title: 2i_ESCs_4Cseq_B4galt6_promoter

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to the mm10 genome using bowtie2 version 2.3.2.
For RNAseq data, the reads were qualified with FastQC tool and trimmed with trim_galore if reads contained adapters. Processed reads were mapped to Ensembl transcriptome version 95 (mm10) by using RSEM . Raw tag counts were extracted from sample.gene.results files and merged together, and then GC-normalized using EDASeq.
For ATACseq data, reads were aligned to mm10 genome by using Bowtie2 with default parameters. Reads mapping to mitochondrial DNA or unassigned sequences were discarded. Finally, concordantly aligned pairs were retained. The BAM files of biological replicates were merged, and peaks were called by using dfilter with the settings of    -bs=100 -ks=50 -pe -lpval=2   . Alignment BAM files were normalized by RPKM and  transformed into read coverage files (bigWig format) by using deepTools.
For ChIPseq data, reads were aligned to mm10 genome by using Bowtie2 with default parameters. Reads mapping to mitochondrial DNA or unassigned sequences were discarded. Finally, concordantly aligned pairs were retained. The peaks were called by using MACS2 with the default parameters. Alignment BAM files normalized by RPKM and  transformed into read coverage files (bigWig format) by using deepTools.
For BL-Hi-C data, were processed with ChIA-PET2 v0.9.2 software with the parameter    -A ACGCGATATCTTATC -B AGTCAGATAAGATAT -s 1 -m 1 -t 4 -k 2 -e 1 -l 15 -S 500    to identify chromatin interactions that annotated with genome mm10. The biological replicates in each group were merged to perform the A/B compartments and TAD analysis. The interaction matrix was generated by HiC-Pro. Normalization was performed by HiCExplorer hicCorrectMatrix (--correctionMethod KR). TADs and TAD boundaries were defined by HiCExplorer hicFindTADs (--correctForMultipleTesting fdr --thresholdComparisons 0.05 --minDepth 120000 --maxDepth 200000 --step 40000) at 40-kb resolution. Compartments were analyzed using HOMER (v.4.10) tools with default parameters at 100 kb resolution. APA analysis was performed using juicer tools.There producibility of BL-Hi-Cdatasets was calculated on pairs of raw Hi-C contact matrices at 100 kb resolution by using HiCRep.
For 4C data, raw paired-end reads were removed with Trim Galore and then subjected to cutadapt (version 3.4) to trim the primer sequence at the 5    end of read 1. Reads that did not contain primer sequences were discarded. Reads were mapped to the mm10 genome using bowtie2 with the following parameters: --very-sensitive --end-to-end --no-unal -X 2000. Bam files were imported into the r3Cseq package (version 1.38.0). Normalized bedgraph files were thus generated and then transformed into bigwig files using the bedGraphToBigWig tool.
Assembly: GRCm38.p6
Library strategy: 4C-seq

source_name: E14 cells

growth_protocol: E14Tg2a (E14) ESCs were cultured in standard culture medium on gelatin-coated dishes without feeder cells: For serum/LIF culture, DMEM high-glucose media supplemented with 15%FBS, 1 mM sodium pyruvate (Gibco), 1% nonessential amino acids (Gibco), 1% GlutaMAX (Gibco), 0.1 mM β-mercaptoethanol (Life Technologies), 1% penicillin-streptomycin (Gibco)，1000 U/mL LIF (Millipore). For 2i/LIF culture, mouse ESCs were cultured in 2i medium as previously described2. In total, 500 mL of 2i medium were prepared with 240 mL of DMEM/F12 (Thermo Fisher Scientific), 240 mL of neurobasal (Thermo Fisher Scientific), 2.5 mL of N2 supplement (Thermo Fisher Scientific), 5 mL of B27 supplement (Thermo Fisher Scientific), 1% GlutaMAX, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, and 1% penicillin-streptomycin, 1000 U/mL LIF, 3 μM CHIR99021 (Selleck), and 1 μM PD0325901 (Selleck). All cells were maintained at 37°C in an incubator with 5% CO2. The medium was changed every day, and the cells were passaged with 0.25% trypsin-EDTA (Gibco). Interconversion of 2i- and serum-ESCs: 2i- and serum-ESCs were cultured on gelatinized plates for 3 days, and were digested with 0.25% trypsin, then 2i-ESCs or serum-ESCs were plated into gelatinized six-well plates with 6-7 × 104 cells per well in serum/LIF or 2i medium. Then change the medium every day.

extract_protocol:
For RNA-seq, total RNAs were extracted with TRIzol® reagent. RNA sequencing libraries were constructed using the VAHTS mRNA-seq V3 Library Prep Kit (Vazyme Biotech). The libraries were denatured and diluted at a proper concentration, then were sequenced on Illumina NovaSeq (Annoroad Gene Technology Co., Ltd). For ATAC-seq, 50,000 cells were harvested and washed once with 50 μL cold PBS. Then the cells were resuspended in 50 μL lysis buffers (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630). Then the suspension of nuclei was centrifuged 500 × g at 4°C for 10 min. The pellet was resuspended with 50 μL transposition reaction mix (10 μL TD buffer, 5 μL Tn5 transposase and 35 μL nuclease-free H2O), and incubated at 37°C for 30 min. Finally, DNA was isolated using MinElute PCR Purification Kit (QIAGEN). ATAC-seq libraries were constructed and were purified with AMPure XP beads (Beckman Coulter). The libraries were denatured and diluted, then were sequenced on HiSeq X-Ten (Annoroad Gene Technology Co., Ltd).  For ChIP-seq,1 × 107 cells were crosslinked with 1% formaldehyde at room temperature for 10 min. Then the reaction was stopped by adding glycine (final concentration, 0.125 M). Crosslinked cells were lysed in ChIP SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl (pH 8.0)) containing 1 × protease inhibitor cocktail and PMSF, then sonicated to achieve a chromatin sized of 200-400 bp. After sonication, the supernatant was diluted with IP buffer and then co-incubated with antibody–Dynabeads protein A/G (1:1 mixed) at 4°C overnight with rotation. Antibodies included：anti-YY1 antibody (Abcam, ab109237)，anti-SMC1 antibody (Bethyl Laboratories, A300-055A).ChIP For Biotin ChIP, cells stably expressed biotin-alone or biotin-TEAD2 were expanded and crosslinked with 1% formaldehyde. Crosslinked cells were sonicated and diluted tenfold with ChIP dilution buffer, and then incubated with M280 streptavidin dynabeads at 4°C for overnight. Streptavidin dynabeads-bound DNA was subsequently washed twice with wash buffer 1 (2% SDS), once with wash buffer 2 (50 mM HEPES (pH 7.5), 1 mM EDTA, 500 mM NaCl, 0.1% sodium deoxycholate, 1% Triton X-100), once with wash buffer 3 (10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate) and then twice with TE wash buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). ChIPed DNA was reverse-crosslinked and purified for DNA library construction followed by sequencing. For BL-HiC, the cells were treated with 1% formaldehyde at room temperature for 10 min followed by quenching with 0.2 M glycine. Nuclei were extracted for subsequent experiments, including digestion with HaeIII (NEB), end-plus-A treatment, proximity ligation with biotin-labeled Bridge Linker, DNA purification and enrichment of biotin-labeled DNA with Dynabeads M-280 streptavidin. The enriched bead-bound DNA was subjected to end repair, adapter ligation, PCR amplification and DNA library construction, followed by sequencing on the Illumina NovaSeq platform (Annoroad Gene Technology Co., Ltd.). For QHR-4C, digested suspensions of 1 × 105 - 1 × 106 cells from tissues were cross-linked with 2% formaldehyde for 10 min and terminated by 0.2 M glycine. The cell pellet was permeabilized and digested with DpnII overnight followed by proximity ligation. Then, DNA under 1000 bp was extracted and sonicated. To enrich ligation events associated with a specific viewpoint, an appropriate amount of sonicated DNA was taken as a template to linearly amplify for 100 cycles using a 5’ biotin-labeled probe of the viewpoint of interest. The amplification products were incubated at 95°C for 5 min, immediately cooled on ice to obtain amplified ssDNA and then enriched with Dynabeads M-280 streptavidin. The bead-bound ssDNA was then ligated with adapters. Finally, QHR-4C libraries were constructed with specific primer pairs (forward primers containing Illumina P5 with sequences near a specific viewpoint and reverse primers containing Illumina P7 with an index and sequences matching the adapter) and then sequenced on the Illumina NovaSeq platform (Annoroad Gene Technology Co., Ltd.).
RNA sequencing libraries were constructed using the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme). ATAC libraries were constructed using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme). BL-Hi-C libraries were constructed into standard illumina libraries. ChIP-seq libraries were constructed using the VAHTSTM Universal DNA Library Prep Kit for Illumina® V2. QHR-4C libraries were constructed into standard illumina libraries.

tag: culture method

value: wildtype


title: sibling-input-rep1

status: Public on Mar 03 2024

type: SRA

city: Wuhan

first: Yunqiao

last: Han

address: Luoyu Road 1037

country: China

institute: Huazhong University of Science and Technology

library_source: transcriptomic

data_processing:
Illumina Casava 1.8 software used for basecalling.
fastp software were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
HISAT2 was used to map reads to zebrafish reference genome (Ensembl GRCz11).
Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software.
StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)). The differentially expressed mRNAs were selected by R package edgeR.
Assembly: GRCz11
Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample

molecule: total RNA

organism: Danio rerio

source_name: trunk region of zebrafish embryos

extract_protocol:
Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent (Invitrogen). The RNA quality and quantity of each sample was assessed using NanoDrop ND-1000 and Bioanalyzer 2100 (Agilent). Total RNAs (20 μg) was depleted of ribosomal RNA by rRNA Depletion Kits (Thermo Fisher Scientific) and Magnesium RNA Fragmentation Module (NEB, cat.e6150) was used to randomly fragment RNA. Anti-m6A antibody (202003, Synaptic Systems) was applied for m6A immunoprecipitation. Then, the RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.1896649).
RNA libraries were prepared for sequencing using standard Illumina protocols
m6A-Seq

tag: tissue

value: trunk region of zebrafish embryos

tag: genotype

tag: treatment

value: no treatment

tag: rip antibody


title: sibling-IP- rep2


title: sibling rep1

data_processing:
Illumina Casava 1.8 software used for basecalling.
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 fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 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.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include raw counts values for each gene and each sample

source_name: the trunk region of zebrafish embryos

extract_protocol:
Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent (Invitrogen). RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies,) and checked using RNase free agarose gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: the trunk region of zebrafish embryos


title: sibling-IP- rep1


title: sibling rep2


title: 2i_d6_WT_Tead2_BL_HiC_rep1

city: guangzhou

first: xiaotao

last: dong

address: 190 Kai Yuan Avenue

institute: Chinese Academy of Sciences

library_source: genomic

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to the mm10 genome using bowtie2 version 2.3.2.
For RNAseq data, the reads were qualified with FastQC tool and trimmed with trim_galore if reads contained adapters. Processed reads were mapped to Ensembl transcriptome version 95 (mm10) by using RSEM . Raw tag counts were extracted from sample.gene.results files and merged together, and then GC-normalized using EDASeq.
For ATACseq data, reads were aligned to mm10 genome by using Bowtie2 with default parameters. Reads mapping to mitochondrial DNA or unassigned sequences were discarded. Finally, concordantly aligned pairs were retained. The BAM files of biological replicates were merged, and peaks were called by using dfilter with the settings of    -bs=100 -ks=50 -pe -lpval=2   . Alignment BAM files were normalized by RPKM and  transformed into read coverage files (bigWig format) by using deepTools.
For ChIPseq data, reads were aligned to mm10 genome by using Bowtie2 with default parameters. Reads mapping to mitochondrial DNA or unassigned sequences were discarded. Finally, concordantly aligned pairs were retained. The peaks were called by using MACS2 with the default parameters. Alignment BAM files normalized by RPKM and  transformed into read coverage files (bigWig format) by using deepTools.
For BL-Hi-C data, were processed with ChIA-PET2 v0.9.2 software with the parameter    -A ACGCGATATCTTATC -B AGTCAGATAAGATAT -s 1 -m 1 -t 4 -k 2 -e 1 -l 15 -S 500    to identify chromatin interactions that annotated with genome mm10. The biological replicates in each group were merged to perform the A/B compartments and TAD analysis. The interaction matrix was generated by HiC-Pro. Normalization was performed by HiCExplorer hicCorrectMatrix (--correctionMethod KR). TADs and TAD boundaries were defined by HiCExplorer hicFindTADs (--correctForMultipleTesting fdr --thresholdComparisons 0.05 --minDepth 120000 --maxDepth 200000 --step 40000) at 40-kb resolution. Compartments were analyzed using HOMER (v.4.10) tools with default parameters at 100 kb resolution. APA analysis was performed using juicer tools.There producibility of BL-Hi-Cdatasets was calculated on pairs of raw Hi-C contact matrices at 100 kb resolution by using HiCRep.
For 4C data, raw paired-end reads were removed with Trim Galore and then subjected to cutadapt (version 3.4) to trim the primer sequence at the 5    end of read 1. Reads that did not contain primer sequences were discarded. Reads were mapped to the mm10 genome using bowtie2 with the following parameters: --very-sensitive --end-to-end --no-unal -X 2000. Bam files were imported into the r3Cseq package (version 1.38.0). Normalized bedgraph files were thus generated and then transformed into bigwig files using the bedGraphToBigWig tool.
Assembly: GRCm38.p6

molecule: genomic DNA

organism: Mus musculus

tag: strain


title: 2i_d6_KO_Tead2_BL_HiC_rep1


title: 2i_d6_4Cseq_B4galt6_promoter


title: WT3

city: chongqing

first: zhou

last: sha

address: 55 University City South Road, Shapingba District, Chongqing, China

institute: chongqing university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: bone marrow

tag: cell type

value: BMDM

value: WT

value: M-CSF induced


title: WT1


title: 2i_d6_KO_Tead2_BL_HiC_rep2


title: 2i_d6_WT_Tead2_BL_HiC_rep2


title: WT2


title: Lysm3

value: Lamtor5 knockdown


title: Lysm2


title: 2i_d6_KO_Tead2_ChIPseq_YY1


title: B11: Standard diet and arsenic-fed, Cecum

city: Dongguan

first: Xin

last: Liu

state: Guangdong

address: No.1 Xincheng Blvd, Songshan Lake National High-tech Industrial Development Zone

department: School of Public Health

institute: Guangdong Medical University

data_processing:
The useful Perl script was used to filter adapter,the low quality reads and the reads whose N base more than 5% for total bases. Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates,DESeq2 v1.6.3 was designed for differential gene expression analysis between two samples with biological replicates, Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes.The GO (Gene Ontology, http://geneontology.org/) and KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.kegg.jp/) enrichment of DEGs were implemented by the hypergeometric test,GO and KEGG terms with q<0.05 were considered to be significantly enriched.
rMATS is a computational tool to detect differential alternative splicing events from RNA-Seq data.
Samtools and bcftools together to call snp and Indel.
Genome_build: ftp://ftp.ensembl.org/pub/release-90/fasta/mus_musculus/dna/
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

source_name: Standard diet and arsenic-fed mice

growth_protocol: The feed for the control group was standard feed for ensuring the nutritional needs of mice. For the test group, to assess the analogbioavailability of arsenic in rice (80%), the arsenical aqueous solution was blended into standard feed material powder and then impacted into granules.The concentration of total arsenic (CtAs) in the feed for the test group was 30 μg g-1, consisting of sodium arsenate (iAsⅤ), sodium arsenite (iAsⅢ), sodium MMA, and sodium DMA (Beijing Century Aoke Biotechnology Co., Ltd. Beijing, China) at proportions of 7.3%, 72.7%, 1.0%, and 19.0%, respectively. The fresh granule feeds weresoon vacuum packaged (50 g per pack for daily use) and stored at –20 °C.

extract_protocol:
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext ® Ultra™ RNA Library Prep Kit for Illumina ® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed.
The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated.

treatment_protocol: Six-week-old SPF male C57BL/6 mice were first acclimatized (7 days) and then separated randomly into two groups (10 mice for each group, control 1‒10 and test 1‒10) forpursuant 60-day exposure experiments. Drinking water and food were available ad libitum (control and test groups were fed standard and arsenic-containing standard feed, respectively).

tag: gender

value: male

value: Cecum

value: Standard diet and arsenic-fed


title: Lysm1


title: serum_ESCs_ATACseq_rep2

value: serum


title: serum_d9_ATACseq_rep2


title: serum_ESCs_ATACseq_rep1


title: serum_d6_ATACseq_rep2


title: serum_d9_ATACseq_rep1


title: serum_d3_ATACseq_rep1


title: M41_TGFB

city: 山东省

first: Haoran

last: Du

state: 山东省

address: wenhuaxi road 44

institute: shandong university

data_processing:
Raw data (raw reads) of fastq 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 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: HISAT2 v2.0.5
Supplementary files format and content: Tab-separated matrix file represents counts and fpkms

organism: Homo sapiens

source_name: kidney organoid

extract_protocol:
RNA libaries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: kidney organoid

tag: cell line

value: Primary cells

value: Kidney cells

tag: organoid

value: TGFB


title: M71_TNFA

value: TNFA


title: M71_CON

value: CON


title: 2i_d6_WT_Tead2_ChIPseq_YY1

value: wildtype


title: M35_TNFA


title: M41_CON


title: M41_TNFA


title: serum_d3_ATACseq_rep2


title: M65_TNFA


title: M71_TGFB


title: M35_CON


title: serum_d6_ATACseq_rep1


title: serum_d15_ATACseq_rep1


title: F64_CON


title: F64_TNFA


title: M65_CON


title: 2i_d6_KO_Tead2_ChIPseq_SMC1


title: 2i_ESCs_ATACseq_rep2


title: serum_d15_ATACseq_rep2


title: serum_d12_ATACseq_rep1


title: F34_TNFA


title: M65_TGFB


title: 2i_ESCs_ATACseq_rep1


title: serum_d12_ATACseq_rep2


title: F34_TGFB


title: 2i_d9_ATACseq_rep2


title: 2i_d9_ATACseq_rep1


title: 2i_d6_ATACseq_rep1


title: D283 Medulloblastoma cell line WT 3

city: Ribeirão Preto

first: Carlos

middle: Alberto

last: Scrideli

state: São Paulo

address: Avenida Bandeirantes 3900

department: Pediatrics

country: Brazil

institute: Ribeirao Preto Medicine School - University of Sao Paulo

data_processing:
Sequencing and base calling: RNA-seq libraries were sequenced on an Illumina HiSeq 2500 equipment (Illumina, San Diego, CA, USA) with base calling by CASAVA software (version 1.8.2, Illumina, San Diego, CA, USA).
Read alignment: Raw data were processed by TrimGalore package (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) to trim the adapters, in following the RNA-seq library reads processed by FastQC tool (Andrews, 2010) and MultiQC (Ewels et al., 2016) and performed analysis of detection of differential expression in D-283Med cell line using processed reads aligned with the reference genome (Genome Reference Consortium Human GRCh38) through STAR package (Dobin and Gingeras, 2015).
Gene specific read counts: Gene specific read counts were determined with to FastQC tool (Andrews, 2010) and MultiQC (Ewels et al., 2016).
Assembly: Reads are in .fastq format and contain the raw base calls from sequencing.
Supplementary files format and content: Gene counts normalized are in .txt format and contain the number of counts normalized abundance measurements using DeSeq for every gene and every sample. VV is WT and KD is Musashi-1 knockdown.

growth_protocol: The pediatric MB cell line D283 Med was maintained in DMEM/F12 medium (Gibco™, Thermo Fisher®, Carlsbad, CA, USA), supplemented with 10% FBS, 100U/ml penicillin, 100 μg/ml streptomycin and kept in a humid atmosphere containing 5% CO2 at 37ºC.

extract_protocol:
Total RNA was extracted using AllPrep DNA/RNA/Protein Mini kit (QIAGEN, Hilden, Germany) and RNA integrity was evaluated by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA), following manufacturer’s. specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: medulloblastoma


title: D283 Medulloblastoma cell line Musashi-1 Knockdown 1

value: MS1 Knockdown


title: D283 Medulloblastoma cell line Musashi-1 Knockdown 3


title: 2i_d6_ATACseq_rep2


title: HP1291-T-Stroma-Xen-D15

city: Buffalo

first: Yue

last: Wu

state: Ny

address: 665 Elm St

country: USA

institute: Roswell Park Cancer Institute Dept or Urology

data_processing:
base pair quality control by fastqc (v0.10.1)
Splieced alignment Bowtie (v1.0.1) and TopHat(V2.0.13) allwoing 1 mismatch per read using joint genome reference strategy (hg19 and mm10 respecitive resSeq UCSC annotations)
Lane replicates mereged with Merge Same Files from Picard (v.1.97)
Second pass QC with RSeQC(v.2.6.3)
read counts proccessed with HTSeq (v0.6.0). Resulting read counts also normalized to TPM
Genome_build: hg19
Supplementary_files_format_and_content: Counts_TPM.csv: TPM counts in csv file with genes as rows and samples as columns,  Counts_Raw.csv: Raw counts in csv file with genes as rows and samples as columns

source_name: Prostate

growth_protocol: Fresh benign prostate tissue specimens were procured from the Pathology Network Shared Resources (PNSR) at Roswell Park Comprehensive Cancer Center (RPCCC).  The protocol (NHR005009) for the use of fresh prostate tissue specimens was approved by the Institutional Review Board (IRB). Male Hsd:Athymic Nude-Fox1nu nude mice (12 weeks of age) were purchased from Envigo (Indianapolis, IN)[24].  Mice were castrated surgically and implanted subcutaneously with silastic tubing (catalog number 508-008 from VWR, Radnor, PA) manually packed with dry testosterone (T) crystals 3-5 days before transplantation with fresh tissue. This procedure standardized the levels of circulating T between mice at levels comparable to circulating T in adult male humans, (i.e., “humanized” mouse hosts) [25].   All experimental procedures were approved by the RPCCC Institutional Animal Care and Use Committee (IACUC) and were performed by trained staff of the RPCCC Mouse Tumor Model Resource (MTMR) core facility under IACUC protocol 1044M.  Fresh prostate tissue specimens were received from the RPCCC PNSR in transport medium that contained Cellgro phenol red-free RPMI1640 medium from Corning life Sciences (Corning, NY) supplemented with 10% charcoal-stripped fetal bovine serum (CS-FBS);  CS-FBS was prepared as described [26].  Tissue was cut into cubes 2-3 mm per side, pieces of tissue to be transplanted were coated with Matrigel from Corning Life Sciences, and the pieces were inserted individually at the subcutaneous site.  A total of 5-8 pieces of tissue were transplanted to each “humanized” mouse.  The resulting xenografts were considered to be established stably after 30 days.

extract_protocol:
Fresh tissue and Primary xenograft tissue was enriched into specific cell types (Epithelial, Endothleial, Stromal) with magnetic bead enrichment from Thermo Fisher Scientific. RNA was isolated from each enriched cell population specimen using miRNease Micro kits from Qiagen (Germantown, MD) following the manufacturer’s instructions, with modification.  RNA was eluted 3 times, each time with 17 μL RNase-free H2O, and all the eluents were combined.  DNase treatment was performed using a Turbo DNA-free Kit from Thermo Fisher Scientific.  After the DNase treatment, RNA was concentrated using an RNA Clean & Concentrator kit from Zymo Research (Irvine, CA).  Quantitative assessment of the total RNA yield was performed using the Qubit Broad Range RNA kit from Thermo Fisher Scientific
Sequencing libraries for each specimen were prepared from 100 ng of total RNA using the TruSeq Stranded Total RNA kit from Illumina Inc.  Ribosomal RNA (rRNA) was depleted from the total RNA, and the remaining RNA was purified and fragmented.  The fragmented RNA was primed for cDNA synthesis and reverse transcribed into a first strand cDNA using random primers.  The RNA templates were removed, and replacement DNA strands were synthesized to generate double stranded DNA (dsDNA) with dTTP incorporated in place of UTP, resulting in blunt-ended dsDNA.  AMPure XP beads from Beckman Coulter (Brea, CA) were used to recover the dsDNA from the second strand reaction mix.  A single ‘A’ nucleotide was then added to the 3’-ends of the blunt fragments.  Multiple indexing adapters that contained a single ‘T’ nucleotide on the 3’- end of the adapters were ligated to the ends of the dsDNA, preparing them for hybridization onto a flow cell.   Adapter ligated libraries were amplified by PCR, purified using Ampure XP beads, and validated for appropriate size on a 4200 TapeStation D1000 Screentape From Agilent Technologies.   The DNA libraries were quantitated using KAPA Biosystems qPCR kits, and a sub-specimen from multiple libraries were pooled at equimolar concentrations, following experimental design criteria.

tag: individual

value: Stroma

value: Xenograft

tag: group

value: Tumor

tag: t-dep status

value: Late T-Dep

tag: qc pass

value: Pass


title: CRS-WT-DR5-12D_3

city: Shenzhen

first: songqiang

last: huang

address: Xili Academy Avenue

institute: Southern University of Science and Technology

data_processing:
All sequence reads were trimmed using Cutadapt and aligned with HISAT2 to Mus musculus GRCm38. After Quality control metrics were finished, expression was performed with RSEM (version 1.2.30).
Assembly: GRCm38
Supplementary files format and content: .xlsx file included FPKM value for each sample

source_name: freshly isolated vHIP

extract_protocol:
Total RNA was immediately extracted using TRIzol reagent according to the manufacturer’s instructions.
RNA integrity was assessed using the RNA Nano 6000 Assay kit on an Agilent Bioanalyzer 2100 system (Agilent Technologies, USA). The library fragments (370 ~ 420 bp in length) were processed with the AMPure XP system (Beckman Coulter, USA).

value: freshly isolated vHIP


title: HP1291-T-Endo-Xen-D15

value: Endo


title: 2i_d3_ATACseq_rep2


title: CRS-WT-DR5-12D_2


title: 2i_d15_ATACseq_rep2


title: D283 Medulloblastoma cell line WT 1

value: WT


title: 2i_d3_ATACseq_rep1


title: 2i_d15_ATACseq_rep1


title: HP1291-T-Epi-Xen-D3

value: Epi

value: Early T-Dep


title: D283 Medulloblastoma cell line WT 2


title: HP1291-T-Endo-Xen-D3


title: D283 Medulloblastoma cell line Musashi-1 Knockdown 2


title: 2i_d12_ATACseq_rep2


title: 2i_d12_ATACseq_rep1


title: HP1291-T-Epi-Xen-D15


title: HP1291-T-Stroma-Xen-D3


title: HP1291-T-Stroma-Xen-Pre

value: Pre-T-Dep


title: F34_CON

value: kidney organoid

value: Primary cells

value: Kidney cells


title: CRS-NKAα1_1


title: serum_ESCs_RNAseq_rep4

value: serum

value: wildtype


title: HP1291-T-Epi-Xen-Pre


title: serum_ESCs_RNAseq_rep3


title: CRS-NKAα1_3


title: HP1271-T-Stroma-Xen-D15


title: serum_ESCs_RNAseq_rep2


title: CRS-WT_2


title: HP1271-T-Epi-Xen-D3


title: HP1271-T-Stroma-Xen-D3


title: KP-1-shPrpf19-2_-1

city: XuHui

first: Shuaihu

last: Li

state: ShangHai

address: No.131 Dongan Road

institute: Fudan University

data_processing:
Raw data processed in vitrual encironment Python 3.10.12 on Linux(Ubuntu 22.04.2)
Sequence reads were trimmed for adapter sequence/low-quality sequence by Cutadapt v4.4(-q 25 --phred33 --length 36 --stringency 3 --paired)
Trimmed sequence were mapped to GRCm39/mm39 using HISAT2 v2.2.1 and the output SAM files were sorted to generate BAM files by samtools v1.17
BAM files were used to generate comma-separated values include raw read counts using StringTie v2.2.1
Assembly: mm39
Supplementary files format and content: Comma-separated values file include raw read counts for KP-1 samples

molecule: polyA RNA

organism: Musculus

growth_protocol: Mouse lung cancer cell lines KP-1 were cultured in Roswell Park Memorial Institute (RPMI) 1640 (meilunbio, MA0215) with 10% FBS and 1% PS (NCM Biotech, C100C5) with 5% CO2 at 37 ℃.

extract_protocol:
Total RNA was extracted from cells using a TRNzol Universal kit (TIANGEN, DP424).
RNA library for RNA-seq was prepared as follows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.

treatment_protocol: KP-1 cells were treated with doxycycline for 3 days for PRPF19 knockdown

value: Non Small Cell Lung Cancer

value: doxycycline induced knockdown


title: HP1271-T-Endo-Xen-D15

value: Xenograft


title: serum_ESCs_RNAseq_rep1


title: KP-1-shPrpf19-2_-3


title: KP-1-shPrpf19-1_-3


title: KP-1-shPrpf19-2_-2


title: HP1275-T-Endo-Xen-D15

value: Tumor


title: HP1275-T-Epi-Xen-D15

value: Late T-Dep


title: HP1275-T-Stroma-Xen-D15

value: Stroma

value: Pass


title: HP1271-T-Epi-Xen-Pre


title: serum_d6_RNAseq_rep2


title: KP-1-shPrpf19-1_-2


title: serum_d9_RNAseq_rep1


title: HP1271-T-Stroma-Xen-Pre


title: HP1275-T-Stroma-Xen-D3


title: serum_d6_RNAseq_rep1


title: KP-1-shPrpf19-1_-1


title: HP1291-T-Endo-Xen-Pre

value: Endo


title: HP1275-T-Epi-Xen-D3


title: serum_d3_RNAseq_rep2


title: serum_d9_RNAseq_rep2


title: HP1271-T-Endo-Xen-Pre


title: HP1271-T-Endo-Xen-D3


title: HP1275-T-Epi-Xen-Pre


title: HP1275-T-Stroma-Xen-Pre


title: KP-1-shLacZ-3

value: WT


title: serum_d3_RNAseq_rep1


title: HP1275-T-Endo-Xen-Pre


title: serum_d15_RNAseq_rep2


title: HP1275-T-Endo-Xen-D3


title: HP1263-T-Stroma-Xen-Pre


title: HP1263-T-Epi-Xen-D15

value: Epi


title: serum_d12_RNAseq_rep1


title: HP1263-T-Endo-Xen-D15


title: HP1263-T-Epi-Xen-D3

value: Early T-Dep


title: serum_d15_RNAseq_rep1


title: serum_d12_RNAseq_rep2


title: HP1263-T-Endo-Xen-D3


title: serum_d0_ko_tead2_RNAseq_rep2


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab + CD19-CD28 (D29), D16

city: Basel

first: Daniel

last: Marbach

address: Grenzacherstrasse 124

department: pRED Pharmaceutical Sciences

country: Switzerland

institute: F. Hoffmann - La Roche Ltd

data_processing:
Base calling was performed with BCL to FASTQ file converter bcl2fastq2 version 2.20.0 (Illumina).
Paired-end reads were mapped onto the human genome (build hg38) with read aligner STAR version 2.7.10a using default mapping parameters.
Read counts for all RefSeq genes were computed using featureCounts version 2.0.1.
Assembly: hg38
Supplementary files format and content: The file raw_counts.txt provides the gene read counts for all samples in tab-separated value format. The first line is a header. The first two columns provide the Entrez Gene ID and Gene Symbol, followed by one column for each sample.

source_name: Tumor

growth_protocol: OCI-Ly18 cells (DSMZ, ACC-699) were cultured in advanced RPMI 1640 (Gibco) containing 10% FBS and 1% GlutaMAX prior to in vivo inoculation

extract_protocol:
Total RNA was extracted from frozen tumor tissues using the Qiagen RNeasy Mini kit. The extracted RNA was quantified with a Qubit 4.0 Fluorometer and its integrity assessed using an Agilent 5300 Fragment Analyzer
RNA sequencing libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit, starting with mRNA enrichment and fragmentation, followed by cDNA synthesis with strand specificity

treatment_protocol: OCI-Ly18 tumor-bearing humanized NSG mice were treated with vehicle (histidine buffer), glofitamab (0.15 mg/kg or 1 mg/kg), and CD19-CD28 (1 mg/kg) once per week intravenously

tag: experimental day

value: D29 (termination)

tag: mouse strain

value: humanized mice

tag: cell injection_route

value: subcutaneous

value: Lymphoma

value: Gazyva + glofitamab + CD19-CD28


title: HP1263-T-Epi-Xen-Pre

value: Pre-T-Dep


title: HP1263-T-Stroma-Xen-D3


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab + CD19-CD28 (D29), D22


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab + CD19-CD28 (D29), D24


title: HP1263-T-Stroma-Initial

value: Fresh


title: HP1263-T-Epi-Initial


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab + CD19-CD28 (D29), D12


title: KP-1-shLacZ-2

value: Non Small Cell Lung Cancer

value: doxycycline induced knockdown


title: KP-1-shLacZ-1


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab + CD19-CD28 (D29), D14

value: Tumor


title: serum_d0_ko_tead2_RNAseq_rep1

tag: culture method

value: serum


title: HP1263-T-Stroma-Xen-D15

value: Stroma

tag: tissue

value: Xenograft

value: Late T-Dep


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab + CD19-CD28 (D29), D11


title: HP1236-T-Stroma-Xen-D15

value: Fail


title: HP1236-T-Epi-Xen-D15

value: Epi


title: 2i_ESCs_RNAseq_rep4

tag: genotype

value: wildtype


title: HP1263-T-Endo-Xen-Pre

value: Endo

value: Pass


title: HP1236-T-Stroma-Xen-D3

value: Early T-Dep


title: HP1236-T-Endo-Xen-D15


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab + CD19-CD28 (D29), D08

value: D29 (termination)

value: humanized mice

value: subcutaneous

value: Lymphoma

tag: treatment


title: 2i_ESCs_RNAseq_rep3


title: HP1236-T-Epi-Xen-D3


title: 2i_ESCs_RNAseq_rep2


title: HP1236-T-Epi-Xen-Pre

value: Pre-T-Dep


title: HP1236-T-Stroma-Xen-Pre


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D29), B23

value: Gazyva + glofitamab


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab + CD19-CD28 (D29), D07

value: Tumor

value: Gazyva + glofitamab + CD19-CD28


title: HP1236-T-Endo-Xen-D3


title: 2i_ESCs_RNAseq_rep1


title: 2i_d9_RNAseq_rep2


title: HP1200-NT-Endo

value: Fresh

value: Non-Tumor


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D29), B22


title: HP1200-NT-Epi


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D29), B21


title: HP1263-T-Endo-Initial


title: HP1200-NT-Stroma

value: Stroma


title: 2i_d9_RNAseq_rep1


title: 2i_d6_RNAseq_rep3


title: HP1195-NT-Stroma-Xen-D15

value: Xenograft

value: Late T-Dep

value: Fail


title: HP1195-NT-Epi-Xen-D15

value: Epi


title: HP1195-NT-Endo-Xen-D15

value: Endo

value: Pass


title: 2i_d6_RNAseq_rep2

value: wildtype


title: HP1195-NT-Stroma-Xen-D3

value: Early T-Dep


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D29), B15

value: D29 (termination)

value: humanized mice

value: subcutaneous


title: 2i_d6_RNAseq_rep1


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D29), B13

value: Lymphoma

value: Gazyva + glofitamab


title: HP1195-NT-Epi-Xen-D3


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D29), B11

value: Tumor


title: HP1195-NT-Epi-Xen-Pre

value: Pre-T-Dep


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D29), B10


title: 2i_d6_ko_tead2_RNAseq_rep1


title: HP1236-T-Endo-Xen-Pre


title: 2i_d6_ko_tead2_RNAseq_rep2


title: HP1184-T-Stroma-Xen-D16


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D29), B09


title: HP1195-NT-Endo-Xen-Pre

value: Non-Tumor


title: 2i_d3_RNAseq_rep4


title: HP1184-T-Epi-Xen-D16


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D29), B06


title: 2i_d3_RNAseq_rep3


title: HP1184-T-Endo-Xen-D16


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D29), B08


title: HP1184-T-Stroma-Xen-D3

value: Stroma


title: HP1184-T-Epi-Xen-D3

value: Xenograft


title: HP1184-T-Stroma-Xen-Pre


title: 2i_d3_RNAseq_rep2


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D29), B05


title: HP1184-T-Endo-Xen-D3


title: 2i_d3_RNAseq_rep1


title: HP1195-NT-Endo-Xen-D3


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab + CD19-CD28 (D21), D20

value: Gazyva + glofitamab + CD19-CD28


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab + CD19-CD28 (D21), D17


title: HP1186-NT-Epi-Xen-D15

value: Late T-Dep

value: Fail


title: HP1186-NT-Stroma-Xen-D3


title: HP1186-NT-Endo-Xen-D3

value: Endo


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab + CD19-CD28 (D21), D10


title: 2i_d3_ko_tead2_RNAseq_rep1


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab + CD19-CD28 (D21), D03


title: 2i_d3_ko_tead2_RNAseq_rep2


title: HP1186-NT-Endo-Xen-Pre


title: HP1186-NT-Endo-Xen-D15


title: HP1186-NT-Stroma-Xen-Pre


title: HP1175-T-Endo-Xen-Post-D17

value: Pass


title: 2i_d15_RNAseq_rep1

value: wildtype


title: HP1175-T-Stroma-Xen-Post-D17


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab + CD19-CD28 (D21), D01


title: HP1175-T-Stroma-Xen-Post-D3

value: Early T-Dep


title: HP1184-T-Endo-Xen-Pre


title: HP1175-T-Endo-Xen-Post-D3


title: 2i_d12_RNAseq_rep1


title: HP1186-NT-Stroma-Xen-D15


title: 2i_d15_RNAseq_rep2


title: HP1175-T-Stroma-Xen-Pre


title: HP1175-T-Epi-Xen-Pre

value: Epi


title: HP1175-T-Epi-Xen-Post-D3


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D21), B24

value: humanized mice


title: HP1175-T-Endo-Xen-Pre


title: Rice root cells - bulk-Whole-6

city: Los Angeles

first: Rachel

last: Shahan

state: California

address: 610 Charles E. Young Dr. S

institute: University of California, Los Angeles

description: Lexogen QuantSeq 3′ FWD RNA-Seq

data_processing:
Reads were aligned to Michigan State University Rice genome v7 with the STAR aligner, deduplicated using UMI-Tools, and counted with HTSeq-Count.
The BAM_COUNTS file were then merged. Reads were normalized, averaged and converted to Log(CPM)  with EdgeR
Assembly: MSU 7.0
Supplementary files format and content: BAM_COUNTS file: HTSeq-Count processed file for each sample
Supplementary files format and content: xlsx file: Integrated and normalized averaged-reads for each gene caculated separately in different root  sections

organism: Oryza sativa

source_name: Root

growth_protocol: X.kitaake was used as wild type. Rice seeds were dehulled, sterilized with 50% bleach for 10 min, and rinsed four to five times with sterile water. All plant growth was in Yoshida’s nutrient solution solidified with gellan gum (Gelzan, Caisson Inc).Growth boxes were kept at 4°C in the dark for 2-3 days until the seeds germinate, then transferred to a percival growth chamber set to 28°C, and consistant light. Rice seedlings were grown in the percival for 1-3 days before harvesting.

extract_protocol:
Sections (root tip to end of lateral root cap: Meristem; end of lateral root cap to the start of root hair elongation: Elongation; 1mm each beyond the start of root hair elongation: Maturation1 and Maturation2) were harvested into 10 μL RNA-later (Ambion) in the lid of a 1.5 ml tube. Samples were frozen in liquid nitrogen and stored at −80.and then processed by grinding with a blue homogenization pestle. RNA was isolated using the Zymo MagBead RNA Isolation kit according to the manufacturer’s protocol (Zymo).
RNA was used as input into the Lexogen QuantSeq 3′ FWD RNA-Seq library preparation procedure according to the manufacturer’s protocol, using the Unique Molecular Identifier (UMI) PCR add-on kit. Libraries were indexed and pooled on an Illumina NextSeq.
Lexogen QuantSeq 3′ FWD RNA-Seq

value: Root

value: All cell types of root

value: WT

tag: developmental stage

value: Whole


title: HP1167-T-Stroma-Xen-Post-D17

value: Tumor


title: Rice root cells - bulk-Whole-5

description: Lexogen QuantSeq 3′ FWD RNA-Seq


title: HP1167-T-Endo-Xen-Post-D17


title: HP1167-T-Stroma-Xen-Post-D10


title: HP1167-T-Stroma-Xen-Post-D3


title: Rice root cells - bulk-Whole-4

description: Lexogen QuantSeq 3′ FWD RNA-Seq


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D21), B01

value: subcutaneous

value: Lymphoma

value: Gazyva + glofitamab


title: Rice root cells - bulk-Whole-3

description: Lexogen QuantSeq 3′ FWD RNA-Seq


title: HP1167-T-Endo-Xen-Post-D10

value: Xenograft


title: HP1167-T-Endo-Xen-Pre

value: Pre-T-Dep


title: 2i_d12_RNAseq_rep2

tag: strain


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D21), B25

tag: cell type


title: OCI-Ly18 cells (s.c.), Vehicle (D21), A05

value: Vehicle


title: HP1167-T-Endo-Xen-Post-D3

value: Endo


title: OCI-Ly18 cells (s.c.), Vehicle (D21), A02


title: Rice root cells - bulk-Whole-2

description: Lexogen QuantSeq 3′ FWD RNA-Seq


title: HP1153-T-Stroma-Xen-Post-D3

value: Stroma

value: Pass


title: HP1153-T-Endo-Xen-Post-D3

value: Early T-Dep


title: OCI-Ly18 cells (s.c.), Vehicle (D21), A01


title: Rice root cells - bulk-Maturation2-6

description: Lexogen QuantSeq 3′ FWD RNA-Seq


title: HP1153-T-Endo-Xen-Pre

value: Fail


title: Rice root cells - bulk-Whole-1

description: Lexogen QuantSeq 3′ FWD RNA-Seq


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab + CD19-CD28 (D19), D19

value: humanized mice

value: Gazyva + glofitamab + CD19-CD28


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D21), B07


title: HP1153-T-Stroma-Xen-Post-D17

value: Late T-Dep


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D21), B03


title: HP1153-T-Epi-Xen-Post-D17

value: Epi


title: Rice root cells - bulk-Maturation2-5

description: Lexogen QuantSeq 3′ FWD RNA-Seq

value: Root

value: All cell types of root

value: WT


title: HP1153-T-Endo-Xen-Post-D17

value: Tumor


title: HP1167-T-Stroma-Xen-Pre


title: HP1153-T-Stroma-Xen-D10


title: Rice root cells - bulk-Maturation2-4

description: Lexogen QuantSeq 3′ FWD RNA-Seq


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab + CD19-CD28 (D19), D09

value: subcutaneous

value: Lymphoma


title: HP1153-T-Stroma-Xen-Pre

value: Xenograft

value: Pre-T-Dep


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab + CD19-CD28 (D19), D06


title: Rice root cells - bulk-Maturation2-3

description: Lexogen QuantSeq 3′ FWD RNA-Seq


title: HP1153-T-Epi-Xen-D10


title: HP1140-T-Stroma-Fresh

value: Fresh


title: HP1140-T-Epi-Fresh


title: Rice root cells - bulk-Maturation2-2

description: Lexogen QuantSeq 3′ FWD RNA-Seq


title: HP1137-T-Epi-Fresh


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D19), B20

value: Gazyva + glofitamab


title: HP1153-T-Endo-Xen-D10

value: Endo


title: Rice root cells - bulk-Maturation2-1

description: Lexogen QuantSeq 3′ FWD RNA-Seq


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab + CD19-CD28 (D19), D04


title: HP1140-T-Endo-Fresh

value: Pass


title: Rice root cells - bulk-Maturation1-6

description: Lexogen QuantSeq 3′ FWD RNA-Seq


title: HP1137-T-Endo-Fresh


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D19), B19


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab + CD19-CD28 (D19), D15


title: Rice root cells - bulk-Maturation1-5

description: Lexogen QuantSeq 3′ FWD RNA-Seq


title: OCI-Ly18 cells (s.c.), Gazyva + glofitamab (D19), B18


title: HP1131-NT-Stroma-Xen-Post-D3

value: Stroma

value: Non-Tumor

value: Early T-Dep


title: Rice root cells - bulk-Maturation1-4

description: Lexogen QuantSeq 3′ FWD RNA-Seq


title: HP1125-NT-Stroma-Xen-Post-D17

value: Late T-Dep

value: Fail


title: HP1125-NT-Stroma-Xen-Post-D3


title: HP1125-NT-Stroma-Xen-Pre


title: OCI-Ly18 cells (s.c.), Vehicle (D19), A09

value: humanized mice

value: Vehicle


title: HP1109-NT-Stroma-Xen-Post-D14


title: HP1104-NT-Stroma-Xen-Post-D3


title: OCI-Ly18 cells (s.c.), Vehicle (D19), A08


title: HP1131-NT-Stroma-Xen-Post-D17


title: HP1137-T-Stroma-Fresh


title: Rice root cells - bulk-Maturation1-1

description: Lexogen QuantSeq 3′ FWD RNA-Seq

value: Root

value: All cell types of root

value: WT


title: OCI-Ly18 cells (s.c.), Vehicle (D19), A07

value: Tumor

value: subcutaneous

value: Lymphoma


title: HP1131-NT-Epi-Xen-Post-D17

value: Epi

value: Xenograft


title: OCI-Ly18 cells (s.c.), Vehicle (D19), A06


title: OCI-Ly18 cells (s.c.), Vehicle (D19), A03


title: HP1131-NT-Endo-Xen-Post-D17

value: Endo


title: Rice root cells - bulk-Elongation-5

description: Lexogen QuantSeq 3′ FWD RNA-Seq

value: Elongation


title: M41, TNFa

library_source: transcriptomic single cell

data_processing:
Raw data (raw reads) of fastq 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 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: HISAT2 v2.0.5
Supplementary files format and content: Tab-separated values files and matrix files

source_name: kidney organoid treated with TNFa

extract_protocol:
RNA libaries were prepared for sequencing using standard Illumina protocols
RNA libraries for scRNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Kidney organoid

value: Primary cells

value: Kidney cells

value: TNFa


title: HP1131-NT-Epi-Xen-Post-D3

value: Non-Tumor

value: Early T-Dep

value: Pass


title: Rice root cells - bulk-Elongation-4

description: Lexogen QuantSeq 3′ FWD RNA-Seq

value: Root


title: HP1131-NT-Endo-Xen-Post-D3


title: Rice root cells - bulk-Maturation1-3

description: Lexogen QuantSeq 3′ FWD RNA-Seq

value: All cell types of root


title: Rice root cells - bulk-Elongation-3

description: Lexogen QuantSeq 3′ FWD RNA-Seq

value: WT


title: M41, CON

source_name: kidney organoid treated without TNFa

value: control


title: H2009-shPRPF19-2_-3

data_processing:
Raw data processed in vitrual encironment Python 3.10.12 on Linux(Ubuntu 22.04.2)
Sequence reads were trimmed for adapter sequence/low-quality sequence by Cutadapt v4.4(-q 25 --phred33 --length 36 --stringency 3 --paired)
Trimmed sequence were mapped to GRCh38/hg38 using HISAT2 v2.2.1 and the output SAM files were sorted to generate BAM files by samtools v1.17
BAM files were used to generate comma-separated values include raw read counts using StringTie v2.2.1
Raw counts were normalized and basemean, log2FoldChange and t-test pvalue were calculated on R 4.2.2
Assembly: hg38
Supplementary files format and content: Comma-separated values file include TPM values, basemean, log2FoldChange and t-test pvalue for H2009 samples

growth_protocol: Human lung cancer cell lines H2009 were cultured in Roswell Park Memorial Institute (RPMI) 1640 (meilunbio, MA0215) with 10% FBS and 1% PS (NCM Biotech, C100C5) with 5% CO2 at 37 ℃.

treatment_protocol: H2009 cells were treated with doxycycline for 3 days for PRPF19 knockdown

value: Non Small Cell Lung Cancer

value: doxycycline induced knockdown


title: HP1125-NT-Epi-Xen-Post-D17

value: Epi

value: Late T-Dep

value: Fail


title: Rice root cells - bulk-Elongation-2

description: Lexogen QuantSeq 3′ FWD RNA-Seq

value: Elongation


title: Rice root cells - bulk-Maturation1-2

description: Lexogen QuantSeq 3′ FWD RNA-Seq


title: Rice root cells - bulk-Elongation-1

description: Lexogen QuantSeq 3′ FWD RNA-Seq


title: H2009-shPRPF19-2_-1


title: HP1125-NT-Epi-Xen-Post-D3

value: Xenograft


title: H2009-shPRPF19-2_-2


title: Rice root cells - bulk-Meristem-6

description: Lexogen QuantSeq 3′ FWD RNA-Seq

value: Meristem


title: HP1125-NT-Endo-Xen-Post-D17

value: Endo


title: Rice root cells - bulk-Elongation-6

description: Lexogen QuantSeq 3′ FWD RNA-Seq


title: H2009-shPRPF19-1_-3


title: Rice root cells - bulk-Meristem-5

description: Lexogen QuantSeq 3′ FWD RNA-Seq


title: H2009-shPRPF19-1_-2


title: HP1125-NT-Endo-Xen-Post-D3


title: HP1125-NT-Endo-Xen-Pre

value: Pre-T-Dep


title: Female whose mother was fed a FASD diet, biological replicate 1

type: RNA

city: Barcelona

first: Marta

last: Cosin Tomas

state: Spain

address: Dr. Aiguader, 88

department: Child Health and environment

country: Spain

institute: ISGlobal

description:
c36j
Cortex of 4-week-old female whose mother was fed a FASD diet, biological replicate 1.
Brain cortex

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures

data_processing: The data were analyzed with Transcriptome Analysis Console 4.0 (TAC 4.0) (Affymetrix default analysis settings, SST-RMA algorithm, comparison CD male vs. FASD male, and comparison CD female vs. FASD female).

label: biotin

source_name: 4-week-old female cortex FASD

label_protocol: Biotin

growth_protocol: Animal experimentation was conducted according to the guidelines of the Canadian Council on Animal Care and approved by the Animal Care Committee of the Research Institute of the McGill University Health Center. Mice were housed in speciﬁc pathogen free facilities with 12h light/dark cycles with food and water ad libitium.

extract_protocol: Total RNA was extracted from frozen cortices of 4-week-old mice using the AllPrep DNA/RNA/miRNA Universal Kit with on-column DNase I treatment (Qiagen).

treatment_protocol: At weaning, wild-type C57BL/6 female mice were placed on amino acid deﬁned Control Diet (CD) (2mg folic acid/kg diet, recommended level for rodents (TD.01369, Harlan Laboratories, Inc., Madison, WI, USA)) or Folic Acid Supplemented Diet (FASD) which contained 5 times the amount of folic acid (10mg folic acid/kg diet, TD.08278, Harlan Laboratories, Inc., Madison, WI, USA). Both diets contained 2.5 g/kg choline bitrate, 3.3 g/kg L-methionine and 1% succinylsulfathiazole, an antibiotic that inhibits folate synthesis by intestinal ﬂora. Five weeks after the start of the diets, females were mated with C57BL/6 males to study offspring. Diets were maintained throughout pregnancy and lactation. We conducted several behavioral tests on offspring before sacrificing them at weaning (4 weeks of age). Brains were collected to conduct gene expression analysis by microarray.

tag: strain/background

value: Cortex

tag: Sex

value: Female

tag: age

value: 4 weeks

tag: maternal diet

value: FASD


title: H2009-shPRPF19-1_-1

tag: cell line


title: Female whose mother was fed a control diet, biological replicate 2

description:
c75m
Cortex of 4-week-old female whose mother was fed a control diet, biological replicate 2.
Brain cortex

source_name: 4-week-old male cortex CD

value: CD


title: Rice root cells - bulk-Meristem-4

description: Lexogen QuantSeq 3′ FWD RNA-Seq

value: Root

value: All cell types of root

value: WT


title: HP1109-NT-Epi-Xen-Post-D14

tag: individual

tag: group

value: Non-Tumor

tag: t-dep status

value: Pass


title: Female whose mother was fed a control diet, biological replicate 3

description:
c59p
Cortex of 4-week-old female whose mother was fed a control diet, biological replicate 3.
Brain cortex


title: Female whose mother was fed a control diet, biological replicate 1

description:
c85m
Cortex of 4-week-old female whose mother was fed a control diet, biological replicate 1.
Brain cortex


title: Rice root cells - bulk-Meristem-3

description: Lexogen QuantSeq 3′ FWD RNA-Seq


title: Male whose mother was fed a FASD diet, biological replicate 4

description:
c74m
Cortex of 4-week-old male whose mother was fed a FASD diet, biological replicate 4.
Brain cortex

source_name: 4-week-old male cortex FASD

value: Male


title: Female whose mother was fed a FASD diet, biological replicate 3

description:
c38n
Cortex of 4-week-old female whose mother was fed a FASD diet, biological replicate 3.
Brain cortex


title: Male whose mother was fed a FASD diet, biological replicate 3

description:
c83i
Cortex of 4-week-old male whose mother was fed a FASD diet, biological replicate 3.
Brain cortex


title: H2009-shLuc-3

value: Non Small Cell Lung Cancer

value: doxycycline induced knockdown


title: Female whose mother was fed a FASD diet, biological replicate 2

description:
c73o
Cortex of 4-week-old female whose mother was fed a FASD diet, biological replicate 2.
Brain cortex


title: HP1109-NT-Endo-Xen-Post-D14

value: Xenograft

value: Late T-Dep

tag: qc pass


title: Male whose mother was fed a control diet, biological replicate

description:
c58i
Cortex of 4-week-old male whose mother was fed a control diet, biological replicate 4.
Brain cortex


title: 1086epi

value: Epi

value: Fresh


title: Rice root cells - bulk-Meristem-1

description: Lexogen QuantSeq 3′ FWD RNA-Seq

value: Meristem


title: H2009-shLuc-1


title: Male whose mother was fed a control diet, biological replicate 2

description:
c84n
Cortex of 4-week-old male whose mother was fed a control diet, biological replicate 2.
Brain cortex

value: Cortex


title: Rps14 + Dim1, 18S rRNA 3'-RACE, biol rep 2

city: Juptier

first: Katrin

last: Karbstein

state: FL

address: 120 Scripps Way

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology

description: Dim1 control, 18S rRNA

library_source: other

data_processing:
Demultiplexed and quality-filtered raw reads (fastq) generated from the NextSeq 500 were trimmed to remove Illumina adapter sequences with Trim Galore! (version 0.6.1, Babraham Bioinformatics). Only reads containing the full linker sequence were retained, and the linker sequences were removed with CutAdapt (version 3.5) using Python version 3.8.3. Quality of trimmed reads was assessed using FastQC (version 0.11.4, Babraham Bioinformatics). Trimmed reads were aligned to the S. cerevisiae 35S rDNA sequence (S288C) from the Saccharomyces Genome Database with Bowtie2 (version 2.2.9). SAMtools (version 1.1.0), BAMtools (version 2.4.0), and BEDtools (version 2.17.0) were used to identify reads aligning to the reference genome and to calculate the read depth or the fraction of reads cleaved at each nucleotide position. For 18S cDNA samples containing a UMI, the program UMI-tools (version 1.1.2, [96]) was used to extract the UMI sequence from each read prior to alignment. The extracted UMI sequence was then used to deduplicate reads after alignment but prior to calculating read depth and cleavage.
Assembly: SGD:S000006486 (Saccharomyces cerevisiae 35S rDNA sequence from the Saccharomyces Genome Database: https://www.yeastgenome.org/locus/S000006486)
Supplementary files format and content: Excel file includes read depth at each nucleotide throughout the reference genome for each sample. One tab per sample.

molecule: other

organism: Saccharomyces cerevisiae BY4741

source_name: Gal::Rps14; Gal::Dim1 + TEF::Rps14 + Cyc1::Dim1

growth_protocol: All cells were grown in YPD media for 8 doublings at 25˚C or 30˚C, shaking at 200 rpm.

extract_protocol:
Cells were harvested between OD 1.0 – 2.0. Ribosomes were purified, ribosomal subunits were separated during purification, and 18S and 25S rRNAs were isolated from from 40S and 60S ribosomal subunits, respectively, by phenol-chloroform-isoamyl alcohol extraction.
rRNA was treated with DNase I and size selected on a denaturing TBE-Urea-PAGE gel. rRNA was extracted from the gel by freeze-thawing the gel pieces in RNA extraction buffer (300 mM NaOAc, 1 mM EDTA, and 0.25% SDS) and ethanol precipitated. rRNA 3’-ends were dephosphorylated using rSAP and ligated to either the Universal miRNA Cloning Linker or ligated to a pre-adenylated linker containing a UMI sequence using truncated T4 RNA ligase K227Q to protect the 3’-end of the rRNAs from degradation and to identify the true rRNA 3’-end after sequencing. Linkers were added in 2-fold excess of rRNA ends. 5’-ends of the DNA linkers and the rRNA were deadenylated by 5’-deadenylase and excess linkers were degraded by DNA-specific RecJf exonuclease. rRNA was reverse transcribed using a linker-specific primer and Protoscript II RT to generate the first strand of cDNA. After RNase H treatment, the second strand was synthesized using an 18S or 25S rRNA-specific forward primer, a linker-specific reverse primer, and Q5 high fidelity DNA polymerase. The forward and reverse second strand synthesis primers contained partial P5 and P7 Illumina sequencing adapters. The cDNA was purified either on a denaturing TBE-Urea-PAGE gel and extracted by freeze-thawing in DNA extraction buffer (300 mM NaCl, 10 mM Tris-HCl (pH 8.0), and 1 mM EDTA) or cleaned up with AMPure XP beads. The purified cDNA was amplified via PCR to generate the final libraries and add the complete P5 and P7 Illumina adapter sequences. Library size and quality were assessed on an Agilent 2100 Bioanalyzer. Validated libraries were pooled at equimolar ratios and loaded onto the NextSeq 500 flow cell.

tag: ribosomal subunit_purified

tag: rrna extracted

tag: cell growth_temperature_(c)

tag: rrna linker

value: Pre-adenylated linker containing a UMI sequence

value: AMPure XP beads


title: Male whose mother was fed a FASD diet, biological replicate 2

description:
c76n
Cortex of 4-week-old male whose mother was fed a FASD diet, biological replicate 2.
Brain cortex

tag: tissue

value: 4 weeks

value: FASD


title: Prostate tissue, M7

city: Boston

first: Christina

last: Sharkey

state: MA

address: 99 Brookline Ave Rm 389

department: Urology

institute: Beth Israel Deaconess Medical Center

description: 10X Genomics

data_processing:
To align the sequencing reads with the mouse mm10 genome, we employed CellRanger V 3.1.0, provided by 10× Genomics. The mapping was performed using the GRCh38 build and ensemble version 92 gene annotation.
We utilized Seurat (v3.5.1)5 to construct data objects from the matrix outputs.
Assembly: mm10
Supplementary files format and content: h5

source_name: Prostate tissue

extract_protocol:
Whole fresh prostate tissues were subjected to a digestion process using collagenase type I supplemented with 10 μM rock inhibitor, 1 nmol Dihydrotestosterone, and DNase I in Hank's Balanced Salt Solution (HBSS) for 2 hours at 37°C. The cells were further treated with TrypLE Express supplemented with 10 μM rock inhibitor for 10 mins at 37°C. The resulting cell solution was neutralized in HBSS supplemented with 5% fetal bovine serum and 1% penicillin-streptomycin solution. Subsequently, the cells were resuspended in Red Blood Cell lysis buffer and incubated for 3 min on ice to remove red blood cells. The single cell suspension was washed with a 0.02% PBS-BSA solution and counted. The viability of cells was between 80%~90%, assessed by Trypan Blue.
To align the sequencing reads with the mouse mm10 genome, we employed CellRanger V 3.1.0, provided by 10× Genomics. The mapping was performed using the GRCh38 build and ensemble version 92 gene annotation.

value: Prostate tissue

tag: treatment

value: HFD


title: neocortical BRAF V600E mutant non-tumoral lesion (NPNL)

city: PARIS

first: Franck

last: Bielle

address: 83 Bd de l'Hopital

department: Paris Brain Institute

country: France

institute: Sorbonne Université

description: 10X Genomics

data_processing:
fastq files were generated using cellranger 4.0.0 mkfastq tool
matrix filles were generated using cellranger 4.0.0 count function, with GRCh38-1.2.0_premrna reference transcriptome with 10000 cells as expected-cells number
output from cellranger was processed into Seurat v4.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: brain

extract_protocol:
Nuclei suspensions were prepared from frozen samples. Nuclei were stained with an anti-uclear protein antibody before to be sorted by FACS.
Libraries were prepared according to Illumina's instructions accompanying the Chromium Next GEM Single Cell 5ʹ Reagent Kits v3.1. Libraries were sequenced on the Chromium Controller (10X Genomics) following the manufacturer's protocols.

value: brain

value: GBM

tag: genotype

value: BRAF mutant V600E


title: Prostate tissue, M5

description: 10X Genomics

tag: strain


title: 1083epi

tag: cell type

value: Non-Tumor

value: Pass


title: Prostate tissue, M3

description: 10X Genomics

value: control


title: Rps14 + Dim1, 18S rRNA 3'-RACE, biol rep 1

description: Dim1 control, 18S rRNA

value: Gal::Rps14; Gal::Dim1 + TEF::Rps14 + Cyc1::Dim1


title: 1083endo

value: Endo


title: Pno1-KKKF + Dim1-E85A, 25S rRNA 3'-RACE, biol rep 2

description: Rio1 bypass condition, 25S rRNA

source_name: Gal::Pno1; Gal::Dim1 + TEF::Pno1-KKKF + Cyc1::Dim1-E85A

value: Universal miRNA Cloning Linker

value: TBE-Urea-PAGE gel extraction


title: Male whose mother was fed a control diet, biological replicate 1

description:
c59j
Cortex of 4-week-old male whose mother was fed a control diet, biological replicate 1.
Brain cortex

tag: strain/background

value: Cortex

tag: Sex

value: Male

value: CD


title: Rice root cells - bulk-Meristem-2

description: Lexogen QuantSeq 3′ FWD RNA-Seq

value: Root

value: All cell types of root

value: WT

tag: developmental stage

value: Meristem


title: hippocampal BRAF V600E mutant non-tumoral lesion (HPNL)

description: 10X Genomics

value: brain


title: Male whose mother was fed a control diet, biological replicate 3

description:
c85i
Cortex of 4-week-old male whose mother was fed a control diet, biological replicate 3.
Brain cortex

tag: age

value: 4 weeks

tag: maternal diet


title: Prostate tissue, M1

description: 10X Genomics

value: Prostate tissue


title: H2009-shLuc-2

tag: cell line

value: Non Small Cell Lung Cancer

value: doxycycline induced knockdown


title: RNAseq_2i_d0_si_Tead4_rep2

data_processing:
Raw reads were qualified with FastQC tool and trimmed with trim_galore if reads contained adapters. Processed reads were mapped to Ensembl transcriptome version 95 (mm10) by using RSEM with parameters “-star”. Raw tag counts were extracted from sample.gene.results files and merged together, and then GC-normalized using EDASeq. The DESeq2 package was used to analyze DEGs. A DEG was defined as a gene with q value < 0.05 and fold change >1.5. The top Gene Ontology (GO) processes were enriched by Metascape web-based platform. Other analysis was performed using glbase.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: E14 mESCs

growth_protocol: For serum/LIF culture, DMEM high-glucose media supplemented with 15%FBS, 1 mM sodium pyruvate (Gibco), 1% nonessential amino acids (Gibco), 1% GlutaMAX (Gibco), 0.1 mM β-mercaptoethanol (Life Technologies), 1% penicillin-streptomycin (Gibco)，1000 U/mL LIF (Millipore). For 2i/LIF culture, mouse ESCs were cultured in 2i medium. In total, 500 mL of 2i medium were prepared with 240 mL of DMEM/F12 (Thermo Fisher Scientific), 240 mL of neurobasal (Thermo Fisher Scientific), 2.5 mL of N2 supplement (Thermo Fisher Scientific), 5 mL of B27 supplement (Thermo Fisher Scientific), 1% GlutaMAX, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, and 1% penicillin-streptomycin, 1000 U/mL LIF, 3 μM CHIR99021 (Selleck), and 1 μM PD0325901 (Selleck). All cells were maintained at 37°C in an incubator with 5% CO2. The medium was changed every day, and the cells were passaged with 0.25% trypsin-EDTA (Gibco).2iL-ESCs and SL-ESCs were cultured on gelatinized plates for 3 days, and were digested with 0.25% trypsin. Then 2iL-ESCs or SL-ESCs were plated into gelatinized six-well plates with 6-7 × 104 cells per well in either serum/LIF or 2i medium. The medium was changed daily. For interconversion of 2iL-ESCs and SL-ESCs, 2iL-ESCs and SL-ESCs were cultured on gelatinized plates for 3 days, and were digested with 0.25% trypsin. Then 2iL-ESCs or SL-ESCs were plated into gelatinized six-well plates with 6-7 × 104 cells per well in either serum/LIF or 2i medium. The medium was changed daily.

extract_protocol:
Total RNAs were extracted with TRIzol® reagent. For quantitative PCR, cDNAs were synthesized with HiScript® III RT SuperMix for qPCR (+gDNA wiper) (Vazyme Biotech).
RNA-seq libraries were constructed using the VAHTS mRNA-seq V3 Library Prep Kit (Vazyme Biotech). The libraries were denatured and diluted at a proper concentration, then were sequenced on Illumina NovaSeq (Annoroad Gene Technology Co., Ltd).

treatment_protocol: siRNAs transfection. siRNAs were designed and synthesized by Shanghai GenePharma (GenePharma, China). Three siRNAs targeting on Tead2, Tead4, Esrrb, Nr5a2 and Tcfcp2l1 genes were designed and synthesized, the most effective siRNA identified by qPCR was used for further experiments. 24 hr prior to transfection, cells were plated onto a 6-well plate at 40%-60% confluence. Transfection was performed with Lipofectamine 2000 (Invitrogen, USA) according to the manufacturer’s protocol. 7.5 μL Lipofectamine 2000 reagent and siRNAs were diluted in Opti-MEM (GIBCO) and incubated at room temperature (RT) for 10 min. Then the mixtures were added to cells, and the final concentration of siRNAs was 50 nM. The medium was replaced 6-8 hr after transfection with fresh culture medium.

value: E14 mESCs

value: Embryonic stem cells

value: ESCs cultured in serum and leukemia inhibitory factor (serum/LIF)


title: CRS-WT-DR5-12D_1

value: freshly isolated vHIP


title: Pno1-KKKF + Dim1-E85A, 25S rRNA 3'-RACE, biol rep 1

description: Rio1 bypass condition, 25S rRNA

value: Gal::Pno1; Gal::Dim1 + TEF::Pno1-KKKF + Cyc1::Dim1-E85A

value: Universal miRNA Cloning Linker

value: TBE-Urea-PAGE gel extraction


title: RNAseq_2i_d0_si_Tead4_rep1


title: A549_shMETTL3_rep3

city: Guangzhou

first: Xia

last: Yang

address: No. 74, Zhongshan 2nd Road

institute: Zhongshan School of Medicine, Sun Yat-sen University

data_processing:
Raw fastq files were trimmed using cutadapt (v 3.0) with parameters -B -b -q 30 -m 20 --trim-n --max-n=0.05.
Trimmed fastq files were mapped to hg19 using hisat2 (v 2.2.1) and converted into bam files using samtools (v 1.13).
Mapped reads were counted using htseq-count (v 0.13.5) for downstream analyses.
Assembly: hg19
Supplementary files format and content: raw counts of all samples and DESeq2 results

growth_protocol: A549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instruction. 12ug of total RNA was used for the construction of sequencing libraries.
The library preparation was performed by commercial services of the LC-BIO Bio-tech ltd (Hangzhou, China).

value: NSCLC

value: METTL3 knockdown


title: Male whose mother was fed a FASD diet, biological replicate 1

description:
c37k
Cortex of 4-week-old male whose mother was fed a FASD diet, biological replicate 1.
Brain cortex

value: Cortex

value: Male

value: FASD


title: BRAF wildtype MTLE-HS

description: 10X Genomics

value: brain

value: GBM

value: BRAF WT


title: 1086endo

tag: individual

value: Endo

value: Fresh

tag: group

value: Non-Tumor

tag: t-dep status

value: Pass


title: CRS-NKAα1_2


title: Pno1-KKKF + Dim1-E85A, 18S rRNA 3'-RACE, biol rep 8

description: Rio1 bypass condition, 18S rRNA

tag: ribosomal subunit_purified

tag: rrna extracted

value: Pre-adenylated linker containing a UMI sequence

value: AMPure XP beads


title: CRS-WT_3

value: freshly isolated vHIP


title: A549_shMETTL3_rep2


title: RNAseq_2i_d0_si_NC_rep2

value: E14 mESCs

value: Embryonic stem cells

value: siNC

value: ESCs cultured in serum and leukemia inhibitory factor (serum/LIF)


title: RNAseq_2i_d0_si_NC_rep1


title: Pno1-KKKF + Dim1-E85A, 18S rRNA 3'-RACE, biol rep 6

description: Rio1 bypass condition, 18S rRNA

value: Gal::Pno1; Gal::Dim1 + TEF::Pno1-KKKF + Cyc1::Dim1-E85A

tag: cell growth_temperature_(c)

tag: rrna linker


title: RNAseq_2i_d6_si_Tead4_rep2

tag: treatment

value: SL-to-2iL transition day 6


title: A549_vector_rep2

value: NSCLC

tag: genotype

value: WT


title: Pno1-KKKF + Dim1-E85A, 18S rRNA 3'-RACE, biol rep 7

description: Rio1 bypass condition, 18S rRNA

tag: strain


title: A549_shMETTL3_rep1

tag: cell type

value: METTL3 knockdown


title: Pno1-KKKF + Dim1-E85A, 18S rRNA 3'-RACE, biol rep 5

description: Rio1 bypass condition, 18S rRNA

value: Universal miRNA Cloning Linker

value: TBE-Urea-PAGE gel extraction


title: A549_vector_rep1


title: Pno1-KKKF + Dim1-E85A, 18S rRNA 3'-RACE, biol rep 4

description: Rio1 bypass condition, 18S rRNA


title: Pno1-KKKF + Dim1-E85A, 18S rRNA 3'-RACE, biol rep 3

description: Rio1 bypass condition, 18S rRNA


title: RNAseq_2i_d6_si_NC_rep2


title: FTO-KO_sh3_input

city: Nanjing

first: yingjie

last: Zhang

address: No.300 Guangzhou Road

institute: Department of Rehabilitation Medicine, the First Affiliated Hospital of Nanjing Medical University

data_processing:
library strategy: meRIP-seq
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted from FTO knockdown GC cells and its negative controls.
MeRIP-seq was carried out with LC-BIO Biotech (Hangzhou, China). Quality and quantity of total RNAs were evaluated with NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). RNA integrity was assessed with Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) with RIN number>7.0 and confirmed by electrophoresis with denaturing agarose gel. Poly(A) mRNA was purified and fragmented into approximately 100-nt fragments. Cleaved RNA fragments were then incubated with an m6A-specific antibody (Synaptic Systems, Goettingen, Germany) in IP buffer at 4°C for 2h. Eluted m6A-containing fragments and untreated input control fragments were converted and stored in our final cDNA library. Paired-end 2×150bp libraries were sequenced on an Illumina Novaseq 6000 platform (LC-Bio Technology CO., Ltd., Hangzhou, China).

value: FTO-KO


title: FTO-KO_sh3_IP

tag: antibody

value: m6A-specific antibody (Synaptic Systems, Goettingen, Germany)


title: Pno1-KKKF + Dim1-E85A, 18S rRNA 3'-RACE, biol rep 2

description: Rio1 bypass condition, 18S rRNA


title: FTO-KO_sh2_IP


title: RNAseq_2i_d21_Tead2_knockout_rep2

value: Tead2 Knockout

value: SL-to-2iL transition day 21


title: Pno1-KKKF + Dim1-E85A, 18S rRNA 3'-RACE, biol rep 1

description: Rio1 bypass condition, 18S rRNA


title: CRS-WT_1

tag: tissue


title: FTO-KO_sh2_input


title: A549_vector_rep3


title: Pno1 + Dim1-E85A, 25S rRNA 3'-RACE, biol rep 2

description: wild type 25S rRNA

source_name: Gal::Pno1; Gal::Dim1 + TEF::Pno1 + Cyc1::Dim1-E85A


title: RNAseq_2i_d15_Tead2_knockout_rep2

value: SL-to-2iL transition day 15


title: RNAseq_2i_d21_Tead2_knockout_rep1


title: Pno1 + Dim1-E85A, 25S rRNA 3'-RACE, biol rep 1

description: wild type 25S rRNA

value: Gal::Pno1; Gal::Dim1 + TEF::Pno1 + Cyc1::Dim1-E85A


title: RNAseq_2i_d6_si_Tead4_rep1

value: E14 mESCs


title: FTO-KO_sh1_input


title: RNAseq_2i_d6_si_NC_rep1

value: Embryonic stem cells


title: FTO-KO_sh1_IP


title: Pno1 + Dim1-E85A, 18S rRNA 3'-RACE, biol rep 8

description: wild type 18S rRNA

value: Pre-adenylated linker containing a UMI sequence

value: AMPure XP beads


title: Pno1 + Dim1-E85A, 18S rRNA 3'-RACE, biol rep 7

description: wild type 18S rRNA


title: ChIPseq_Tead2_AviTag_knock_in_2iL_ESCs_input

data_processing:
After trimming the adaptor sequence with Cutadapt, ChIP-seq reads were aligned to mm10 genome using Bowtie2 with the default parameters. Reads mapping to mitochondrial DNA or unassigned sequences were discarded. Finally, concordantly aligned pairs were retained. The peaks were called using MACS2 (Zhang et al, 2008) with the default parameters. Alignment BAM files were converted into read coverage files (bigWig format) using deepTools (Ramírez et al., 2016).  Peak overlap was done by using bedtools (v2.25.0). Differential peaks were called by MACS2 bdgdiff function with the default parameters. Motif analysis of ChIP-seq peaks was performed by using Homer.
Assembly: mm10
Supplementary files format and content: Normalized bigWig and peak file for each sample.

growth_protocol: For serum/LIF culture, DMEM high-glucose media supplemented with 15%FBS, 1 mM sodium pyruvate (Gibco), 1% nonessential amino acids (Gibco), 1% GlutaMAX (Gibco), 0.1 mM β-mercaptoethanol (Life Technologies), 1% penicillin-streptomycin (Gibco)，1000 U/mL LIF (Millipore). For 2i/LIF culture, mouse ESCs were cultured in 2i medium. In total, 500 mL of 2i medium were prepared with 240 mL of DMEM/F12 (Thermo Fisher Scientific), 240 mL of neurobasal (Thermo Fisher Scientific), 2.5 mL of N2 supplement (Thermo Fisher Scientific), 5 mL of B27 supplement (Thermo Fisher Scientific), 1% GlutaMAX, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, and 1% penicillin-streptomycin, 1000 U/mL LIF, 3 μM CHIR99021 (Selleck), and 1 μM PD0325901 (Selleck). All cells were maintained at 37°C in an incubator with 5% CO2. The medium was changed every day, and the cells were passaged with 0.25% trypsin-EDTA (Gibco).For interconversion of 2iL-ESCs and SL-ESCs, 2iL-ESCs and SL-ESCs were cultured on gelatinized plates for 3 days, and were digested with 0.25% trypsin. Then 2iL-ESCs or SL-ESCs were plated into gelatinized six-well plates with 6-7 × 104 cells per well in either serum/LIF or 2i medium. The medium was changed daily.

extract_protocol:
For ChIP, cells stably expressed biotin-alone or biotin-TEAD2 were expanded and crosslinked with 1% formaldehyde. Crosslinked cells were sonicated and diluted tenfold with ChIP dilution buffer, and then incubated with M280 streptavidin dynabeads at 4°C overnight. Streptavidin dynabeads-bound DNA was subsequently washed twice with wash buffer 1 (2% SDS), once with wash buffer 2 (50 mM HEPES (pH 7.5), 1 mM EDTA, 500 mM NaCl, 0.1% sodium deoxycholate, 1% Triton X-100), once with wash buffer 3 (10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate) and then twice with TE wash buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). ChIPed DNA was reverse-crosslinked and purified for DNA library construction followed by sequencing. For CUT&Tag, 100,000 cells were harvested and washed twice with 200 µL of wash buffer. 10 µL concanavalin A beads (Bangs Laboratories) were added per sample and incubated at room temperature for 15 min. Then, 100 µL of dig-wash buffer containing 2 mM EDTA and 1 µg of primary antibody were added. The primary antibody incubation was performed on a rotating platform at 4°C overnight. Two hundred microliters of dig-wash buffer were added to remove the unbound antibodies. Then, the reaction was incubated with pAG-Tn5 (homemade) at 4°C for 2 hr. Two hundred microliters of dig-med buffer were added to remove unbound pAG-Tn5 protein. Next, the cells were resuspended in 100 µL of tagmentation buffer and incubated at 37°C for 1 hr. To stop tagmentation, 2.25 µL of 0.5 M EDTA, 2.75 µL of 10% SDS and 0.5 µL of 20 mg/mL proteinase K were added and incubated at 55°C for 30 min and then at 70°C for 30 min to inactivate proteinase K. Then, DNA was extracted. The antibodies included H3K27ac (Active Motif, 39133), H3K4me1 (Active Motif, 39297).
ChIP-seq libraries were constructed using the VAHTSTM Universal DNA Library Prep Kit for Illumina® V2 (Vazyme Biotech). After PCR library amplification, size selection of adaptor-ligated DNA was performed using Agencourt AMPure XP Beads (Beckman Coulter). The libraries were sequenced on the Illumina NovaSeq or Hiseq X-ten platform (Annoroad Gene Technology Co., Ltd.).  To generate the CUT&Tag libraries, 21 µL DNA were mixed with 2 µL of a universal i5 and a uniquely barcoded i7 primer (Buenrostro et al, 2015a) using a different barcode per sample. A volume of 25 µL of NEBNext high-fidelity 2 × PCR master mix (NEB) was added and mixed. The sample was placed in a thermocycler with a heated lid using the following cycling conditions: 72°C for 5 min (gap filling); 98°C for 30 s; 14 cycles of 98°C for 10 s and 63°C for 30 s; final extension at 72°C for 1 min; and hold at 8°C. Post-PCR clean-up was performed by adding 1 × volume of Ampure XP beads (Beckman Counter), and the libraries were incubated with beads at room temperature for 15 min, washed twice gently with 80% ethanol, and eluted in 25 µL of 10 mM Tris (pH 8.0). The libraries were sequenced on Illumina NovaSeq (Annoroad Gene Technology Co., Ltd.).

treatment_protocol: The CRISPR/Cas9 system was used to genetically generate Tead2-FLAG-AviTag knock-in ESC lines, 2iL-ESC lines with mutation of TEAD2 motifs in the B4galt6 promoter region, and  Tead2-knockout SL-ESC lines

value: AviTag-knock-in

value: ESCs cultured in serum-free medium with LIF and two inhibitors (PD0325901 and CHIR99021) (2i/LIF)


title: RNAseq_2i_d15_Tead2_knockout_rep1


title: WT_Con3_input


title: Biotin_ChIPseq_Tead2_AviTag_knock_in_SL_ESCs

value: ESCs cultured in serum and leukemia inhibitory factor (serum/LIF)


title: Pno1 + Dim1-E85A, 18S rRNA 3'-RACE, biol rep 6

description: wild type 18S rRNA


title: WT_Con2_input

value: WT


title: Pno1 + Dim1-E85A, 18S rRNA 3'-RACE, biol rep 5

description: wild type 18S rRNA


title: 4Cseq_B4galt6_promoter_2iL_ESCs_Tead2_motif_mutant_rep2

data_processing:
Adaptor sequences in raw paired-end reads were removed with Trim Galore and then subjected to cutadapt (version 3.4) to trim the primer sequence at the 5’ end of read 1. Reads that did not contain primer sequences were discarded. Reads were mapped to the mm10 genome using bowtie2 with the following parameters: --very-sensitive --end-to-end --no-unal -X 2000. Bam files were imported into the r3Cseq package (version 1.38.0). Normalized bedgraph files were thus generated and then transformed into bigwig files using the bedGraphToBigWig tool
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: 4C-seq

growth_protocol: For 2i/LIF culture, mouse ESCs were cultured in 2i medium. In total, 500 mL of 2i medium were prepared with 240 mL of DMEM/F12 (Thermo Fisher Scientific), 240 mL of neurobasal (Thermo Fisher Scientific), 2.5 mL of N2 supplement (Thermo Fisher Scientific), 5 mL of B27 supplement (Thermo Fisher Scientific), 1% GlutaMAX, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, and 1% penicillin-streptomycin, 1000 U/mL LIF, 3 μM CHIR99021 (Selleck), and 1 μM PD0325901 (Selleck). All cells were maintained at 37°C in an incubator with 5% CO2. The medium was changed every day, and the cells were passaged with 0.25% trypsin-EDTA (Gibco).For interconversion of 2iL-ESCs and SL-ESCs, 2iL-ESCs and SL-ESCs were cultured on gelatinized plates for 3 days, and were digested with 0.25% trypsin. Then 2iL-ESCs or SL-ESCs were plated into gelatinized six-well plates with 6-7 × 104 cells per well in either serum/LIF or 2i medium. The medium was changed daily.

extract_protocol:
Briefly, digested suspensions of 1 × 105 - 1 × 106 cells from tissues were cross-linked with 2% formaldehyde for 10 min and the reaction was terminated by 0.2 M glycine. The pellet was permeabilized and digested with DpnII overnight followed by proximity ligation. Then, DNA under 1000 bp was extracted and sonicated. To enrich ligation events associated with a specific viewpoint, an appropriate amount of sonicated DNA was taken as a template to linearly amplify for 100 cycles using a 5’ biotin-labeled probe of the viewpoint of interest. The amplification products were incubated at 95°C for 5 min, immediately cooled on ice to obtain amplified ssDNA and then enriched with Dynabeads M-280 streptavidin. The bead-bound ssDNA was then ligated with adapters
QHR-4C libraries were constructed with specific primer pairs (forward primers containing Illumina P5 with sequences near a specific viewpoint and reverse primers containing Illumina P7 with an index and sequences matching the adapter) and then sequenced on the Illumina NovaSeq platform (Annoroad Gene Technology Co., Ltd.).

treatment_protocol: Tead2-knockout SL-ESC lines and 2iL-ESCs with mutated TEAD2 motifs by using CRISPR/Cas9

value: TEAD2 motif mutant


title: WT_Con2_IP


title: Biotin_ChIPseq_Tead2_AviTag_knock_in_2iL_ESCs


title: Pno1 + Dim1-E85A, 18S rRNA 3'-RACE, biol rep 4

description: wild type 18S rRNA

value: Universal miRNA Cloning Linker


title: 4Cseq_B4galt6_promoter_2iL_ESCs_Tead2_motif_mutant_rep1


title: WT_Con1_IP


title: Pno1 + Dim1-E85A, 18S rRNA 3'-RACE, biol rep 1

description: wild type 18S rRNA

value: TBE-Urea-PAGE gel extraction


title: 4Cseq_B4galt6_promoter_2i_d6_Tead2_knockout_rep1

value: SL-to-2iL transition day 6


title: REL-14 DP Rep 3

status: Public on Mar 02 2024

city: Worcester

first: Michelle

middle: A

last: Kelliher

state: Massachusetts

address: 364 Plantation Street, Lazare Research Building, 470H

institute: UMass Chan Medical School

description: Not included in this study

data_processing:
Reads were aligned to hg38 using Star and annotated with gencode.v34.primary_assembly
FastQC and MultiQC were used for raw reads quality control and QoRTs for post-alignment quality control
Aligned exon reads were counted toward gene expression with FeatureCounts with default settings
Differential expression analysis was performed with DESeq2
Significantly differentially expressed genes were filtered using FDR<0.05 and absolute log2 fold change > 1.0
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM for each Sample

source_name: Spleen

growth_protocol: 10^6 relapsed PDX cells were engrafted into NOD scid gamma mice

extract_protocol:
RNA was harvested using RNAeasy mini plus kit (Qiagen) and subsequently stored at -80C prior to amplification and QC
RNA libraries for RNA-seq were prepared using SMARTer RNA amplification kit and ultra low input mRNA non-directional library preparation

value: Spleen

value: REL-14 PDX

value: Leukemic cells


title: Pno1 + Dim1-E85A, 18S rRNA 3'-RACE, biol rep 2

description: wild type 18S rRNA


title: 4Cseq_B4galt6_promoter_2i_d6_Tead2_knockout_rep2

city: guangzhou

first: xiaotao

last: dong

address: 190 Kai Yuan Avenue

institute: Chinese Academy of Sciences

value: Tead2 Knockout


title: Pno1 + Dim1-E85A, 18S rRNA 3'-RACE, biol rep 3

description: wild type 18S rRNA

value: Gal::Pno1; Gal::Dim1 + TEF::Pno1 + Cyc1::Dim1-E85A


title: REL-14 DP Rep 2_B

description: Not included in this study


title: REL-14 hL-IC Rep 3

description: Not included in this study


title: REL-14 DP Rep 2


title: REL-14 DP Rep 1


title: REL-14 hL-IC Rep 2_B

description: Not included in this study


title: WT_Con3_IP

value: m6A-specific antibody (Synaptic Systems, Goettingen, Germany)


title: REL-14 hL-IC Rep 2


title: WT_Con1_input


title: REL-13 DP Rep 1

value: REL-13 PDX


title: REL-13 hL-IC Rep 2


title: REL-14 hL-IC Rep 1


title: REL-13 hL-IC Rep 3


title: REL-13 hL-IC Rep 1


title: P5ciRNA

city: Hangzhou

first: Ningning

last: Xie

address: 1 Xueshi Road

institute: Women’s Hospital, School of Medicine, Zhejiang University

data_processing:
To perform analysis on mRNAs, the initial step involved utilizing Cutadapt and Perl scripts to eliminate reads containing adaptor contamination, low-quality bases, and unclear bases. Then, FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was employed for the purpose of confirming the sequence quality. The standard-compliant reads were mapped to the human genome by Bowtie2 and Tophat2. The assembled mapped reads of each specimen were processed by deployingStringTie.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include raw count values for each sample.

source_name: placenta

extract_protocol:
Isolation of the total RNA was performed using Trizol Reagent (Invitrogen, USA).
Two libraries were constructed for the purpose of whole transcriptome sequencing. The TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA) were employed to create the small RNA library. A 1 µg of total RNA was utilized in accordance with the provided protocol. Following the completion of library preparation, the created libraries underwent sequencing by employing the Illumina Hiseq2000 platform, employing a single-end configuration with a read length of 1×50 bp. For mRNA and circRNA library, first, ribosomal RNA was depleted, and the remaining RNA was fragmented. Following the purification process, the poly(A)– or poly(A)+ RNA fractions were subjected to fragmentation by means of divalent cations at an increased temperature. Additionally, the construction of the cDNA library was carried out utilizing the mRNA-Seq sample preparation kit (Illumina, San Diego, CA, USA).Finally, the paired-end sequencing was conducted on the Illumina NovaSeq 6000 system with a 2 × 150 bp read length (LC Bio, China).

value: placenta


title: P3ciRNA


title: REL-13 DP Rep 2


title: C4ciRNA


title: P1ciRNA


title: P2ciRNA


title: C5ciRNA


title: REL-13 DP Rep 3


title: C1ciRNA


title: C3ciRNA


title: P4ciRNA


title: C2ciRNA


title: SH_SY5Y_DMSO_1

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60).  GEMM mouse samples were mapped to mm10 and other samples were mapped to hg38 (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (  M22 for GEMM mouse samples; r31, GRCh38.p12 for other samples).
Assembly: GRCh38 (hg38) or GRCm38 (mm10)
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files

growth_protocol: The cells were cultured in RPMI 1640 supplemented with 10% Fetal Bovine Serum, 1% L-Glutamine, and 1% Penicillin/Streptomycin at 37 °C in an atmosphere of 5% CO2. Transgenic TH-Mycn/AlkF1178L mice were housed with temperature and 12h light /12h dark cycle controlled under specific-pathogen-free conditions (SPF) at the St Jude Children’s Research Hospital mouse facility.

extract_protocol:
Total RNA extraction from cells and tumor tissues was performed using the RNeasy Mini Kit (74106, Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

treatment_protocol: The generation of QC6352-resistant BE2C cells was established by exposing the parental BE2C cells to QC6352 in sequential, increasing concentrations of QC6352 (0.1, 0.2, 0.5, 1, 2, and 2.5 µM; each concentration was incubated for 5-7 days). The final concentration of QC6352 was 2.5 µM. GIMEN and SH-SY5Y cells were treated DMSO or QC6352 100 nM for 48 hours. GIMEN cells were overexpressing MYCN or vector. For the tumor samples from TH-MYCN/ALKF1178L mouse model, the tumors were either treated with vehicle or QC6352 25 mg/kg.

value: neuroblastoma

value: DMSO


title: GIMEN_MYCN_2

source_name: GIMEN

value: GIMEN

value: MYCN overexpression

value: overexpressing MYCN


title: GIMEN_RFP_2

value: control

value: vector control


title: GIMEN_QC6352_2


title: GIMEN_DMSO_2


title: GIMEN_DMSO_1


title: GIMEN_QC6352_1


title: GIMEN_MYCN_1


title: BE2C-QC6352R_1

tag: phenotype

value: QC6352 resistant

value: QC6352 2.5uM resistant


title: SH_SY5Y_DMSO_2


title: BE2C_Ctrl_2

value: ctrl


title: SH_SY5Y_QC6352_1


title: BE2C-QCR-02

data_processing:
The ATAC-seq raw reads were aligned to the human reference genome (hg38) using BWA (version 0.7.12-r1039) to and then removed duplicated reads with Picard (version 1.65), with only properly paired uniquely mapped reads were extracted by samtools (version 1.3.1 parameters used were -q 1 -f 2 -F 1804) .  Reads mapping to mitochondrial DNA were excluded from the analysis. All mapped reads were offset by +4 bp for the + strand and -5 bp for the  – strand.
Nucleosome free reads was used  to generate bigwig files and call eanriched regions. MACS2 (version 2.2.7.1) parameters are  “-q 0.01 –nomodel –extsize 200 –shift 100 -f BEDPE --keep-dup all”.
Assembly: GRCh38 (hg38)
Supplementary files format and content: narrowPeak

source_name: Brain

growth_protocol: BE2C cells were cultured in 1X Roswell Park Memorial Institute (RPMI) 1640  supplemented with 10% Fetal Bovine Serum , 1% L-Glutamine , and 1% Penicillin/Streptomycin. The generation of QC6352-resistant BE2C cells was established by exposing the parental BE2C cells to QC6352 in sequential, increasing concentrations of QC6352 (0.1, 0.2, 0.5, 1, 2, and 2.5 µM; each concentration was incubated for 5-7 days). The final concentration of QC6352 was 2.5 µM.

extract_protocol:
Library preparations for ATAC-seq were based on a published protocol with minor modifications. Briefly, cells (100,000 per sample) were harvested and washed with 150 ul ice-cold Dulbecco's Phosphate-Buffered Saline (DPBS) containing protease inhibitor (PI). Nuclei were collected by centrifugation at 500 g for 10 minutes at 4 °C after cell pellets were resuspended in lysis buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 containing 0.1% NP-40 and PI). Nuclei were incubated with Tn5 transposon enzyme in transposase reaction mix buffer (Illumina) for 30 min at 37 °C. DNAs were purified from the transposition sample by using Mini-Elute PCR purification kit (28004, Qiagen) and measured by Qubit.
Polymerase chain reaction (PCR) was performed to amplify with High-Fidelity 2X PCR Master Mix [72°C/5 mins + 98 °C /30 s + 12 × (98 °C /10 s + 63 °C/30 s + 72 °C/60 s) + 72 °C/5 min]. The libraries were purified using the Mini-Elute PCR purification kit (Qiagen). ATAC-seq libraries were pair-end sequenced on HiSeq4000 (Illumina) in the Hartwell Center at St Jude Children's Research Hospital, Memphis, TN, USA.

treatment_protocol: The experiment was done using parental (0.025% DMSO) and QC6352-resistant BE2C cells (maintained in 2.5 µM of QC6352).

value: Brain

value: neuroblast


title: BE2C-QC6352R_2


title: BE2C-QCR-01


title: BE2C-ctrl-02


title: BE2C_Ctrl_1


title: SKNAS_siKDM4C90_2

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60),  mapped to human genome assembly (hg38) (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (r31, GRCh38.p12) .
Assembly: GRCh38(hg38)
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files

source_name: cell line

growth_protocol: BE2C, KELLY and SKNAS cells were cultured with RPMI 1640 media supplemented with 100 U/mlpenicillin/streptomycin and 10% fetal bovine serum. Cells were maintained at 37 °C in an atmosphere of 5% CO2.

extract_protocol:
For siRNA knockdown, cells were treated with siCtrl or siKDM6B for 72h.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

value: SKNAS

value: siKDM4C #90


title: GIMEN_RFP_1


title: SKNAS_siKDM4B_68


title: SKNAS_siKDM4B_67


title: SKNAS_siKDM4C90_1


title: SKNAS_siKDM4A36_1

value: siKDM4A #36


title: SKNAS_siCtrl2_2

value: siCtrl


title: SKNAS_siCtrl2_1


title: KELLY_siKDM4C90_2

value: KELLY


title: KELLY_siKDM4B_67


title: KELLY_siKDM4A36_2


title: KELLY_siKDM4B_68


title: KELLY_siKDM4A36_1


title: KELLY_siCtrl2_2


title: KELLY_siKDM4C90_1


title: KELLY_siCtrl2_1


title: BE2C_siKDM4C90_2


title: BE2C_siKDM4A36_1


title: BE2C-ctrl-01


title: BE2C_siKDM4B_68


title: BE2C_siKDM4A36_2


title: BE2C_siCtrl2_2