utilizing the BWA software, we mapped the clean data to miRBase 22.0 Homo Sapiens miRNA database and GRCH38 genome.
(miRNA) count counting
Genome_build: GRCh38 / miRBase 22.0
Supplementary_files_format_and_content: TXT files contain counts for each sample

source_name: gingiva

extract_protocol:
(rRNA-free RNA) Total RNA was extracted from cell or animal tissue by Trizol reagent(Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200(Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
(miRNA) Total RNA was extracted from cell or animal tissue by Trizol reagent(Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200(Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit(Qiagen) and the purification result was validated by Gel electrophoresis.
(rRNA-free RNA) RNA libraries were prepared for sequencing using standard Illumina protocols
(miRNA) RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Gingiva biopsy samples from the periodontitis patients were collected from the sulcular region that included the connective tissues and gingival epithelium facing towards the sulcus. For the control group participants, similar biopsy specimens of healthy gingiva were taken while extracting teeth that were either impacted or required extraction or for the orthodontic treatment. Two gingival samples (one for redondoviruses detection, and the other for RNA sequencing) were collected from each participant and were immediately frozen with liquid nitrogen, then stored at −80°C.

value: gingiva

tag: periondontitis

value: negative

tag: redondoviridae infection

tag: fraction

value: miRNA


title: C130 miRNA

description: All.miRNA.mature.Counts.exp.txt


title: WT_input rep1


title: Sample D2: Ri rep2


title: Mockgraft_1

value: scion leaves

value: Micro Tom

value: Water


title: Sample B2: WT rep2

value: Willd type


title: BABA12_T2_Leaf_WGBS_2

library_source: genomic

data_processing:
Whole genome bisulfite sequencing (WGBS) datasets (fastq files) were trimmed using Trimmomatic (Bolger et al., 2014) to remove adapter sequences
High-quality trimmed sequences were aligned against the Tomato ITAG4.0 reference genome using Bismark (Krueger & Andrews, 2011). Duplicated reads were collapsed into one read.
Chloroplast sequences was used to estimate the bisulfite conversion.
To account for non-converted DNA, we applied a correction according to Catoni and Zabet 2021 (https://doi.org/10.1007/978-1-0716-1134-0_21). Briefly, the number of methylated reads were decreased as: m*= max(0, m – nc) (where m* is the corrected number of methylated reads, m is the raw number of methylated reads, n is the total number of reads and c is the conversion rate).
Assembly: ITAG4.0
Supplementary files format and content: For each sample, the CX_Report generated by Bismark is provided (Krueger et al. 2011, Bioinformatics).

molecule: genomic DNA

extract_protocol:
DNA was extracted from 100 mg of ground frozen leaf and fruit tissue using Qiagen DNeasy Plant Mini Kit (Qiagen) following the manufacturer’s instructions and resuspended in 30 μL pure water.
All library preparation and sequencing was conducted by Novogene using NovaSeq 6000 PE150. After quality control, positive control DNAs were added into the DNAs which were then fragmented into 200-400 bp using Covaris S220 and bisulfite treated (Accel-NGS Methyl-Seq DNA Library Kit for illumina, Swift). Ligation of methylation sequencing adapters, size selection and PCR amplification was then performed before illumina sequencing for 20 million paired reads per sample with 30 x sequencing depth.

treatment_protocol: At two-weeks, 1/3 of plants were soil drenched with 5 mM BABA (catalogue number A4420-148 7, Sigma Aldrich) to provide a final concentration of 0.5 mM in the soil. All other plants were treated with the same volume of water. One week after BABA treatment, seedlings were removed from soil, roots were gently washed, and seedlings were replanted in new compost. At twelve weeks, 1/3 of plants were soil treated to a final concentration of 0.5 mM BABA. The remaining 1/3 of plants were left as water controls.

value: leaves

tag: developmental stage

value: 12 wpg

tag: treatment

value: BABA 12 wpg


title: B111 miRNA

description: All.miRNA.mature.Counts.exp.txt

value: positive


title: Sample B1: WT rep1


title: B126 miRNA

description: All.miRNA.mature.Counts.exp.txt


title: BABA2_T2_Leaf_WGBS_3

value: BABA 2 wpg


title: AL-GSHEE4

city: hefei

first: Yue

last: Zhao

institute: univerisity of science and techonology of china

description:
AL-CTRL1234vsAL-GSHEE1234_count.xlsx
bulk RNA for NK cells

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, 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 Hisat2 v2.2.1 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.2.1.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: FPKM values and gene count for each Sample

source_name: peripheral blood

extract_protocol:
For bulk RNA-seq analysis of human peripheral blood NK cells, we sorted NK cells from peripheral blood using the Human NK Cell Isolation Kit (Miltenyi Biotec) or flow cytometric sorting with a purity of more than 95%. Total intracellular RNA was extracted using TRIzol (Invitrogen).
RNA libraries for RNA-seq were prepared using VAHTS® Universal V8 RNA-seq Library Prep Kit or Fast RNA-seq Lib Prep Kit V2 following manufacture's protocols.

treatment_protocol: NK cells purified from peripheral blood were treated in vitro with BSO for 72 h; NK cells purified from peripheral blood of patients with acute leukemia were treated in vitro with GSHEE for 12h.

value: peripheral blood

value: NK cells

tag: subject status

value: acute leukemia patient

value: GSHEE


title: BABA12_T2_Leaf_WGBS_1


title: BABAgraft_3

tag: treatment scion

value: BABA treated


title: T24KO1_NSG3

value: human bladder cancer cell line

value: PIN1 knockout


title: AL-GSHEE3


title: A101 miRNA

description: All.miRNA.mature.Counts.exp.txt

value: gingiva

value: miRNA


title: BABA12_T2_Leaf_WGBS_3

value: Micro Tom


title: A124 miRNA

description: All.miRNA.mature.Counts.exp.txt


title: AL-GSHEE2


title: F-len CGGBP1 rep 3

type: RNA

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

description: Gene expression after 48 hrs of transfection the truncated form

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327).

scan_protocol: The microarray slide was scanned on a G2600D scanner (Agilent Technologies).

data_processing: Images were quantified using Agilent Feature Extraction Software . Feature extracted raw data was analyzed using Agilent GeneSpring GX software.

source_name: F-len CGGBP1 rep 3

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (Part No. 5190-0424). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: HEK293T cells were were grown in DMEM supplemented with 10% FBS and 1% antibiotic-antimycotic at 37°C and 5% CO2.

extract_protocol: RNA was extracted using Trizol precipitation and was then purified using Qiagen’s RNeasy mini kit (74106). The concentration and purity of the RNA extracted were evaluated using the Nanodrop Spectrophotometer (Thermo Scientific; 1000).  The integrity of the extracted RNA were analysed on the Bioanalyzer (Agilent; 2100).

treatment_protocol: HEK293T cells were transduced with the following shRNA lentiviruses: non-targeting (CT), CGGBP1-targeting (KD for selected domains: shA targetting the N-terminal of CGGBP1 for C-term truncated form over-expression and shB targetting the C-terminal of CGGBP1 for N-term truncated form over-expression). For stable transduction, control- and CGGBP1-shmiR transduced cells were selected with 10 ug/ml puromycin for a week. CT cells were then transfected with F-len overexpression plasmid using Polyplus JetOptimus (cat #101000051) transfection reagent (5ug plasmid per 10cm dish). HEK293T shB and shA cells were transfected with N-term and C-term over-expression plasmids respectively using the same protocol as for F-len.


title: C130 rRNA-free RNA

description: All.counts.exp_mRNA_lncRNA.txt/all.counts.exp_circRNA.txt

value: negative

value: rRNA-free RNA


title: AL-GSHEE1


title: C126 rRNA-free RNA


title: Water_T2_Leaf_WGBS_2

value: leaves

value: Water


title: Water_T2_Leaf_WGBS_3

value: 12 wpg


title: B126 rRNA-free RNA

value: positive


title: AL-CTRL4


title: Water_T2_Leaf_WGBS_1


title: F-len CGGBP1 rep 2

source_name: F-len CGGBP1 rep 2


title: AL-CTRL3


title: B111 rRNA-free RNA


title: F-len CGGBP1 rep 1

source_name: F-len CGGBP1 rep 1


title: BABA2_T1_Leaf_WGBS_3

value: 2 wpg

value: BABA 2 wpg


title: BABA2_T2_Leaf_WGBS_1


title: BABA2_T1_Leaf_WGBS_2


title: A101 rRNA-free RNA


title: BABA2_T2_Leaf_WGBS_2


title: C-term truncation rep 2

source_name: C-term truncation rep 2


title: C-term truncation rep 3

source_name: C-term truncation rep 3


title: BABA2_T1_Leaf_WGBS_1


title: AL-CTRL1

value: peripheral blood

value: NK cells


title: A124 rRNA-free RNA


title: sham3

city: Wenzhou

first: Liangen

last: Lin

state: Zhejiang

address: No. 299 Guan Road, Louqiao Street, Ouhai District

institute: wenzhou people's hospital

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: rn6
Supplementary files format and content: FPKM, count values for each Sample

organism: Rattus norvegicus

source_name: lung

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp pashIRed-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: lung

value: sham


title: Water_T1_Leaf_WGBS_3


title: dAdo 12h rep3

city: Cologne

first: Gregor

last: Langen

address: Zuelpicher Str. 47b

department: Institute for Plant Sciences

country: Germany

institute: University of Cologne

data_processing:
Sequenced reads were pseudoaligned to Arabidopsis TAIR10 transcriptome and counted using kallisto 0.44 -b 100 --single
Processed data file: read counts from tximport
Assembly: TAIR10

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Surface-sterilized seeds were germinated and grown on ½ MS  (with vitamins, pH 5.7) with 1 % (w/v) sucrose and 0.4 % (w/v) Gelrite under short day conditions (8 h light, 16 h dark) with 130 μmol m-2 s-1 of light and 22 °C/18 °C. 7-day-old seedlings were transferred from plates to individual wells of 24-well plates containing 0.5 mL liquid ½ MS medium supplemented with 0.5% (w/v) sucrose, followed by  5 additional days in liquid culture.

extract_protocol:
Total RNA was extracted using the TRIzol and DNA digested with DNase I.
Stranded mRNA-seq Libraries were prepared according to the manufacturer’s instructions (Vazyme Biotech Co., Nanjing, China)

treatment_protocol: The medium was replaced with 1 mL 500 µM dAdo in 2.5 mM MES buffer pH 5.6, or 2.5 mM MES buffer pH 5.6.

value: seedlings

tag: age

value: 12 days

value: dAdo 12h


title: N-term truncation rep 3

source_name: N-term truncation rep 3


title: N-term_ChIP

data_processing:
Adapter trimming and Quality filtering of paired reads using fastp version 0.23.4 at default parameters
Paired end-to-end alignment using Bowtie2 at default parameters after imposing a read length constraint of minimum 100bp and maximum 1000bp. Alignment mean read length = 222bp for N-term_MeDIP, 218bp for C-term_MeDIP, 203bp for F-len_MeDIP, 228bp for Input (MeDIP). 191bp for N-term_ChIP and 151bp for Input (ChIP).
Bigwigs were created using bamCoverage by deeptools version 3.5.1 at default parameters in bin size of 50bp
Assembly: hg38 unmasked
Supplementary files format and content: Bigwig

growth_protocol: HEK293T and human fibroblasts cells were grown in DMEM supplemented with 10 % FBS and 1% antibiotic-antimycotic at 37°C and 5% CO2.

extract_protocol:
1. MeDIP-Seq: After 72 h of transfection, cells over-expressing N-term & C-term truncated forms and F-len CGGBP1 were harvested for genomic DNA isolation using phenol-chloroform-isoamyl alcohol extraction method. Genomic DNA was sonicated to obtain 700-1000 bp fragments. 1µg fragment DNA was end repaired using NEBNext Ultra II End Repair/dA-Tailing Module (NEB #E7546). PCR adapters from Oxford Nanopore Technologies (ONT #SQK-PSK004) were ligated to end repaired DNA using NEB Blunt/TA Ligase Master Mix (NEB #M0367). 1x MeDIP master mix (10 mM Sodium Phosphate Buffer, 0.14 M NaCl and 0.05% TritonX-100) was added to adapter ligated DNA which was then denatured at 95℃ for 5 mins followed by snap chilling on ice. An antibody cocktail against 5-methylcytosine (EMD Millipore #MABE146, Sigma #SAB2702243 and Novus Biologicals #NBP2–42813) was added to snap-chilled DNA and was incubated at 4℃ overnight. Protein G Plus/Protein A Agarose beads were added to the mix followed by incubation at room temperature for 2 h. Then beads were collected by centrifugation in a separate tube and were washed thrice with 1x MeDIP master mix buffer and were subjected to Proteinase K (Sigma #P2308) digestion at 56℃ for 2 h. The slurry was centrifuged and immunoprecipitated DNA in the supernatant was collected into new tubes. This DNA was subjected to 18 cycles of PCR using whole genome primers (ONT #SQK-PSK004) and LongAmp Hot Start Taq 2X Master Mix (NEB #M0533). 2. ChIP-Seq: The N-term, C-term, and FL-CGGBP1 were over-expressed in HEK293T-shB-KD, HEK293T-shA-KD, and HEK293T-CT cells, respectively. Cells were harvested for ChIP after being transfected for 72 hours. The cells were harvested using a scrapper after being crosslinked with 4% formaldehyde for 10 minutes at 37°C. They were then quenched with glycine (125 mM). Thermo Fisher Scientific #87785's 1x Halt Protease inhibitor cocktail, EDTA-free, was added to SDS lysis buffer (50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS) and the mixture was lysed for 30 minutes on ice with periodic flick-mixing. After that, DNA was sonicated for 20 cycles of 30 seconds ON and 30 seconds OFF to create DNA fragments that ranged in length from 0.15 to 0.35 kb. The fragmented DNA was diluted in ChIP-dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 167 mM NaCl) after taking out 10% DNAseparately as input. In order to pre-clear chromatin, Protein G Plus/Protein A Agarose beads (Merck Millipore #IP05) were incubated for 4hours at 4°C. After that, the DNA was incubated for an overnight period at 4°C with gentle tumbling with an antibody cocktail targeted against the N-term(Invitrogen #PA5-57317, Abcam #ab176814, Abclonal #AE005 directed towardsthe FLAG-tagged N-term). Protein G Plus/Protein A Agarose beads were then added to collect the antibodies, and the mixture was tumble-incubated for an hour at room temperature. After that, the beads were pelleted and washed with the following four buffers: LiCl IP wash buffer (0.25 M LiCl, 1% IGEPAL (NP40), 1% sodium deoxycholate, 1 mM EDTA, and 10 mM Tris–HCl); low-salt IP wash buffer (0.1% SDS, 1% Triton X–100, 2 mM EDTA, 20 mM Tris–HCl and 150 mM NaCl); and two washes of TE buffer (10 mM Tris–HCl and 1 mM EDTA). An elution buffer (1% SDS and 0.1 M NaHCO3) was used to elute the immunoprecipitated DNA in a 500ul total volume. 200 mM NaCl was added to eluted DNAand incubatedfor 8 hours at 65°C forreverse-crosslinking. Next, for one hour at 45°C, Proteinase K (Sigma #P2308) was added to the DNA along with 10 mM EDTA, 0.1 M Tris-HCl pH 6.8, and 0.1 mg/ml for protein digestion. After adding 10% v/v 3M sodium acetate at pH 5.2, ethanol precipitation was used to purify the ChIP DNA.
1. MeDIP-Seq: Library preparation was done using NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (NEB #E7645, #E7103) as per manufacturer’s instruction. DNA was quantified using Qubit and quality assessment was done using TapeStation. DNA was sequenced on Illumina HiSeq 2500 platform. 2. ChIP-Seq: Library preparation was done using NEXTFlex Rapid DNA Sequencing Bundle (NEXTflex, #5188-12) as per manufacturer’s instruction. DNA was quantified using Qubit and quality assessment was done using TapeStation. DNA was sequenced on Illumina NovaSeq 6000 platform.
MeDIP-Seq & ChIP-Seq

treatment_protocol: HEK293T cells were transduced with the following shRNA lentiviruses: non-targeting (CT), CGGBP1-targeting (KD for selected domains: shA targetting the N-terminal of CGGBP1 for C-term truncated form over-expression and shB targetting the C-terminal of CGGBP1 for N-term truncated form over-expression). For stable transduction, control- and CGGBP1-shmiR transduced cells were selected with 10 ug/ml puromycin for a week. CT cells were then transfected with Full-length overexpression plasmid using Polyplus JetOptimus (cat #101000051) transfection reagent (5ug plasmid per 10cm dish). HEK293T shB and shA cells were transfected with N-term and C-term over-expression plasmids respectively using the same protocol as for Full-length.

tag: antibody

value: Invitrogen #PA5-57317, Abcam #ab176814, Abclonal AE005


title: sham2

tag: tissue


title: sham1


title: dAdo 12h rep2

tag: ecotype


title: Water_T1_Leaf_WGBS_2

value: Micro Tom


title: C-term truncation rep 1

source_name: C-term truncation rep 1


title: AL-CTRL2

tag: cell type

value: acute leukemia patient


title: IR3

value: ischemia-reperfusion (IR)


title: N-term truncation rep 1

source_name: N-term truncation rep 1


title: HaCaT cells treated with 3.6 µM BGJ398 for 5 h, second replicate

city: Zürich

first: Debora

last: Stefanova

address: Otto-Stern Weg 7

department: DBIOL

country: Switzerland

institute: ETH Zürich

data_processing:
he counts were generated by theSoftware Kallisto (version  0.44.0). Aggregation to gene level counts and normalizationwas performed with our R package ezRun (https://zenodo.org/records/5653448).
genome build: GRCm38.p6, The gene model annotations were obtainedfrom GENCODE Release_M23 downloaded on 2019-11-05.
Supplementary files format and content: Normal counts

source_name: HaCaT

growth_protocol: HaCaT cells are grown in DMEM (10% FBS) until confluency in a cell incubator.

extract_protocol:
Cells were washed with PBS one time, then total RNA from was isolated using the IBI Scientific RNA isolation kit (IBI Scientific, Dubuque, IO; IB47303) following the manufacturer`s protocol.
The quality of the isolated RNA was determined with a Fragment Analyzer (Agilent, Santa Clara, California, USA). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. The TruSeq Stranded mRNA (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were poly A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR.  The quality and quantity of the enriched libraries were validated using the Fragment Analyzer (Agilent, Santa Clara, California, USA).  The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20.
Cluster Generation and Sequencing: The Novaseq 6000 (Illumina, Inc, California, USA) was used for cluster generation and sequencing according to standard protocol.  Sequencing were paired end at 2 X150 bp or single end 100 bp.

treatment_protocol: Cell medium was replaced with DMEM (5 % FBS) containing either vehicle or 10 µM AZD4547 or 3.6 µM BGJ398 and incubated for 5 h

value: HaCaT

value: keratinocytes

value: wild type


title: Water_T1_Leaf_WGBS_1

source_name: leaves

value: leaves

value: Water


title: dAdo 12h rep1


title: buffer 12h rep3

value: mock 12h


title: N-term_Input

value: not applicable


title: BABA12_Fruit_WGBS_3

source_name: red fruits

value: red fruits

value: 15 wpg

value: BABA 12 wpg


title: BABA12_Fruit_WGBS_2


title: IR2

value: lung


title: N-term truncation rep 2

source_name: N-term truncation rep 2


title: HaCaT cells treated with 3.6 µM BGJ398 for 5 h, first replicate


title: IR1


title: buffer 12h rep1

value: seedlings

value: 12 days


title: I_post_C3

value: I-post-C


title: HaCaT cells treated with 3.6 µM BGJ398 for 5 h, third replicate


title: HaCaT cells treated with 10 µM AZD4547 for 5 h, second replicate


title: dAdo 3h rep3

value: dAdo 3h


title: BABA2_Fruit_WGBS_3

value: Micro Tom

value: BABA 2 wpg


title: dAdo 3h rep2


title: I_post_C2


title: BABA12_Fruit_WGBS_1


title: I_post_C1


title: HaCaT cells treated with DMSO for 5 h, third replicate

value: HaCaT

value: DMSO


title: HaCaT cells treated with 10 µM AZD4547 for 5 h, first replicate

value: keratinocytes

value: wild type


title: dAdo 3h rep1


title: HaCaT cells treated with 10 µM AZD4547 for 5 h, third replicate


title: BABA2_Fruit_WGBS_1


title: buffer 12h rep2


title: BABA2_Fruit_WGBS_2


title: Fatbody_KUMstrain, MockBlood_Day7, scRNAseq

city: Paris

first: Thomas

last: Vial

address: 28 rue du Docteur Roux

country: France

institute: Institut Pasteur

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
STARsolo raw output files were individually read into RStudio (R version 4.3.2 from 2023-10-31) and processed using Seurat (Seurat v5.0.1) and SingleCellExperiment (version 1.24.0). Samples were converted to Seurat objects and SingleCellExperiment objects. A first filter was applied by using the DropletUtils::barcodeRanks function (DroptletUtils version 1.22.0): the knee point of the barcoderank was used as a cutoff to remove empty and /or bad quality droplets with a total UMI number under this value (cf : table with inflection per sample).
Assembly: AaegL5
Supplementary files format and content: Tab-separated values files and matrix files

organism: Aedes aegypti

source_name: fatbody

growth_protocol: Experiments were conducted with Ae. aegypti mosquitoes derived from a wild-type colony originating from Kumasi, Ghana105. Mosquitoes were reared under controlled conditions (28°C, 12-hour light/12-hour dark cycle and 70% relative humidity). Prior to performing the experiments, their eggs were hatched synchronously in a SpeedVac vacuum device (Thermo Fisher Scientific) for 45 minutes. Their larvae were reared in plastic trays containing 1.5 L of tap water and supplemented with Tetramin (Tetra) fish food at a density of 200 larvae per tray. After emergence, adults were kept in BugDorm-1 insect cages (BugDorm) with permanent access to 10% sucrose solution.

extract_protocol:
A cold dissociation method was used for the mosquito midgut and fat body, adapting protocols originally developed for dissociating Anopheles sp. midgut into single-cell suspensions suitable for scRNAseq (DOI: dx.doi.org/10.17504/protocols.io.j8nlke246l5r/v1, remove the private link prior to publication). Mosquitoes were dissected on ice and pools of 7 organs collected in a drop of ice-cold SF900 III media (Sigma-Aldrich). Each organ was sectioned into 3 smaller pieces using spring scissors (Fine science tools). Sectioned organs were transferred immediately to a chambered coverglass well (Thermo scientific) containing 500ul of dissociation media (SF900 III media supplemented with 10mg/ml Bacillus licheniformis protease (Sigma-Aldrich) and 25 unit/ml DNaseI (Sigma)) for 15 minutes in the dark on ice. Tissues were then gently triturated using 15 back-and-forth pipetting motions. After 5 minutes, 100uL of supernatant containing dissociated cells was collected and transferred to a collection tube containing 45 mL of SF900 III media on ice. The dissociation well was supplemented with 100uL of fresh dissociation media and incubated for 10 min in the dark on ice. Tissues were triturated again, and 100uL of supernatant transferred to the collection tube. Three to four more dissociation rounds were performed until only single cells remained.  The collection tube was then spun at 300g for 15 min at 4°C. The pellet was resuspended gently in 900 ul ice-cold SF900 II media and filtered through Flowmi cell strainers (Sigma) with a 40 um porosity for midguts and 70 um porosity for fat bodies. The resulting cell suspension was spun at 300 g for 5 min at 4°C and resuspended in 30 ul of PBS 1x-BSA 0,04%.
Library was performed according to manufacter's instruction (Single Cell 5' Kit v2 dual index,10x Genomics).

treatment_protocol: Five- to 7-day-old female mosquitoes were deprived of 10% sucrose solution 18-24 hours before exposure to an artificial blood meal consisting of a 2:1 mix of washed rabbit erythrocytes (BCL) supplemented with 10 mM adenosine triphosphate (Sigma) and Leibovitz’s L-15 medium (Gibco) supplemented with supplemented with 0.1% penicillin/streptomycin (pen/strep; Gibco ThermoFisher Scientific), 2% tryptose phosphate broth (TBP; Gibco Thermo Fischer Scientific), 1× non-essential amino acids (NEAA; Life Technologies) and 10% fetal bovine serum (FBS; Life Technologies).  Mosquitoes were exposed to the blood meal for 15 min through a desalted pig-intestine membrane using an artificial feeder (Hemotek Ltd) set at 37°C. Fully engorged females were incubated at 28°C, 70% relative humidity and under a 12-hour light-dark cycle with permanent access to 10% sucrose.

value: fatbody

value: fat body cells

tag: age at_treatment

value: 5-7 day-old female

value: blood meal

tag: collection time

value: 7 days after blood meal


title: buffer 3h rep2

value: mock 3h


title: HaCaT cells treated with DMSO for 5 h, first replicate

tag: cell line

tag: genotype


title: HaCaT cells treated with DMSO for 5 h, second replicate


title: Fatbody_KUMstrain, MockBlood_Day2, scRNAseq

description: 10X Genomics

value: 2 days after blood meal


title: Water_Fruit_WGBS_2

value: red fruits

value: 15 wpg

value: Water


title: Midgut_KUMstrain, MockBlood_Day7, scRNAseq

description: 10X Genomics

source_name: midgut

value: midgut

value: midgut cells


title: Water_Fruit_WGBS_1

value: Micro Tom


title: buffer 3h rep1

value: seedlings

value: 12 days


title: P7-lymph node-ST

city: Nanjing

first: kun

last: xu

address: 300 Guangzhou Road

institute: Department of Oncology, The First Affiliated Hospital of Nanjing Medical University

data_processing:
Spatial transcriptomics raw sequencing data was processed using the Space Ranger v1.2.2 (10x Genomics) with the GRCh38 genome assembly as reference and transcript counts quantified for each annotated gene within every spot.
Using Space Ranger’s count, reads were aligned to the GRCh38 reference genome, and transcript counts quantified for each annotated gene within every spot. The resulting UMI count matrices (genes × spots) were then provided as input to Seurat suite (version 3.2.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: Genes by barcode counts matrices in HDF5 binary data format, PNG of all replicate images (tissue_hires_image), JSON file containing scaling factors that converts pixel positions (scalefactors_json.json), and text file containing spot barcode position information (tissue_positions_list).

molecule: polyA RNA

source_name: lymph node

extract_protocol:
For Visium, the section was cut at 10 µm thickness and mounted onto Visium slide capture areas. Sequencing libraries were prepared following the manufacturer’s protocol. After tissue staining, bright-field images were taken as described in the Spatial Transcriptomics procedure. Tissue permeabilization was performed for 12 minutes, as established in the TO assay. The Visium Spatial Gene Expression Slide & Reagent kit (10X Genomics) was used to generate sequencing libraries for Visium samples.
Visium spatial gene expression libraries were prepared for sequencing using 10x Genomics protocols.

value: untreated

tag: tnm stage

tag: molecular typing

value: luminal B


title: Base editing efficiency of linear gRNA with AC10 linker at 9 gene sites  with dCas12f-ABE(L-AC10 group), repeat2

status: Public on Nov 16 2024

first: Kechen

last: Chen

state: Guangdong

address: Shatai South Road

institute: Southern Medical University

data_processing:
Sample indexes were removed by trim_galore(0.6.10).
BAM files were generated by alignment to the reference genomic regions using the Bowtie2(2.5.1).
The substitution at each base was calculated with CRISPResso(2.2.12).
Assembly: hg38
Supplementary files format and content: Quantification of A to G substitution at each target position.

source_name: HEK293T cell line

growth_protocol: HEK293T cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
The HEK293T transfected cells were washed with 1x PBS, and harvested by addition of lysis buffer with proteinase K, 55℃ overnight. And then the genomic DNA was extracted with the steps of ethanol precipitation.
The targeted genome regions of interest were amplified with the first round PCR by Gold Medal Mix to add unique indexes for each sample. Each sample was then amplified by the second round PCR using P5 and P7 primers. All PCR products were mixed into one pot and purified by DNA Clean Beads.

treatment_protocol: In 24-well plates, HEK293T cells were transfected with 16ng gRNA plasmids and 484ng dCas12f-ABE or Cas12f-ABE plasmids.

value: HEK293T cell line

value: Human embryonic Kidney


title: Base editing efficiency of linear gRNA with AC10 linker at 9 gene sites  with dCas12f-ABE(L-AC10 group), repeat3


title: Base editing efficiency of linear gRNA with AC10 linker at 9 gene sites  with dCas12f-ABE(L-AC10 group), repeat1


title: Midgut_KUMstrain, MockBlood_Day2, scRNAseq

description: 10X Genomics

value: 5-7 day-old female


title: Base editing efficiency of linear gRNA with AC10 linker at 9 gene sites  with Cas12f-ABE(L-AC10 group), repeat3


title: Base editing efficiency of linear gRNA with AC10 linker at 9 gene sites  with Cas12f-ABE(L-AC10 group), repeat2


title: Water_Fruit_WGBS_3


title: Base editing efficiency of linear gRNA with AC10 linker at 9 gene sites  with Cas12f-ABE(L-AC10 group), repeat1


title: Base editing efficiency of linear gRNA with AC5 linker at 9 gene sites  with dCas12f-ABE(L-AC5 group), repeat1


title: Base editing efficiency of linear gRNA with AC5 linker at 9 gene sites  with Cas12f-ABE(L-AC5 group), repeat3


title: Base editing efficiency of linear gRNA with AC5 linker at 9 gene sites  with dCas12f-ABE(L-AC5 group), repeat3


title: Base editing efficiency of linear gRNA with AC5 linker at 9 gene sites  with Cas12f-ABE(L-AC5 group), repeat2


title: buffer 3h rep3


title: Base editing efficiency of linear gRNA with AC5 linker at 9 gene sites  with Cas12f-ABE(L-AC5 group), repeat1


title: Base editing efficiency of circular gRNA with AC10 linker at 9 gene sites with dCas12f-ABE(C-AC10 group), repeat2


title: Base editing efficiency of linear gRNA with AC5 linker at 9 gene sites  with dCas12f-ABE(L-AC5 group), repeat2


title: Base editing efficiency of circular gRNA with AC10 linker at 9 gene sites with dCas12f-ABE(C-AC10 group), repeat1


title: Base editing efficiency of circular gRNA with AC10 linker at 9 gene sites with Cas12f-ABE(C-AC10 group), repeat2


title: Base editing efficiency of circular gRNA with AC10 linker at 9 gene sites with dCas12f-ABE(C-AC10 group), repeat3


title: Base editing efficiency of circular gRNA with AC10 linker at 9 gene sites with Cas12f-ABE(C-AC10 group), repeat3


title: Base editing efficiency of circular gRNA with AC5 linker at 9 gene sites with dCas12f-ABE(C-AC5 group), repeat1


title: Base editing efficiency of circular gRNA with AC5 linker at 9 gene sites with dCas12f-ABE(C-AC5 group), repeat3


title: Base editing efficiency of circular gRNA with AC5 linker at 9 gene sites with dCas12f-ABE(C-AC5 group), repeat2


title: Base editing efficiency of circular gRNA with AC5 linker at 9 gene sites with Cas12f-ABE(C-AC5 group), repeat3


title: Base editing efficiency of circular gRNA with AC10 linker at 9 gene sites with Cas12f-ABE(C-AC10 group), repeat1


title: Base editing efficiency of circular gRNA with AC5 linker at 9 gene sites with Cas12f-ABE(C-AC5 group), repeat2


title: Base editing efficiency of normal gRNA at 9 gene sites with dCas12f-ABE(Normal group), repeat3


title: Base editing efficiency of normal gRNA at 9 gene sites with dCas12f-ABE(Normal group), repeat1


title: Base editing efficiency of normal gRNA at 9 gene sites with Cas12f-ABE(Normal group), repeat2


title: Base editing efficiency of normal gRNA at 9 gene sites with Cas12f-ABE(Normal group), repeat3


title: Base editing efficiency of normal gRNA at 9 gene sites with dCas12f-ABE(Normal group), repeat2


title: Base editing efficiency of circular gRNA with AC5 linker at 9 gene sites with Cas12f-ABE(C-AC5 group), repeat1


title: Base editing efficiency at 9 gene sites(blank group), as a negative control for dCas12f-ABE, repeat3


title: Base editing efficiency of normal gRNA at 9 gene sites with Cas12f-ABE(Normal group), repeat1


title: Base editing efficiency at 9 gene sites(blank group), as a negative control for dCas12f-ABE, repeat2


title: Base editing efficiency at 9 gene sites(blank group), as a negative control for Cas12f-ABE, repeat2


title: HD05; HD6; GEX

city: Taoyuan

first: Chuang-Wei

address: No. 5, Fusing St

country: Taiwan

institute: cgmh

description: 10X Genomics

data_processing:
Sequence Alignment
Quality Control
Gene Expression Quantification
Normalization
Differential Expression Analysis
Assembly: Genome Build
Supplementary files format and content: CSV/TSV

source_name: PBMC

growth_protocol: Not applicable as this study involves clinical samples from patients rather than in vitro cell cultures

extract_protocol:
Not applicable for growth or treatment as per the study design
Sample Collection,Cell Lysis,RNA Extraction
RNA Quality Check,cDNA Synthesis,Second-Strand Synthesis,End Repair and A-Tailing,Adapter Ligation,Library Amplification
Strategy,Barcoding

value: PBMC

tag: individual

value: healthy people number 05


title: Base editing efficiency at 9 gene sites(blank group), as a negative control for Cas12f-ABE, repeat3


title: HD04; HD5; GEX

description: 10X Genomics

treatment_protocol: Not applicable for growth or treatment as per the study design

value: healthy people number 04


title: HD02; HD3; GEX

description: 10X Genomics

value: healthy people number 02


title: Base editing efficiency at 9 gene sites(blank group), as a negative control for dCas12f-ABE, repeat1


title: HD03; HD4; GEX

description: 10X Genomics

value: healthy people number 03


title: NH4Cl plus TGF-β treatment, replicate 2, RNAseq

city: Manhasset

first: Lopa

last: Mishra

state: NY

address: 350 Community Drive

institute: The Feinstein Institutes for Medical Research & Cold Spring Harbor Laboratory

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed.
Assembly: hg38 for human samples
Supplementary files format and content: tab-delimited text files include fpkm values for each sample from the treated HCT116 cells

source_name: colon

extract_protocol:
For RNA-seq, RNA was extracted from HCT116 cells under different conditions using the RNeasy Plus Mini kit. RNA quality and concentration were assessed using the Thermo Scientific Nanodrop spectrophotometer before RNA sequencing.
About 1 μg of RNA was used to generate barcoded sequencing libraries. Novogene Corporation performed library preparation.

value: colon cancer cell line

value: colon

value: NH4Cl + TGF-β


title: NH4Cl treatment, replicate 2, RNAseq


title: NH4Cl treatment, replicate 1, RNAseq


title: NH4Cl treatment, replicate 3, RNAseq


title: NH4Cl plus TGF-β treatment, replicate 1, RNAseq


title: TGF-β treatment, replicate 3, RNAseq

value: TGF-β


title: TGF-β treatment, replicate 2, RNAseq


title: tomato fruit pericarps, slalkbh2-28, rep3

city: Beijing

first: Leilei

last: Zhou

address: Xianshan street

institute: Institute of Botany, Chinese Academy of Sciences

data_processing:
The uniquely mapped reads with a MAPQ ≥ 13 were assembled by Cufflinks. Gene expression was calculated as fragments per kilobase of exon per million mapped fragments (FPKM) by Cuffdiff. Differentially expressed genes between samples were defined with a cutoff criterion of FPKM fold change ≥ 1.5 and P value < 0.05.
Assembly: SL 3.0
Supplementary files format and content: txt files include gene expression values (FPKM) for each sample.

source_name: fruit pericarps

extract_protocol:
Total RNA was extracted by using the hot-phenol method from the wild-type and slalkbh2 mutant (slalkbh2-25 and slalkbh2-28) fruits at the mature green (MG) stage. mRNAs were isolated from the total RNA and then fragmented, followed by RNA-seq library construction.
For library construction, 50 ng of fragmented mRNAs were used for library construction with NEBNext ultra RNA library prepare kit for illumina (NEB, E7530). High-throughput sequencing was performed on the illumina HiSeq X sequencer with a paired-end read length of 150 bp according to the standard protocols.

value: fruit pericarps


title: tomato fruit pericarps, slalkbh2-28, rep2


title: tomato fruit pericarps, slalkbh2-28, rep1


title: TGF-β treatment, replicate 1, RNAseq


title: Ctrl, replicate 3, RNAseq

value: No treatment


title: Base editing efficiency at 9 gene sites(blank group), as a negative control for Cas12f-ABE, repeat1


title: Ctrl, replicate 2, RNAseq


title: tomato fruit pericarps, slalkbh2-25, rep2


title: NH4Cl plus TGF-β treatment, replicate 3, RNAseq


title: tomato fruit pericarps, WT, rep3

value: WT


title: NC6

city: shanghai

first: D

last: Jie

state: shanghai

address: yangpu

institute: Changhai Hospital

data_processing:
First, the Raw Data is filtered, and the filtered high-quality sequence (Clean Data) is compared to the reference genome of the species.According to the comparison results, the expression amount of each gene was calculated. On this basis, the samples were further analyzed by expression difference analysis, enrichment analysis and cluster analysis. The transcription sequence was reconstructed by splicing the above Reads.
Assembly: Homo_sapiens.GRCh38.dna.primary_assembly.fa
Supplementary files format and content: expression.xlsx

source_name: control

extract_protocol:
Conventional tissue RNA extraction method
After the completion of the library construction, PCR amplification was used to enrich the library fragments, and then the library was selected according to the fragment size, the library size was 450bp. Then, the library was inspected by Agilent 2100 Bioanalyzer, and the total concentration and effective concentration of the library were detected. Then, according to the effective concentration of the library and the amount of data required by the library, the libraries containing different Index sequences (each sample adds a different Index, and finally distinguish the data of each sample according to the Index) are mixed proportionally. The hybrid library was uniformly diluted to 2nM, and the single strand library was formed by alkali denaturation.After RNA extraction, purification, and library construction, the libraries were Paired-end (PE) sequenced using Next-Generation Sequencing (NGS) based on the Illumina sequencing platform.

value: control


title: tomato fruit pericarps, WT, rep2


title: tomato fruit pericarps, WT, rep1


title: tomato fruit pericarps, slalkbh2-28, m6A-seq IP, rep3

data_processing:
For data analysis, FastQC tool (version 0.11.7) was utilized to assess the quality of raw reads, Cutadapt (version 1.16) was used to trim the adaptors and low-quality bases with a score < 20, and Trimmomatic (version 0.30) was used to filter out the short reads with a length < 18 nucleotides or reads containing ambiguous nucleotides.
The obtained clean reads were aligned to the tomato reference genome SL 3.0 by Burrows-Wheeler Aligner (version 0.30), and only uniquely mapped reads with a mapping quality (MAPQ) ≥ 13 were retained. MACS software (version 2.0.10) was adapted to identify high-confidence m6A peaks with a stringent cutoff threshold for MACS-assigned false discovery rate (FDR) < 0.05.
PeakAnalyzer (version 2.0) was applied to annotate high-confidence peaks to the tomato genome annotation file. Integrated Genome Browser (version 9.0.2) was used for the visualization of m6A peaks according to the standard protocols.
Differentially methylated peaks were identified by the m6A site differential algorithm [ref num] with a criterion of fold change in m6A enrichment ≥ 1.5 and P value < 0.05. m6A motifs were analyzed by HOMER (version 4.7) with a restricted length of six nucleotides.
Assembly: SL 3.0
Supplementary files format and content: Tab-delimited bw files include read distributions along gene transcripts for each sample.

extract_protocol:
Total RNA was extracted by using the hot-phenol method from the wild-type and slalkbh2 mutant (slalkbh2-25 and slalkbh2-28) fruits at the mature green (MG) stage. mRNAs were isolated from the total RNA and then fragmented, followed by immunoprecipitation with specific anti-m6A antibody (Synaptic Systems, 202003).
For library construction, 50 ng of immunoprecipitated mRNAs or pre-immunoprecipitated mRNAs (input control) were used for library construction with NEBNext ultra RNA library prepare kit for illumina (NEB, E7530). High-throughput sequencing was performed on the illumina HiSeq X sequencer with a paired-end read length of 150 bp according to the standard protocols.

value: slalkbh2-28 mutant


title: NC2


title: NC4


title: tomato fruit pericarps, slalkbh2-28, m6A-seq IP, rep2


title: tomato fruit pericarps, slalkbh2-28, m6A-seq IP, rep1


title: DG6

source_name: Endometriosis lesions

value: Endometriosis lesions


title: NC1


title: tomato fruit pericarps, slalkbh2-28, m6A-seq input, rep1


title: tomato fruit pericarps, slalkbh2-28, m6A-seq input, rep2


title: DG5


title: tomato fruit pericarps, slalkbh2-28, m6A-seq input, rep3


title: tomato fruit pericarps, slalkbh2-25, m6A-seq IP, rep2

value: slalkbh2-25 mutant


title: DG4


title: Ctrl, replicate 1, RNAseq


title: DG3


title: tomato fruit pericarps, slalkbh2-25, m6A-seq IP, rep3


title: DG2


title: tomato fruit pericarps, slalkbh2-25, rep1


title: tomato fruit pericarps, slalkbh2-25, m6A-seq IP, rep1


title: tomato fruit pericarps, slalkbh2-25, m6A-seq input, rep2


title: NC5


title: NC3


title: tomato fruit pericarps, slalkbh2-25, m6A-seq input, rep1


title: tomato fruit pericarps, slalkbh2-25, rep3


title: 1321N1_nt_12h_rep3

city: Vienna

first: Giulio

last: Superti-Furga

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
NGS reads were mapped to the Genome Reference Consortium GRCh38 assembly via “Spliced Transcripts Alignment to a Reference” (STAR, v2.7.9a) utilizing the “basic” GENCODE transcript annotation from version 43 (February 2023) as reference transcriptome. STAR was run with options recommended by the ENCODE project. NGS read alignments overlapping GENCODE exon features were counted with the Bioconductor (v3.16) GenomicAlignments (v1.34.0) package via the summarizeOverlaps function in Union mode, ignoring secondary alignments and alignments not passing vendor quality filtering, and alignments were counted strand-specifically in feature (i.e., gene, transcript, and exon) orientation. Exon-level counts were aggregated to gene-level counts.
Assembly: Genome Reference Consortium GRCh38 assembly
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and 100 U/ml penicillin and 0.1 mg/ml streptomycin

extract_protocol:
Total RNA was isolated using the QIAGEN RNeasy kit including the on-column DNase I digestion.
RNA-sequencing libraries were generated following the QuantSeq 3’- mRNA-Seq FWD library preparation protocol (Lexogen). Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the 2100 Bioanalyzer instrument (Agilent).
QuantSeq 3'-mRNA sequencing (Lexogen)

treatment_protocol: Cells were treated with 2.3 µM cadmium chloride, 2.55 µM sodium metaarsenite or 20 µM mercury chloride in full medium.

value: Non-treated


title: DG1


title: 1321N1_nt_6h_rep3


title: tomato fruit pericarps, slalkbh2-25, m6A-seq input, rep3


title: 1321N1_nt_24h_rep3


title: 1321N1_nt_3h_rep3


title: tomato fruit pericarps, WT, m6A-seq IP, rep2


title: tomato fruit pericarps, WT, m6A-seq IP, rep1


title: 1321N1_nt_24h_rep2


title: 1321N1_nt_12h_rep2


title: 1321N1_nt_90min_rep3


title: tomato fruit pericarps, WT, m6A-seq input, rep1


title: tomato fruit pericarps, WT, m6A-seq input, rep2


title: 1321N1_nt_3h_rep2


title: 1321N1_nt_90min_rep2


title: 1321N1_nt_24h_rep1


title: tomato fruit pericarps, WT, m6A-seq input, rep3


title: 1321N1_nt_12h_rep1


title: 1321N1_nt_6h_rep2


title: Medulloblastoma frozen tumor, SHH, M098RB03

first: Mathilde

last: Filser

address: 26 rue d'Ulm

department: Genetics Department

institute: Institut Curie

data_processing:
Downstream analysis relied on a custom bioinformatic pipeline called NanoCliD, available on GitHub (https://github.com/InstituteCurieClinicalBioinformatics/NanoCliD). Methylation calling was performed using Nanopolish 0.14.0, and the Guppy 5.0.17 data processing toolkit facilitated the conversion of FAST5 files to FASTQ files. Sequences were aligned to the reference genome hg19 with Minimap 2.24-r1122. CNV Calling was performed, adapted from NanoDX7, using QDNASeq and DeepTools v3.5.1 (Fig 1b). The obtained copy number profiles were then manually analyzed, focusing on key alterations encountered in medulloblastoma which are chromosome 6 monosomy, GLI2, MYC, MYCN, MYCL, SNCAIP and OTX2 amplifications, loss of chromosome 9q and 10q and isochromosome 17.
For each sample, Nanopore sequencing methylation data werre compared to the 3,905 publicly available Illumina arrays (Accession series GSE109381 updated version; https://www.ncbi.nlm.nih.gov/gds), corresponding to the v11b4 Heidelberg classifier (https://www.molecularneuropathology.org/mnp/). The NanoDx pipeline7 was integrated into NanoCliD for tumor classification. The CpG called during Nanopore sequencing were cross-referenced with those from the 850,000 covered by the EPIC array to retain only common sites. Random forest algorithm was employed to obtain methylation profiling, enabling tumor assignment to a group based on the analyzed CpG overlapping those of Illumina arrays (as illustrated in Fig. 2). The score, representing the sample's passage through the algorithm's decision trees, was obtained by counting each class returned by each tree. As described by other teams before, Aa random forrest score above 0.15 was considered satisfactory for reliable classification7. Uniform Manifold Approximation and Projection (UMAP) (Fig. 2) and t-distributed Stochastic Neighbor Embedding (t-SNE) were also generated for each sample for visualization.
Assembly: hg19
Supplementary files format and content: MethylationTables.tar.gz : list of tsv files obtained after methylation calling
Library strategy: Nanopore whole genome long read sequencing

source_name: Brain Tumor

extract_protocol:
DNA were extracted from frozen MB samples using the standard phenol-chloroform procedure. The quality and quantity of DNA were assessed using Nanodrop (Thermo Fisher Scientific) and Qubit (Thermo Fisher Scientific). Quantification of DNA was performed using the Qubit Fluorometer (Quant-iT dsDNA BR Assay Kit; Thermo Fisher Scientific) and quality assessment was carried out using TapeStation (Genomic DNA screenTape; Agilent) following the manufacturer’s instructions.
For whole-genome Nanopore sequencing, DNA libraries were prepared using the SQK-RBK004 rapid barcoding kit from Oxford Nanopore Technologies. Two types of flow cells were used: MinION R9.4.1 (FLO-MIN106D) and Flongle R9.4.1 (FLO-FLG001). For MinION flow cells, 400 ng of DNA were tagmented, barcoded, repaired, and pooled in batches of six samples before adaptor ligation. Sequencing involved multiplexing six libraries, with each batch taking 48 to 72 hours per MinION R9.4.1 flow cell. For Flongle flow cells, the same SQK-RBK004 kit (Oxford Nanopore Technologies) was used, but 200 ng of DNA per tumor sample was sequenced individually on a Flongle flow cell for 24 hours. All sequencing was performed on MinION Mk1B or Mk1C devices, and sequencing runs were initiated and monitored using MinKnow software from Oxford Nanopore Technologies.

value: Brain Tumor

value: Medulloblastoma


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M098RB02


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M102RB08


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M100RB07


title: tomato fruit pericarps, WT, m6A-seq IP, rep3


title: 1321N1_nt_6h_rep1


title: 1321N1_nt_3h_rep1


title: Medulloblastoma frozen tumor, Group 3, M112RB05


title: Medulloblastoma frozen tumor, SHH, M096RB01


title: 1321N1_Hg_24h_rep3

value: 24h with 20 µM mercury chloride


title: Medulloblastoma frozen tumor, SHH, M095RB05


title: Medulloblastoma frozen tumor, SHH, M095RB06


title: Medulloblastoma frozen tumor, WNT, M098RB01


title: 1321N1_nt_90min_rep1


title: 1321N1_Hg_12h_rep3

value: 12h with 20 µM mercury chloride


title: 1321N1_Hg_6h_rep3

value: 6h with 20 µM mercury chloride


title: Medulloblastoma frozen tumor, SHH, M095RB04


title: Medulloblastoma frozen tumor, SHH, M095RB03


title: 1321N1_Hg_90min_rep3

value: 1.5h with 20 µM mercury chloride


title: Medulloblastoma frozen tumor, SHH, M095RB02


title: 1321N1_Hg_24h_rep2


title: 1321N1_Hg_12h_rep2


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M092RB03


title: 1321N1_Hg_6h_rep2


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M090RB11


title: Medulloblastoma frozen tumor, Group 3, M091RB12


title: 1321N1_Hg_3h_rep2

value: 3h with 20 µM mercury chloride


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M089RB10


title: 1321N1_Hg_12h_rep1


title: 1321N1_Hg_90min_rep2


title: 1321N1_Hg_24h_rep1


title: Medulloblastoma frozen tumor, SHH, M087RB10


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M088RB09


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M087RB11


title: 1321N1_Hg_6h_rep1


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M085RB04


title: 1321N1_Hg_3h_rep1


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M083RB08


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M085RB02


title: 1321N1_Hg_90min_rep1


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M085RB05


title: 1321N1_Hg_3h_rep3


title: Medulloblastoma frozen tumor, WNT, M081RB09


title: 1321N1_Cd_24h_rep3

value: 24h with 2.3 µM cadmium chloride


title: 1321N1_Cd_6h_rep3

value: 6h with 2.3 µM cadmium chloride


title: Medulloblastoma frozen tumor, Group 3, M082RB01


title: 1321N1_Cd_3h_rep3

value: 3h with 2.3 µM cadmium chloride


title: 1321N1_Cd_90min_rep3

value: 1.5h with 2.3 µM cadmium chloride


title: 1321N1_Cd_24h_rep2


title: Medulloblastoma frozen tumor, Group 3, M080RB04


title: 1321N1_Cd_6h_rep2


title: Medulloblastoma frozen tumor, SHH, M080RB03


title: 1321N1_Cd_3h_rep2


title: 1321N1_Cd_12h_rep3

value: 12h with 2.3 µM cadmium chloride


title: 1321N1_Cd_90min_rep2


title: Medulloblastoma frozen tumor, WNT, M080RB01


title: 1321N1_Cd_12h_rep1


title: Medulloblastoma frozen tumor, WNT, M079RB10


title: 1321N1_Cd_3h_rep1


title: Medulloblastoma frozen tumor, Group 3, M079RB12


title: Medulloblastoma frozen tumor, Group 4, M079RB09


title: 1321N1_Cd_24h_rep1


title: Medulloblastoma frozen tumor, SHH, M079RB11


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M081RB07


title: 1321N1_Cd_90min_rep1


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M080RB06


title: 1321N1_As_6h_rep3

value: 6h with 2.55 µM sodium metaarsenite


title: 1321N1_Cd_6h_rep1


title: 1321N1_As_24h_rep3

value: 24h with 2.55 µM sodium metaarsenite


title: Medulloblastoma frozen tumor, Group 4, M078RB06


title: Medulloblastoma frozen tumor, WNT, M078RB05


title: 1321N1_As_12h_rep3

value: 12h with 2.55 µM sodium metaarsenite


title: Medulloblastoma frozen tumor, WNT, M079RB08


title: 1321N1_Cd_12h_rep2


title: 1321N1_As_3h_rep3

value: 3h with 2.55 µM sodium metaarsenite


title: Medulloblastoma frozen tumor, Group 4, M078RB04


title: Medulloblastoma frozen tumor, WNT, M080RB02


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M080RB05


title: 1321N1_As_90min_rep3

value: 1.5h with 2.55 µM sodium metaarsenite


title: 1321N1_As_24h_rep2


title: Medulloblastoma frozen tumor, Group 4, M078RB03

value: Brain Tumor


title: 1321N1_As_12h_rep2


title: Medulloblastoma frozen tumor, Group 4, M078RB01

value: Medulloblastoma


title: 1321N1_As_6h_rep2


title: Medulloblastoma frozen tumor, SHH, M077RB12


title: Medulloblastoma frozen tumor, Group 4, M077RB11


title: 1321N1_As_90min_rep2


title: Medulloblastoma frozen tumor, Group 4, M077RB09


title: 1321N1_As_12h_rep1


title: Medulloblastoma frozen tumor, SHH, M077RB10


title: 1321N1_As_24h_rep1


title: Medulloblastoma frozen tumor, Group 3, M077RB08


title: Medulloblastoma frozen tumor, Group 4, M077RB07


title: 1321N1_As_6h_rep1


title: 1321N1_As_90min_rep1


title: Medulloblastoma frozen tumor, SHH, M076RB04


title: Medulloblastoma frozen tumor, SHH, M076RB06


title: Medulloblastoma frozen tumor, Group 4, M076RB03


title: Medulloblastoma frozen tumor, Group 3, M076RB02


title: Medulloblastoma frozen tumor, SHH, M076RB05


title: 1321N1_As_3h_rep1


title: Medulloblastoma frozen tumor, WNT, M078RB02


title: UTUC71

city: Suita

first: Akinaru

last: Yamamoto

state: Outside U.S./Canada

address: Yamadaoka, 2-2

institute: Osaka University Graduate School of Medicine

data_processing:
Gene expression values for tumor samples were estimated from the RNA-seq data using the Genomon pipeline (https://github.com/ Genomon-Project/genomon-docs/tree/v2.0).
Alignment was performed using the STAR aligner (v.2.5.2a) against the hg19 human genome.
The BAM files, named Aligned.sortedByCoord.out.bam, which were generated via STAR, were utilized to quantify expression data using GenomonExpression.
Assembly: hg19
Supplementary files format and content: text file includes raw counts for each Sample

source_name: UTUC tissue

extract_protocol:
Total RNA was extracted from each sample stored in RNAlater (-20 °C) using the RNeasy mini kits (QIAGEN).
The 100-bp RNA fraction was utilized to construct cDNA libraries using the TruSeq Stranded mRNA Prep kit (Illumina), following the manufacturer’s protocol.

value: UTUC tissue

value: cancer


title: Medulloblastoma frozen tumor, Group 4, M076RB01


title: AN77

source_name: adjacent normal tissue

value: adjacent normal tissue

value: normal


title: UTUC76


title: UTUC77


title: AN76


title: UTUC75


title: 1321N1_As_3h_rep2


title: Medulloblastoma frozen tumor, WNT, M075RB11


title: AN75


title: Medulloblastoma frozen tumor, Group 3, M075RB10


title: UTUC74


title: Medulloblastoma frozen tumor, Group 3, M075RB08


title: Medulloblastoma frozen tumor, Group 3, M075RB07


title: UTUC72


title: AN73


title: Medulloblastoma frozen tumor, WNT, M074RB04


title: AN71


title: Medulloblastoma frozen tumor, WNT, M074RB03


title: Medulloblastoma frozen tumor, SHH, M075RB09


title: UTUC70


title: Medulloblastoma frozen tumor, SHH, M075RB12


title: AN72


title: AN69


title: UTUC69


title: Medulloblastoma frozen tumor, WNT, M071RB02


title: Medulloblastoma frozen tumor, Group 3, M074RB06


title: Medulloblastoma frozen tumor, WNT, M074RB01


title: UTUC68


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M071RB01


title: AN68


title: Medulloblastoma frozen tumor, SHH, M068RB04


title: Medulloblastoma frozen tumor, Group 3, M074RB02


title: Medulloblastoma frozen tumor, Group 3, M074RB05


title: UTUC67


title: UTUC73


title: AN70


title: AN74


title: AN67


title: Medulloblastoma frozen tumor, SHH, M067RB03


title: UTUC66


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M060RB07


title: Medulloblastoma frozen tumor, WNT, M073RB11


title: cE14M3, 12L, snRNAseq

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

country: Canada

institute: Memorial University of Newfoundland

description: 10x Genomics

data_processing:
The demultiplexing, alignment, filtering, barcoding, and UMI counting were done using the 10x Genomics Cell Ranger v7.2.0 pipeline. (https://www.10xgenomics.com/support/software/cell-ranger/7.2)
All the steps are mentioned here; https://github.com/ziahasanz/lc_paper/
Assembly: mRatBN7.2
Supplementary files format and content: matrix (.h5) and AnnData (.h5ad) files

source_name: Locus coeruleus

extract_protocol:
Nuclei were isolated from the dissected frozen Locus coeruleus (LC) of two groups of rats, AAV-GFP and AAV-htauE14, using the 10x Genomics Chromium Nuclei Isolation with RNAse Inhibitor Kit.
Library construction was completed using the Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics). The libraries were then sequenced (paired-end) on the Illumina NovaSeq 6000.
snRNA-seq

tag: strain

value: Locus coeruleus

value: Brain cells

tag: Sex

value: Male


title: cE14M2, 11L, snRNAseq

description: 10x Genomics

tag: treatment


title: UTUC65


title: UTUC64


title: AN64


title: Medulloblastoma frozen tumor, WNT, M057RB04


title: AN65


title: AN63


title: cE14F3, 9L, snRNAseq

description: 10x Genomics

value: Female


title: Medulloblastoma frozen tumor, SHH, M058RB05


title: UTUC63


title: cE14M1, 10L, snRNAseq

description: 10x Genomics


title: UTUC62


title: Medulloblastoma frozen tumor, Group 3, M054RB01


title: cE14F2, 8L, snRNAseq

description: 10x Genomics


title: cE14F1, 7L, snRNAseq

description: 10x Genomics


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M052RB02


title: UTUC60


title: cGFPM3, 6L, snRNAseq

description: 10x Genomics

value: AAV-GFP


title: AN60


title: Medulloblastoma frozen tumor, Group 4, M050RB09


title: UTUC59


title: AN61


title: AN66


title: cGFPM2, 5L, snRNAseq

description: 10x Genomics


title: Medulloblastoma frozen tumor, Group 4, M056RB03


title: AN59


title: Medulloblastoma frozen tumor, Group 3, M055RB02


title: cGFPM1, 4L, snRNAseq

description: 10x Genomics


title: UTUC57


title: Medulloblastoma frozen tumor, Group 4, M047RB05


title: cGFPF3, 3L, snRNAseq

description: 10x Genomics


title: AN62


title: UTUC61


title: UTUC56


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M047RB06


title: AN58


title: AN56


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M047RB01


title: UTUC55


title: cGFPF2, 2L, snRNAseq

description: 10x Genomics


title: AN55


title: UTUC54


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M046RB12


title: cGFPF1, 1L, snRNAseq

description: 10x Genomics


title: JM8.N4 mESC, wild-type, ZNF143 ChIP-seq Input, rep. 2

city: Cambridge

first: Domenic

last: Narducci

state: MA

address: Building 56 Room 787B, 32 Vassar Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for NovaSeq output.
Paired end reads were aligned to a concatenation of the UCSC mm39 and hg38 genomes using bowtie2 v2.2.5 with --no-mixed --no-discordant.
Uniquely aligned reads were filtered for PCR duplicates using sambamba markdup. Reads for each condition were randomly subsambled using normalization factors based on hg38 spike-in. Normalization factors were corrected using the ratio of human to mouse read counts in corresponding input samples.
Assembly: mm39;hg38
Supplementary files format and content: bigwig file has data based on all uniquely aligning non-duplicate reads

growth_protocol: mESCs were cultured under 5% CO2 at 37°C under feeder-free conditions. The mESCs were grown in medium consisting of KnockOut DMEM (ThermoFisher #10829-018) supplemented with 15% FBS, 1000 U/mL LIF (homemade), 1 mM MEM Non-Essential Amino Acid Solution (ThermoFisher #11140050), 2 mM GlutaMAX supplement (ThermoFisher #35050061), 100 μg/mL Penicillin-Streptomycin (ThermoFisher #15140122), 0.1 mM 2-mercaptoethanol (ThermoFisher #31350010), 10 μM MEK inhibitor (Tocris #PD0325901), and 3 μM GSK inhibitor (Sigma-Aldrich #SML1046) on plates pre-coated with sterile 0.1% gelatin (Sigma-Aldrich, G1890). The mESCs were passaged every 2 days by dissociation with TrypLE Express Enzyme (ThermoFisher #12605028), and half the medium was replaced daily.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 mins. Following quenching, chromatin was sonicated and then reverse crosslinked. Naked DNA was further sonicated to the 400-800bp range.
DNA from ZNF143 ChIP, CTCF ChIP, or input chromatin was used to prepare libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with a number of PCR cycles according to the manufacturer's protocol on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified twice using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR and pooled in a 1:1 ratio. Following qPCR quantification, libraries were submitted for sequencing.

treatment_protocol: For depletion of ZFP143 in the clone A and clone B cell lines, the cells were incubated in media containing 100 μM 5-Ph-IAA (MedChemExpress #HY-134653) and 300 nM HaloPROTAC3 (Promega # GA3110), and for depletion of CTCF in the same lines the, the cells were incubated in media containing 100 nM dTAG-13 (Tocris # 6605) for 3 hours. For the depletion of ZFP143 in the clone D cell line, the cells were incubated in media containing 100 nM dTAG-13, and for the depletion of ZNF143 in the clone 30 HEK293T cell line, the cells were incubated in media containing 500 μM IAA for 3 hours.

value: Mouse embryonic stem cell

tag: spike-in reference_organism

value: Homo sapiens

tag: spike-in cell_line

tag: chip antibody

tag: antibody info

value: Wild-type

tag: time


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M046RB10

tag: tissue


title: UTUC53


title: AN54


title: AN57


title: AN53


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M046RB07

tag: cell type


title: JM8.N4 mESC, wild-type, ZNF143 ChIP-seq Input, rep. 1


title: UTUC58


title: UTUC52


title: JM8.N4 mESC, clone D timecourse ∆ZFP143 24h, CTCF ChIP-seq Input, rep. 2

value: Clone D, Homozygous ZFP143-SNAPftag-FKBP12(F36V)-V5, Homozygous FLAG-HaloTag-CTCF

value: 100nM dTAG-13

value: 24 hours


title: AN52


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M045RB03

value: Brain Tumor


title: AN51


title: UTUC51


title: Medulloblastoma frozen tumor, Group 4, M045RB02

value: Medulloblastoma


title: UTUC50

value: UTUC tissue


title: JM8.N4 mESC, clone D timecourse ∆ZFP143 12h, CTCF ChIP-seq Input, rep. 2

value: 12 hours


title: AN50

value: adjacent normal tissue


title: UTUC49

value: cancer


title: Medulloblastoma frozen tumor, Group 3, M045RB01


title: JM8.N4 mESC, clone D timecourse untreated, CTCF ChIP-seq Input, rep. 2


title: AN49

value: normal


title: UTUC47


title: Medulloblastoma frozen tumor, SHH, M043RB04


title: JM8.N4 mESC, clone D timecourse ∆ZFP143 24h, CTCF ChIP-seq Input, rep. 1


title: AN47


title: Medulloblastoma frozen tumor, SHH, M079RB07


title: Medulloblastoma frozen tumor, SHH, M043RB02


title: UTUC46


title: AN46


title: JM8.N4 mESC, clone D timecourse ∆ZFP143 12h, CTCF ChIP-seq Input, rep. 1


title: AN45


title: Medulloblastoma frozen tumor, SHH, M039RB11


title: JM8.N4 mESC, clone D timecourse ∆ZFP143 6h, CTCF ChIP-seq Input, rep. 1

value: 6 hours


title: UTUC45


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M039RB09


title: UTUC44


title: JM8.N4 mESC, clone D timecourse ∆ZFP143 6h, CTCF ChIP-seq Input, rep. 2


title: JM8.N4 mESC, clone D timecourse untreated, CTCF ChIP-seq Input, rep. 1


title: AN44


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M035RB01


title: UTUC43


title: AN43


title: JM8.N4 mESC, wild-type, ZNF143 ChIP-seq, rep. 2


title: Medulloblastoma frozen tumor, SHH, M033RB07


title: UTUC41


title: JM8.N4 mESC, wild-type, ZNF143 ChIP-seq, rep. 1


title: Medulloblastoma frozen tumor, SHH, M027RB08


title: AN41


title: UTUC39


title: AN39


title: JM8.N4 mESC, clone D timecourse ∆ZFP143 24h, CTCF ChIP-seq, rep. 2

value: CTCF

value: Millipore-Sigma (#07-725)


title: Medulloblastoma frozen tumor, SHH, M027RB07


title: UTUC38


title: AN38


title: Medulloblastoma frozen tumor, Group 3, M022RB07


title: UTUC37


title: AN37


title: JM8.N4 mESC, clone D timecourse ∆ZFP143 6h, CTCF ChIP-seq, rep. 2


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M019RB03


title: AN36


title: UTUC36


title: JM8.N4 mESC, clone D timecourse untreated, CTCF ChIP-seq, rep. 2


title: Medulloblastoma frozen tumor, SHH, M019RB01


title: JM8.N4 mESC, clone D timecourse ∆ZFP143 24h, CTCF ChIP-seq, rep. 1


title: AN35


title: UTUC35


title: UTUC33


title: Medulloblastoma frozen tumor, SHH, M018RB11


title: Medulloblastoma frozen tumor, SHH, M018RB12


title: JM8.N4 mESC, clone D timecourse ∆ZFP143 12h, CTCF ChIP-seq, rep. 1


title: UTUC34


title: AN33


title: Medulloblastoma frozen tumor, SHH, M018RB10


title: AN34


title: UTUC32


title: JM8.N4 mESC, clone D timecourse untreated, CTCF ChIP-seq, rep. 1


title: UTUC31


title: AN31


title: JM8.N4 mESC, clone D timecourse ∆ZFP143 12h, CTCF ChIP-seq, rep. 2


title: Medulloblastoma frozen tumor, SHH, M018RB09


title: Medulloblastoma frozen tumor, SHH, M018RB07


title: AN30


title: Medulloblastoma frozen tumor, SHH, M017RB03


title: UTUC29


title: AN29


title: UTUC27


title: AN28


title: Medulloblastoma frozen tumor, SHH, M016RB12


title: AN27


title: UTUC28


title: Medulloblastoma frozen tumor, Group 4, M016RB11


title: JM8.N4 mESC, clone D timecourse ∆ZFP143 6h, CTCF ChIP-seq, rep. 1


title: AN26


title: Medulloblastoma frozen tumor, Group 4, M016RB09


title: AN32


title: Medulloblastoma frozen tumor, WNT, M016RB10


title: AN24


title: UTUC24


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M015RB06


title: UTUC26


title: UTUC30


title: UTUC25


title: AN23


title: Medulloblastoma frozen tumor, Group 4, M015RB03


title: AN22


title: UTUC23


title: Medulloblastoma frozen tumor, SHH, M015RB01


title: Lung-OC2

first: liu

last: cihang

address: Xueyuan Road

institute: Peking University Health Science Center

data_processing:
The Dropseq core computational pipeline15 was used for processing next-generation sequencing reads of the scRNA-seq data. STAR (version 2.5.2a) was used for mapping. Reads were aligned to the mm10 genome reference (provided by the Dropseq group via the Gene Expression Omnibus (GEO) accession code GSE63269). For cell filtering, we considered all barcodes with more than 200 genes detected within the top 1200 barcodes by total UMI counts.
After demultiplexing of bcl files with Bcl2fastq v.2.20.0.422 (Illumina) and quality control, paired-end scRNA-seq FASTQ files were processed on the Seven Bridges Genomics platform with default parameters. Downstream analysis was conducted in R v.4.1.0 with the package Seurat v.4.0.3. All Seurat objects (one for each of the multiplexed samples) were merged and subjected to the same quality filtering. Cells with fewer than 200 or more than 4,000 detected genes were excluded from the analysis. After log normalization, the count data were scaled regressing for mitochondrial reads, and principal component analysis (PCA) was performed based on the 2,000 most variable features. Clustering and UMAP visualization were performed on the merged dataset using 30 principal components and a resolution of 0.5 for the shared nearest neighbour clustering algorithm. The clusters were annotated manually on the basis of marker gene expression.
To extract cluster markers, FindAllMarkers was executed with logfc.threshold and min.pct cut-offs set to 0.25. Top-ranked genes (by log fold change; logFC) were extracted for illustration. For differential gene expression, FindMarkers was applied with logfc.threshold and min.pct set to 0.1. Genes were subsequently filtered on the basis of Bonferroni-adjusted P < 0.05. The R package clusterProfiler (V.3.11.1) is used for KEGG pathway and GO annotation analysis, with parameters set to PValueCutoff = 0.05, PAdjustMethod = BH, QValueCutoff = 0.05, MingsSize = 10, and MaxGSSize = 500. The results were filtered for significantly enriched gene sets (Bonferroni-adjusted P < 0.05).
Assembly: mm10
Supplementary files format and content: The processed WTA files contained gene-barcode matrix that showed the barcoded cells and gene expression counts. In these matrices, each row represents a barcoded cell name, and each column represents a gene name. Thus, the analysis of the expression level of each gene in each cell was available.

molecule: nuclear RNA

source_name: Lung

extract_protocol:
After mice anesthetized, brain and liver tissue were perfused with sterile saline from the left to the right ventricle of the heart, lung tissue was perfused with sterile saline from the right to the left ventricle of the heart. Subsequently, all tissue was cut into pieces and frozen in liquid nitrogen. Single nucleus was isolation according to the BD instruction. In brief, transferred tissue into a 1.5 ml centrifuge tube, added 200 ul lysis buffer, cut the tissue with scissors, and transferred it to a Dounce homogenizer, added another 300 ul of lysis buffer, and used tight fitting pestle (Type A and B) to disaggregate tissue pieces with 20 strokes or until no chunks of tissue are observed. Incubated cell suspension on ice for 1 minute, then terminated the reaction by adding 500 ul of clean solution, followed by filtered through a 40um cell strainer, then cleaned the strainer with 1ml of clean solution. Finally, centrifuged cell suspension at 500 g for 5 min at 4°C, discarded the supernatant and resuspended the nuclei with sample buffer, and performed microscopic microscopy with trypan blue.
Whole-transcriptome analyses of WT and cKO mouse brain, liver and lung were performed using the BD Rhapsody Single-Cell Analysis System (BD Biosciences). Cells were pooled from three mice per sample. Nucleus isolation procedures are described above. Then the single cell nuclei were isolated using the BD Rhapsody HT Xpress Single-Cell Analysis System (BD Biosciences, 666625) according to the instructions. Nuclei suspensions were loaded into BD Rhapsody microtiter plates (BD Biosciences, 666262) to enable isolation of single-cell nuclei, and nuclei were captured, lysed, and mRNA collected using BD Rhapsody Enhanced Cartridge Reagent Kit (BD Biosciences, 664887). Thirty thousand cells per sample were loaded into a Rhapsody cartridge (BD Biosciences, 633733) and processed following the manufacturer’s instructions. Then cDNA libraries were prepared using the BD Rhapsody Whole Transcriptome Analysis Amplification Kit (BD Biosciences, 633801) following the BD Rhapsody System mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol (BD Biosciences). Concentrations were determined using a Qubit Fluorometer with the Qubit dsDNA HS Kit (Thermo, Q32851). Sequencing was performed in paired-end mode (2 × 150 cycles) on a DNBSEQ-T7 with DNBSEQ-T7RS (FCL PE150) Reagent Kit chemistry.

value: Lung

value: cKO

value: 24 month-old


title: Lung-OC3


title: Lung-OC1


title: AN21


title: Medulloblastoma frozen tumor, Group 4, M014RB10


title: AN20


title: UTUC20


title: Medulloblastoma frozen tumor, WNT, M013RB06


title: AN25


title: Lung-OW3

value: WT


title: UTUC19


title: AN19


title: Medulloblastoma frozen tumor, Group 4, M015RB05


title: Medulloblastoma frozen tumor, SHH, M013RB05


title: Medulloblastoma frozen tumor, Group 3, M012RB12


title: UTUC18


title: Lung-OW2


title: Lung-OW1


title: UTUC17


title: Liver-OC3

source_name: Liver

value: Liver


title: AN17


title: AN18


title: UTUC16


title: UTUC22


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M012RB10


title: Liver-OC2


title: Medulloblastoma frozen tumor, SHH,M012RB11


title: UTUC21


title: AN16


title: UTUC15


title: Liver-OC1


title: AN15


title: Medulloblastoma frozen tumor, SHH, M048RB12


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M012RB09


title: AN14


title: UTUC14


title: Liver-OW3


title: Liver-OW2


title: AN13


title: Medulloblastoma frozen tumor, Group 3, M012RB08


title: UTUC13


title: Medulloblastoma frozen tumor, WNT, M012RB07


title: UTUC12


title: Liver-OW1


title: AN12


title: AN11


title: Medulloblastoma frozen tumor, SHH, M011RB06


title: Brain-OC3

source_name: Brain

value: Brain


title: AN10


title: Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M011RB05


title: UTUC10


title: Medulloblastoma frozen tumor, Group 4, M011RB04


title: UTUC9


title: UTUC8


title: Medulloblastoma frozen tumor, SHH, M011RB02


title: AN8


title: UTUC7


title: Medulloblastoma frozen tumor, WNT, M011RB01


title: UTUC6


title: Brain-OW2


title: AN6


title: UTUC5


title: Medulloblastoma frozen tumor, Group 4, M010RB11


title: Medulloblastoma frozen tumor, SHH, M010RB10


title: UTUC11


title: AN5


title: Brain-OW1


title: Brain-OC2


title: UTUC4


title: bladder treated with BBN10

data_processing:
The sequenced reads were mapped to mouse reference genome sequences (GRCm38/mm10) using TopHat2 v2.1.1
Raw counts were calculated using feature counts v2.0.0.
Fragments per kilobase of exons per million mapped fragments were calculated using Cuffdiff v2.2.1.
Assembly: mm38
Supplementary files format and content: text file includes raw counts for each Sample

source_name: bladder

extract_protocol:
Total RNA was extracted from each sample stored in RNAlater (-20 °C) using the miRNeasy Mini Kit (QIAGEN).
The library preparation was performed using a combination of the SMARTerHT (TaKaRa) and NexteraXT (Illumina) kits, following the TAKARA protocol.

value: bladder

tag: tissue region

value: BBN


title: Brain-OC1


title: Medulloblastoma frozen tumor, SHH, M010RB09

value: Brain Tumor

value: Medulloblastoma


title: AN3


title: Medulloblastoma frozen tumor, WNT, M010RB08


title: bladder treated with BBN9


title: Brain-OW3


title: AN2


title: UTUC1

value: UTUC tissue


title: non-cancer side of upper urinary tract treated with BBN9

source_name: left ureter

value: left ureter

value: non-cancer side of upper urinary tract


title: UTUC2

value: cancer


title: Medulloblastoma frozen tumor, WNT, M010RB07


title: Medulloblastoma frozen tumor, Group 4, M009RB06


title: AN7

value: adjacent normal tissue

value: normal


title: cancer side of upper urinary tract treated with BBN9

source_name: right ureter

value: right ureter

value: cancer side of upper urinary tract


title: AN1


title: SOR+NOB2

city: Houston

first: Kristin

last: Mahan

address: 1825 Pressler St

department: MDD

institute: UTHealth science

data_processing:
Raw data (raw reads) of fastq format were firstly processed through Novogene 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
Reference genome and gene model annotation files were downloaded fromgenome websitedirectly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-endclean 2 reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Andthen FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis of twoconditions/groups (two biological replicates per condition) was performed using the DESeq2R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: Microsoft Excel 97-2003 Worksheet (.xls)

growth_protocol: HepG2 cells were cultured in Eagle's Minimal Essential Medium, supplemented with 10% fetal bovine serum, 100 units/ml of penicillin G sodium, and 100 μg/ml of streptomycin.

extract_protocol:
RNA was isolated using TRIzol reagent, followed by TRIzol cleanup column following manufacturer protocols.
RNA library was formed by polyA capture (or rRNA removal) and reverse transcription of cDNA using Novogene’s Transcriptome Sequencing services

treatment_protocol: Cells were treated with Vehicle control,5µM NOB or 2µM SOR, or a combination of both

value: human liver cancer cell

value: SOR+NOB


title: Medulloblastoma frozen tumor, WNT, M009RB05


title: AN4


title: SOR+NOB3


title: UTUC3


title: Medulloblastoma frozen tumor, Group 4, M009RB02


title: SOR2

value: SOR


title: SOR+NOB1


title: cancer side of upper urinary tract treated with BBN8

value: WT


title: SOR3


title: bladder treated with BBN8


title: cancer side of upper urinary tract treated with BBN10


title: Medulloblastoma frozen tumor, Group 3, M009RB01


title: normal bladder treated with tap water3

value: normal bladder

value: No


title: SOR1


title: NOB3

value: NOB


title: Medulloblastoma frozen tumor, Group 4, M008RB12

value: Brain Tumor


title: NOB1


title: NOB2


title: normal upper urinary tract treated with tap water6

value: normal upper urinary tract


title: Medulloblastoma frozen tumor, Group 3, M008RB11

value: Medulloblastoma