title: HepG2, siFBL, FUBP1 RIP, rep2

status: Public on Apr 20 2025

city: Chicago

first: Boyang

last: Gao

state: IL

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

description:
Library name: siFBL_RIP_rep2
FUBP1RIP.FBLKD.wholetable.csv

data_processing:
Adapters were trimmed by cutadapt -m 20 -a NNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -U 3. Samples with adapter trimming were uploaded. Samples were mapped by hisat2, and alternative splicing was analyzed by rmats. RIP-seq enrichment were measured by DESeq2 after counting reads on each gene with featureCounts
the processed data column header information is in the 'processed_data_readme.txt'
Assembly: hg38
Supplementary files format and content: txt, rmats of SE occurrence
Supplementary files format and content: csv, DESeq2 of FUBP1 RIP-seq

extract_protocol:
For RNA-seq, HepG2 cell RNA was harvested by TRIzol™ reagent.  For RIP-seq, samples were  lysed by iCLIP lysis buffer (50 mM Tris pH 7.5, 100 mM NaCl, 1% NP-40 substitute, 0.1% SDS, 0.5% sodium deoxycholate, 100 × protein inhibitor cocktail and 100 × SUPERase•In™ RNase Inhibitor) at 4℃ for 15 mins with rotation, followed by centrifugation at 13,000 g for 15 mins. Protein G beads (Invitrogen, 10009D) were conjugated with 16 μg FUBP1 antibody (abcam, ab192867) by incubation at 4℃ for 1hr, then washed and mixed with lysate supernatant to rotate at 4℃ for 4 hrs. Beads were washed for three times with CLIP wash buffer (50mM Tris pH 7.5, 300 mM KCl, 0.05% NP-40 substitute, 1000 × protein inhibitor cocktail and 1000 × SUPERase•In™ RNase Inhibitor) and eluted by proteinase K digestion (Thermo Scientific, EO0491). Input samples harvested before immunoprecipitation was also digested with proteinase K for RNA recovery.
The purified RNA was constructed for library with SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian.

treatment_protocol: In the siRNA-mediated knockdown assay, cells at ~90% confluency were passaged at 1:4 ratio into 15 cm plates. Within 16 hours after passaging, 60 μL Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen, 13778150) and 200 pmol siRNA were diluted in 1mL Opti-MEM™ I Reduced Serum Medium (Gibco, 31985070), respectively. The solutions were mixed together and incubated at room temperature for 5 mins before added into the cell culture. Knockdown reactions for fewer cells were scaled down based on the bottom area of culture plates. The siRNA used in this paper include siControl (Qiagen, 1027310), siFBL (Qiagen, SI04164951), siControl2 (Invitrogen, 4390846) and siFUBP1(Invitrogen, s16966). Cells were harvested 48 hours post transfection. U3 KD was conducted with U3 ASO (mU*mC*mA*mC*mC*T*T*C*A*C*C*C*T*C*T*mC*mC*mA*mC*mU) controlled by GFP ASO (mC*mU*mG*mC*mC*A*T*C*C*A*G*A*T*C*G*mU*mU*mA*mU*mC). Transfection was done by Lipofectamine™ 3000 transfection reagents (Invitrogen, L3000015), where 600 pmol ASO and 8 μL P3000™ reagents were added to 125 μL Opti-MEM™ medium. In parallel, 6 μL Lipofectamine™ 3000 reagents were diluted in 125 μL Opti-MEM™ medium. The two mixtures were mixed together and incubated at room temperature for 10 min, and then added to 2 mL media in a 6-well plate well. HepG2 cells corresponding to 1/3 of a 10 cm plate at ~90% confluency were then added to the transfected media. Cell were cultured for 72 hours before harvest.

value: siFBL FUBP1 RIP


title: HepG2, siCtrl, FUBP1 RIP, rep2

type: SRA

country: USA

description:
Library name: siCtrl_RIP_rep2
FUBP1RIP.FBLKD.wholetable.csv

library_source: other

molecule: other

organism: Homo sapiens

tag: cell line

tag: treatment

value: siCtrl FUBP1 RIP


title: HepG2, siFBL, FUBP1 RIP, rep1

description:
Library name: siFBL_RIP_rep1
FUBP1RIP.FBLKD.wholetable.csv


title: HepG2, siFBL, input, rep2

description:
Library name: siFBL_input_rep2
Input-SE.MATS.JC.txt

value: siFBL input


title: HepG2, siCtrl, input, rep2

description:
Library name: siCtrl_input_rep2
Input-SE.MATS.JC.txt

value: siCtrl input


title: HepG2, siCtrl, FUBP1 RIP, rep1

description:
Library name: siCtrl_RIP_rep1
FUBP1RIP.FBLKD.wholetable.csv


title: HepG2, siCtrl, input, rep1

description:
Library name: siCtrl_input_rep1
Input-SE.MATS.JC.txt


title: HepG2, U3 ASO, rep3

description:
Library name: U3KD_rep3
U3KD-SE.MATS.JC.txt

library_source: transcriptomic

molecule: polyA RNA

value: U3 ASO


title: HepG2, U3 ASO, rep2

description:
Library name: U3KD_rep2
U3KD-SE.MATS.JC.txt


title: HepG2, U3 ASO, rep1

description:
Library name: U3KD_rep1
U3KD-SE.MATS.JC.txt


title: HepG2, GFP ASO, rep3

description:
Library name: GFP_rep3
U3KD-SE.MATS.JC.txt

value: GFP ASO


title: HepG2, siFUBP1, rep2

description:
Library name: siFUBP1_rep2
siFUBP1.SE.MATS.JC.txt


title: HepG2, GFP ASO, rep2

description:
Library name: GFP_rep2
U3KD-SE.MATS.JC.txt


title: HepG2, siCtrl2, rep1

description:
Library name: siCtrl2_rep1
siFUBP1.SE.MATS.JC.txt


title: HepG2, PAR-CLIP, FUBP1, rep2

description: Library name: PAR-CLIP-FUBP1-rep2

data_processing:
*library strategy: PAR-CLIP-seq
Reads were trimmed by cutadapt with parameter "-m 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT". Reads with adapter trimmed were uploaded as raw reads. Samples were mapped with hisat2. For PAR-CLIP samples, reads were deduplicated by picard markduplicate. Read 1 were then selected and filtered with mapping quality of 30, followed by wavClusteR analysis.
Assembly: hg38
Supplementary files format and content: bigwig

molecule: total RNA

extract_protocol:
For PAR-CLIP, two replicates of 150 million HepG2 cells were cultured with 200 μM 4SU for 14 hrs. Cells were crosslinked by 365 nm UV at 1500 J/m2 twice. For CLIP-seq, 3 replicates of 150 million HepG2 cells were crosslinked by 254 nm UV at 1500 J/m2 for three times. Samples were harvested and lysed by iCLIP lysis buffer (50 mM Tris pH 7.5, 100 mM NaCl, 1% NP-40 substitute, 0.1% SDS, 0.5% sodium deoxycholate, 100 × protein inhibitor cocktail and 100 × SUPERase•In™ RNase Inhibitor) at 4℃ for 15 mins with rotation. To release FUBP1 proteins associated with the chromatin, cell lysate was supplemented with 1% SDS, sonicated at 30% amplitude with 2s:4s cycles for 1 min on ice. The lysate was 10-fold diluted by iCLIP lysis buffer without SDS, centrifuged to save the supernatant, and treated with 0.2 U/μL RNase T1 (Thermo, EN0642) at 22℃ for 15 mins before quenched on ice for 5 mins. Protein G beads (Invitrogen, 10009D) were conjugated with 20 μg FUBP1 antibody (abcam, ab192867) by incubation at 4℃ for 1hr, then washed and mixed with RNase T1-treated lysate to rotate at 4℃ for 4 hrs. Beads were washed for three times with CLIP wash buffer (50mM Tris pH 7.5, 300 mM KCl, 0.05% NP-40 substitute, 1000 × protein inhibitor cocktail and 1000 × SUPERase•In™ RNase Inhibitor), digested by 10 U/μL RNase T1 at 22℃ for 8 mins, before they were washed by CLIP High salt buffer (50mM Tris pH 7.5, 500 mM KCl, 0.05% NP-40 substitute, 1000 × protein inhibitor cocktail and 1000 × SUPERase•In™ RNase Inhibitor) and PNK buffer without DTT for 3 times each and underwent end repair by T4 PNK (NEB, M0201L), then eluted by proteinase K digestion (Thermo Scientific, EO0491). For CLIP-seq, 2% input samples were harvested before incubation with antibody-conjugated protein G beads, treated with 10 U/μL RNase T1 at 22℃ for 8 mins, followed by proteinase K digestion and end repair in the next.
Library was constructed by  NEBNext® Small RNA Library Prep Set (NEB, E7330S). PAR-CLIp was sequenced by Illumina NovaSeq 6000 with paired-end 50 bp. CLIP-seq was sequenced by Illumina NovaSeq X with single-end 100 bp.


title: HepG2, siFUBP1, rep3

description:
Library name: siFUBP1_rep3
siFUBP1.SE.MATS.JC.txt


title: HepG2, GFP ASO, rep1

description:
Library name: GFP_rep1
U3KD-SE.MATS.JC.txt


title: HepG2, siFUBP1, rep1

description:
Library name: siFUBP1_rep1
siFUBP1.SE.MATS.JC.txt


title: HepG2, PAR-CLIP, FUBP1, rep1

description: Library name: PAR-CLIP-FUBP1-rep1


title: Deac1_0d_Control_rep1

status: Public on Apr 21 2025

city: Geneva

first: Hongrui

last: Wang

state: NY

address: 630 W. North Street

department: School of Integrative Plant Science, Horticulture section

institute: Cornell University

data_processing:
FastQC for quality control
BBDuk for removing adaptors and poly-A following the pipeline suggested by the manufacturer (https://www.lexogen.com/quantseq-data-analysis/)
STAR for gene level quantification using ‘-quantMode GeneCounts’
Low count gene filterig based on 'total gene count greater than sample number'
DESeq2 for variance stabilization transformation and gene expression normalization
WGCNA for gene co-expression analysis, noise gene filtering, module eigengene visualization and contrast generation
GSEA for pathway enrichment analysis
Assembly: Vitis vinifera 12X.v2 genome with VCost.v3 annotation
Supplementary files format and content: One matrix table with raw gene counts for every gene and every sample without any filtering

organism: Vitis vinifera

source_name: bud

extract_protocol:
Total RNA was extracted using SpectrumTM Plant Total RNA Kit (Sigma Aldrich, St Louis, MO, USA) following the protocol suggested by the manufacturer
Libraries were constructed with Lexogen QuantSeq 3’mRNA-Seq Prep Kit (Lexogen, Greenland, NH, USA) following standard practices as a service provided by Cornell University Institute of Genomic Diversity (Ithaca, NY, USA). Sequencing of the libraries was accomplished using NextSeq500 (Illumina, Inc., San Diego, CA, USA) with 95 samples per lane at Cornell University Institute of Biotechnology (Ithaca, NY, USA). The read length was 85 bp.

tag: tissue

value: bud

tag: genotype

value: Riesling

tag: deacclimation assay

tag: days

value: Control


title: HepG2, siFBL, input, rep1

description:
Library name: siFBL_input_rep1
Input-SE.MATS.JC.txt


title: hBMSCs, MSC-3BSGHOT3 (Corresponding to the LT/BSG group in the article)

city: Shenzhen

first: Mengke

last: Fan

address: 1068 Xueyuan Avenue, Xili Shenzhen University City,

country: China

institute: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences

description: Library name: Sample 12

data_processing:
RNA-seq
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: hBMSCs

growth_protocol: Human bone marrow mesenchymal stem cells (hBMSCs) were maintained in MEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

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.

treatment_protocol: hBMSCs were cultured with BSG extracts under moderate hyperthermia (42℃, 5%CO2）or regular  atmosphere (37℃, 5%CO2 )

value: hBMSCs

tag: cell type

value: mesenchymal stem cells

value: WT

value: osteogenic differentiation

tag: batch


title: hBMSCs, MSC-3BSGHOT1 (Corresponding to the LT/BSG group in the article)

description: Library name: Sample 10


title: hBMSCs, MSC-3BSG1 (Corresponding to the BSG group in the article)

description: Library name: Sample 7


title: hBMSCs, MSC-3BSG2 (Corresponding to the BSG group in the article)

description: Library name: Sample 8


title: hBMSCs, MSC-HOT3 (Corresponding to the LT group in the article)

description: Library name: Sample 6


title: hBMSCs, MSC-3BSGHOT2 (Corresponding to the LT/BSG group in the article)

description: Library name: Sample 11


title: hBMSCs, MSC-3BSG3 (Corresponding to the BSG group in the article)

description: Library name: Sample 9


title: hBMSCs, MSC-HOT2 (Corresponding to the LT group in the article)

description: Library name: Sample 5


title: HepG2, siCtrl2, rep2

description:
Library name: siCtrl2_rep2
siFUBP1.SE.MATS.JC.txt


title: hBMSCs, MSC-HOT1 (Corresponding to the LT group in the article)

description: Library name: Sample 4


title: HepG2, siCtrl2, rep3

description:
Library name: siCtrl2_rep3
siFUBP1.SE.MATS.JC.txt


title: hBMSCs, NC3 (Corresponding to the Control group in the article)

description: Library name: Sample 3


title: hBMSCs, NC1 (Corresponding to the Control group in the article)

description: Library name: Sample 1


title: m_HO53-24H-3

city: Reykjavik

first: Iwona

middle: Teresa

last: Myszor

address: Vatnsmyrarvegur 16

country: Iceland

institute: University of Iceland

data_processing:
Illumina NovaSeq 6000
Kallisto version 0.45.0
sleuth R package version 0.30
Assembly: Ensembl GRCh38
Supplementary files format and content: Kallisto h5 and tsv abundance measurements

source_name: bronchus

growth_protocol: BCi-NS1.1 cell line (BCi) was cultured in Bronchial/Tracheal Epithelial cell growth medium (BEGM) supplemented with retinoic acid and Penicillin-Streptomycin (20 U/ml, 20 µg/ml, respectively) at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted using NucleoSpin RNA kit (Machinery-Nagel).
The quality (RIN score) and quantity of isolated total RNA samples was assessed using the DNA 5K/RNA chip for the LabChip GX (Perkin-Elmer). cDNA libraries derived from Poly-A mRNA were generated using Illumina´s TruSeq RNA v2 Sample Prep Kit. Briefly, Poly-A mRNA was isolated from total RNA samples (0.2–1 μg input) using hybridization to Poly-T beads. The Poly-A mRNA was fragmented at 94°C, and first-strand cDNA was prepared using random hexamers and the SuperScript II reverse transcriptase. Following second-strand cDNA synthesis, end repair, addition of a single A base, indexed adaptor ligation, AMPure bead purification, and PCR amplification, the resulting cDNA sequencing libraries were measured on the LabChip GX, diluted to 3 nM and stored at -20 °C.

treatment_protocol: Cells were seeded in triplicates and treated with HO53 compound the next day after seeding. The treatment was performed by adding HO53 compound to BEGM medium to obtain 75 µM final concentration. Samples in triplicates were collected after 4 h, 8 h and 24 h. Untreated cells served as control collected after 24 h.

value: bronchus

value: bronchial epithelial cells

tag: culture

value: monolayer (undifferentiated cells)


title: m_HO53-24H-2


title: 143B cells, M-BSG2  (Corresponding to the 5-MNP-BSG group in the article)

description: Library name: Sample 8

growth_protocol: 143B cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

treatment_protocol: 143B cells were cultured with injectable magnetothermal bioactive systems (5-MNP-BSG) under alternating magnetic field (20A; 500H)

value: osteosarcoma cells


title: 143B cells, BSG3  (Corresponding to the BSG group in the article)

description: Library name: Sample 6


title: 143B cells, BSG1  (Corresponding to the BSG group in the article)

description: Library name: Sample 4


title: 143B cells, BSG2  (Corresponding to the BSG group in the article)

description: Library name: Sample 5


title: 143B cells, M-BSG3  (Corresponding to the 5-MNP-BSG group in the article)

description: Library name: Sample 9


title: 143B cells, M-BSG1  (Corresponding to the 5-MNP-BSG group in the article)

description: Library name: Sample 7


title: 143B cells, M-BSG-Hot3  (Corresponding to the 5-MNP-BSG (+) group in the article)

description: Library name: Sample 12


title: 143B cells, M-BSG-Hot1  (Corresponding to the 5-MNP-BSG (+) group in the article)

description: Library name: Sample 10


title: 143B cells, NC2  (Corresponding to the Control group in the article)

description: Library name: Sample 2


title: 143B cells, M-BSG-Hot2  (Corresponding to the 5-MNP-BSG (+) group in the article)

description: Library name: Sample 11


title: 143B cells, NC3  (Corresponding to the Control group in the article)

description: Library name: Sample 3


title: 143B cells, NC1  (Corresponding to the Control group in the article)

description: Library name: Sample 1


title: m_HO53-24H-1


title: m_HO53-8H-3


title: m_HO53-4H-2


title: hBMSCs, NC2 (Corresponding to the Control group in the article)

description: Library name: Sample 2


title: m_HO53-4H-1


title: m_Ctrl-24h-3

value: untreated - 24h


title: m_HO53-8H-1


title: m_Ctrl-24h-2


title: m_HO53-4H-3


title: m_Ctrl-24h-1


title: Sample5_24hrs_Clu

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

data_processing:
Basecalls performed using illumina's bcl2fastq
Sequenced reads were trimmed for adaptor sequence, low complexity and low quality sequences. Then reads were aligned to Ensembl GRCh38.p10 genome assembly using STAR 2.7.8a with following parameters: '--outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif'
Counts were generated by Rsubread 2.8.0
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: count file was generated by 'featureCounts' from Rsubread package. The numbers are raw counts.

source_name: Peripheral blood

growth_protocol: CD34+ stem/progenitor cells from PV patients were incubated for 24 hours in X-VIVO medium (Lonza) with 2mM L-glutamine, 10ng/mL SCF, 50ng/mL TPO, 10ng/mL FLT3.

extract_protocol:
Total RNA was purified with the RNeasy Plus Micro Kit (Qiagen) following manufacturer’s instructions.
RNA-sequencing was performed as specified in Picelli et al 2014 using the NovaSeq sequencing platform (Illumina).

treatment_protocol: The PV stem/progenitor cells were treated with clusterin (CLU) (20µg/mL) or IKK-16 (2µM) or both, CLU (20µg/mL) and IKK-16 (2µM), or HU (100µM) or solvent control for 24 hours.

tag: disease state

value: Patient5 with Polycythemia vera

value: Peripheral blood

value: Hematopoietic stem/progenitor cells

tag: ex vivo treatment

value: CLU treated


title: Sample5_24hrs_HU

value: HU treated


title: Sample5_24hrs_IKK16

value: IKK-16 treated


title: Sample5_24hrs_control

value: Solvent control


title: Sample5_24hrs_CluIKK16

value: CLU and IKK-16 treated


title: Sample4_24hrs_CluIKK16

value: Patient4 with Polycythemia vera


title: Sample4_24hrs_HU


title: Sample4_24hrs_control


title: Sample4_24hrs_Clu


title: Sample4_24hrs_IKK16


title: HEepG2-shPCCB-4

city: Shanghai

first: Liu

last: Fangfang

address: No. 555, Zuchongzhi Road, Pudong New Area, Shanghai, China

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

description:
Library name: Sample8
Column name in Kpm_RNAseq_FPKM.csv: KD4

data_processing:
Raw FASTQ files were quality checked using FastQC (v0.11.9) Reads were aligned to the hg38 reference genome using hisat2 (v2.2.1) Gene counts were quantified using featureCounts (v2.0.3) Differential expression genes were analyzed using edgeR (v3.40.2)
Assembly: hg38
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: HepG2 cells were maintained in DMEM supplemented containing 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were cultured in an incubator containing 5% CO2 at 37 oC with suitable humidity.

extract_protocol:
RNA was harvested by ANOROAD (Beijing, China).
RNA libraries for RNA-seq were prepared using VAHTS  Universal  V6  RNA-seq  Library Prep  Kit  for  Illumina ® (NR604-01/02) following manufacturer's protocols.

value: hepatocellular carcinoma

value: PCCB konckdown


title: HEepG2-shNT-4

description:
Library name: Sample4
Column name in Kpm_RNAseq_FPKM.csv: NT4

value: WT


title: Sample3_24hrs_HU

value: Patient3 with Polycythemia vera


title: HEepG2-shNT-3

description:
Library name: Sample3
Column name in Kpm_RNAseq_FPKM.csv: NT3


title: Sample3_24hrs_IKK16


title: Sample3_24hrs_CluIKK16


title: HEepG2-shPCCB-3

description:
Library name: Sample7
Column name in Kpm_RNAseq_FPKM.csv: KD3


title: HEepG2-shPCCB-2

description:
Library name: Sample6
Column name in Kpm_RNAseq_FPKM.csv: KD2


title: HEepG2-shNT-1

description:
Library name: Sample1
Column name in Kpm_RNAseq_FPKM.csv: NT1


title: Sample2_24hrs_HU

value: Patient2 with Polycythemia vera


title: Brain_TBI_RVG-nSTM2

city: xi'an

first: Xun

last: Wu

state: Shaanxi

address: No.1 Xinsi Road, Baqiao District

institute: fourth military medical school

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2.2.4 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
RNAs differential expression analysis was performed by DESeq2 software between two different groups
Assembly: Ensembl_release101
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Mus musculus

source_name: brain

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000.

value: brain


title: Sample3_24hrs_Clu


title: Sample2_24hrs_CluIKK16


title: Brain_TBI_RVG-nSTM3


title: Brain_TBI_RVG-nSTM1


title: m_HO53-8H-2

value: bronchus

value: bronchial epithelial cells

value: monolayer (undifferentiated cells)


title: Brain_TBI_RVG-vector3

value: TBI


title: Brain_TBI_RVG-vector2


title: Sample2_24hrs_Clu

value: Peripheral blood

value: Hematopoietic stem/progenitor cells


title: Brain_TBI_RVG-vector1


title: HEepG2-shPCCB-1

description:
Library name: Sample5
Column name in Kpm_RNAseq_FPKM.csv: KD1


title: HEepG2-shNT-2

description:
Library name: Sample2
Column name in Kpm_RNAseq_FPKM.csv: NT2


title: Brain_Sham3

value: Sham


title: Brain_Sham2


title: Brain_Sham1


title: BV2_LPS3

value: microglial cells

value: LPS


title: Sample1_24hrs_HU

value: Patient1 with Polycythemia vera

value: HU treated


title: Sample1_24hrs_CluIKK16

value: CLU and IKK-16 treated


title: BV2_LPS2


title: BV2_LPS1


title: SpretB6_iPSCs_C6

city: New York

first: Daniel

last: Medina Cano

email: medinacd@mskcc.org, dmcdmc156@gmail.com

state: New York

address: 411E 67th St

department: Developmental Biology

institute: MSKCC

description: Library name: SP6

data_processing:
The fastq files were mapped to the mouse mm10 genome
Salmon (Patro et al, 2017) was used to associate the mapped reads to their transcirpts
Assembly: mm10
Supplementary files format and content: Gene counts per sample, un-normalized (salmon output).

source_name: Mouse iPSCs

growth_protocol: F1 iPSCs were generated as previously described (Medina-Cano et al, biorxiv 2024, doi https://doi.org/10.1101/2024.09.30.615887)

extract_protocol:
iPSCs were extracted for bulk RNA-seq as previously described (Medina-Cano et al, biorxiv 2024, doi https://doi.org/10.1101/2024.09.30.615887)
The libraries were constucted as described in (Medina-Cano et al, biorxiv 2024, doi https://doi.org/10.1101/2024.09.30.615887) - RNASeq-Ribodepletion, sequenced to 80M reads depth per sample

treatment_protocol: iPSCs were treated as previously described (Medina-Cano et al, biorxiv 2024, doi https://doi.org/10.1101/2024.09.30.615887)

value: Mouse iPSCs

value: iPSCs

value: Mouse stem cells

tag: genotype background


title: SpretB6_iPSCs_C4

description: Library name: SP4


title: Sample1_24hrs_control

value: Solvent control


title: Sample3_24hrs_control

value: Patient3 with Polycythemia vera


title: SpretB6_iPSCs_C3

description: Library name: SP3


title: BV2_Vehicle3

value: Vehicle


title: Sample2_24hrs_IKK16

value: Patient2 with Polycythemia vera

value: IKK-16 treated


title: PwkB6_iPSCs_C1

description: Library name: PW1


title: PwkB6_iPSCs_C3

description: Library name: PW3


title: PDLSC,VO-Ohpic3,24h

city: Bangkok

first: Suphalak

last: Phothichailert

state: --None--

address: 34  Henri-Dunant, Wang Mai, Pathumwan

country: Thailand

institute: Chulalongkorn University

description:
Library name: V3
RNA-Seq of homo sapiens

data_processing:
Read quality was checked with a FastQC (V0.10.1)
Different expression gene analysis were used DESeq2 (V1.6.3), Deseq (V1.18.0), EdgeR (V3.4.6), and Cuffdiff (V2.2.1)
Assembly: GRch38.107
Supplementary files format and content: tab-delimited text file includes rawreads count values for each sample

source_name: Peridontal ligament

growth_protocol: ThePDLSC were extracted from PDL tissue and cultured in High glucose Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, 1% of Penicillin (100 U/mL), Streptomycin (100 mg/mL) and incubated at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated using a RNeasy Plus Mini Kit with DNase I treatment. Total RNA quantity and quality were examined using a Nanodrop.
Library quality assurance was conducted using an Cutadapt (V1.9.1)

treatment_protocol: PDLSCs were treated with 5 uM VO-OHpic for 24h

value: Peridontal ligament

value: Periodontal ligament stem cells

value: Wild-type

value: VO-Ohpic treatment


title: PwkB6_iPSCs_C2

description: Library name: PW2


title: PDLSC,VO-Ohpic2,24h

description:
Library name: V2
RNA-Seq of homo sapiens


title: MolfB6_iPSCs_C2

description: Library name: MO2


title: Sample2_24hrs_control

value: Peripheral blood

value: Hematopoietic stem/progenitor cells


title: BV2_Vehicle2

value: microglial cells


title: BV2_Vehicle1


title: PDLSC,VO-Ohpic1,24h

description:
Library name: V1
RNA-Seq of homo sapiens


title: MolfB6_iPSCs_C1

description: Library name: MO1


title: PDLSC,Control3,24h

description:
Library name: GM3
RNA-Seq of homo sapiens

value: Untreatment


title: Sample1_24hrs_Clu

value: Patient1 with Polycythemia vera

value: CLU treated


title: Sample1_24hrs_IKK16


title: CastB6_iPSCs_C6

description: Library name: CA6

value: Mouse iPSCs

value: iPSCs


title: BV2_Mettl3_KO_LPS2-input

data_processing:
fastp software (https://github.com/OpenGene/fastp) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. And sequence quality of IP and Input samples were verified using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and RseQC (http://rseqc.sourceforge.net/).
Then we used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genomeMus musculus(Version: v101). Peak calling and diff peak analysis were performed by R package exomePeak2 (https://bioconductor.org/packages/release/bioc/html/exomePeak2.html), and peaks were annotated by intersection with gene architecture using R package ANNOVAR (http://www.openbioinformatics.org/annovar/). MEME (http://meme-suite.org) and HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif finding followed by localization of the motif with respect to peak summit.
And StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all transcripts and genes from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)). The differentially expressed transcripts and genes were selected with log2 (fold change) ≥ 1 or log2 (fold change) ≤ -1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: Ensembl_release101
Supplementary files format and content: tab-delimited text file includes peak
Library strategy: meRIP-seq

extract_protocol:
Total RNAs were extracted from neuroblastoma cells using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al. DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210)
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq 6000 platform

value: Mettl3 KO


title: CastB6_iPSCs_C3

description: Library name: CA3

value: Mouse stem cells


title: CastB6_iPSCs_C4

description: Library name: CA4


title: BV2_Mettl3_KO_LPS3-input


title: SpretB6_C3

description: Library name: SB3_IGO_16878_B_3_S4_L002

data_processing:
The fastq files were mapped to the mouse mm10 genome for visualization purposes
Additional quantification data is included as supplementary information in the associated manuscript
Assembly: mm10
Supplementary files format and content: Allele-specific counts per gene for each sample subdivided by whether they map to the B6 or the Spret genome. Counts are size-normalized.

source_name: Mouse epiblast stem cells

growth_protocol: EpiSC-derived organoids were generated from SpretB6 lines as previously described (Medina-Cano et al, biorxiv 2024, doi https://doi.org/10.1101/2024.09.30.615887)

extract_protocol:
EpiSC-derived organoids were extracted for bulk RNA-seq as previously described (Medina-Cano et al, biorxiv 2024, doi https://doi.org/10.1101/2024.09.30.615887)
The libraries were constucted as described in (Medina-Cano et al, biorxiv 2024, doi https://doi.org/10.1101/2024.09.30.615887) - RNASeq-Ribodepletion, sequenced to 80M reads depth per sample

treatment_protocol: EpiSC-derived organoids were treated from SpretB6 lines as previously described (Medina-Cano et al, biorxiv 2024, doi https://doi.org/10.1101/2024.09.30.615887)

value: Mouse epiblast stem cells

value: Epiblast stem cells


title: PDLSC,Control2,24h

description:
Library name: GM2
RNA-Seq of homo sapiens


title: BV2_Mettl3_KO_LPS1-input


title: Dox,rep3

first: Jiahao

last: Li

address: No. 800 Dongchuan Road, Shanghai

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

data_processing:
The quality-filtered reads were mapped to the Arabidopsis thaliana genome (TAIR10) using TopHat2 v2.1.0.
Normalized RPKM (Reads Per Kilobase of transcript per Million mapped reads) value for each annotated gene was then obtained using Cufflinks v2.2.1.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file includes RPKM values for each sample.

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Wild type plants were grown for 10 days on solid 1/2 MS medium.

extract_protocol:
Total RNA was extracted from these seedlings using TRIzol reagent.
Sequencing libraries were generated using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (NR604-01/02).

treatment_protocol: Wild type plants grown on 1/2 MS medium supplemented without (control) or with 5 μg/mL Dox for 10 days.

value: Seedling

tag: ecotype

value: Wild type

value: Doxycycline


title: HepG2, CLIP-seq, FUBP1 CLIP, siFBL, rep3

description: Library name: CLIP_FUBP1CLIP_siFBL_rep3

data_processing:
*library strategy: CLIP-seq
Reads were trimmed by cutadapt with parameter "-m 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT". Reads with adapter trimmed were uploaded as raw reads. Samples were mapped with hisat2. For PAR-CLIP samples, reads were deduplicated by picard markduplicate. Read 1 were then selected and filtered with mapping quality of 30, followed by wavClusteR analysis.
Assembly: hg38
Supplementary files format and content: bigwig

value: siFBL


title: BV2_Mettl3_KO_LPS3-IP


title: MolfB6_iPSCs_C3

description: Library name: MO3


title: SpretB6_C2

description: Library name: SB2_IGO_16878_B_2_S5_L002


title: Dox,rep2


title: HepG2, CLIP-seq, FUBP1 CLIP, siFBL, rep2

description: Library name: CLIP_FUBP1CLIP_siFBL_rep2


title: BV2_Mettl3_KO_LPS2-IP


title: SpretB6_C1

description: Library name: SB1_IGO_16878_B_1_S6_L002


title: PDLSC,Control1,24h

description:
Library name: GM1
RNA-Seq of homo sapiens

value: Peridontal ligament

value: Periodontal ligament stem cells

value: Wild-type


title: Control,rep3

value: Control


title: BV2_Mettl3_KO_LPS1-IP

value: microglial cells


title: 5726-TVA-B

city: NEW YORK

first: Alexander

last: Tsankov

address: 1425 Madison Ave

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
We initiated our analysis by aligning the raw fastq files to the customized mouse genome reference mm10, which included the Rfp sequence. This alignment process was executed using CellRanger v5.0.0 by 10X Genomics. Following alignment, we used the CellRanges algorithm to filter count matrices. Cells with less than 400 genes, fewer than 1000 UMI (unique molecular identifier), or over 25% mitochondrial gene expression were excluded. Subsequent data processing and analysis were conducted using the Seurat v4.2.2 R package. The data was normalized using the NormalizeData function, utilizing the normalization.method = 'LogNormalize' parameter. For dimensionality reduction, we focused on the top 2,000 variable features, using functions such as FindVariableFeatures, ScaleData, and RunPCA. Ultimately, we generated UMAPs based on the top 15 principal components (PCs).
To subcluster the immune compartment, we employed the R package Harmony to address batch effects stemming from technical variations across replicates. De novo clustering was carried out using the Louvain algorithm at multiple resolutions (0.2, 0.4, 0.8, 2, 3, 5, 8) within the KNN graph space. For high-level cell type annotation, we iteratively and semi-supervisedly assigned de novo discovered clusters to cell types based on the expression of established marker genes defining each cluster. The annotation of cell subtypes at a lower level followed a similar approach to the high-level annotation, with additional assistance from de novo marker discovery utilizing the Seurat FindMarkers function and Wilcoxon Rank Sum test.
To identify clusters enriched with doublets, we searched for cell clusters that exhibited the expression of canonical markers for two or more distinct cell types and a higher count of genes/UMI. These identified clusters were subsequently excluded from further analysis.
Cell-level proliferation analysis was performed using the Seurat function CellCycleScoring, which utilized a curated list of murine cell cycle genes. Subsequently, cells were categorized as 'cycling' or 'non-cycling' based on whether their S-phase score or G2M-score exceeded a threshold of 0.10 for the tumor compartment and immune compartment.
To identify modules of co-expressed genes, we employed the R package scWGCNA (https://github.com/smorabit/scWGCNA). Initially, we computed metacells, each comprising 100 cells (k=100), utilizing the construct_metacells function. For module identification, we utilized the blockwiseConsensusModules function with the following parameter settings: for tumor cells analysis we used softPower = 12, deepSplit = 2, and mergeCutHeight = 0.20, max_shared = 25, minModuleSize = 25, metacells_k = 40, nfeatures = 5,000 genes; for microglia analysis we used softPower = 12, deepSplit = 4, and mergeCutHeight = 0.20, max_shared = 25, minModuleSize = 50, metacells_k = 60, nfeatures = 10,000 genes; for MDMs/monocytes analysis we used softPower = 12, deepSplit = 4, and mergeCutHeight = 0.20, max_shared = 25, minModuleSize = 25, metacells_k = 50, nfeatures = 10,000 genes; and for T/NK cells analysis we used softPower = 12, deepSplit = 2, and mergeCutHeight = 0.20, max_shared = 25, minModuleSize = 25, metacells_k = 60, nfeatures = 5,000 genes. To capture module characteristics, indicating normalized average expression of genes within each WGCNA module, module scores were computed using the Seurat function ‘AddModuleScore’. For Trajectory analysis using RNA velocity we used the scVelo package (v0.3.2, Python 3.9.13) and follow there protocol. our single-cell data UMAP embedding, along with metadata information, was incorporated into the loom files to present the RNA velocity trajectory with associated meta information. The UMAP was generated using the scv.pl.velocity_embedding_stream function from scVelo.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain tumor

extract_protocol:
Tumors were dissected from the brain, minced into pieces < 1 mm3, and digested with an enzymatic mixture that includes papain (0.94 mg/ml, Worthington, LS003120), EDTA (0.18 mg/ml, Sigma, E6758), cysteine (0.18 mg/ml, Sigma, A8199), and DNase I (60 μg/ml, Roche, 11284932001) in 2 ml HBSS (Gibco, 14175-095). Tumor tissues were kept at 37°C for 15 minutes with occasional agitation. The digestion was terminated with the addition of 2 ml Ovomucoid (0.7 mg/ml, Worthington, LS003086). Following digestion, single cells were passed through a 70 μm cell strainer, centrifuged, and resuspended in 30% Percoll (GE Healthcare, 17-0891-01) solution containing 10% FBS (Hyclone SH30396.03). Cells were separated by centrifugation at 800g for 15 minutes at 4°C. The pellet was resuspended in RBC lysis buffer (BioLegend, 420301) for 1 min at 37°C before they were centrifuged at 450g for 5 min. The pellet was resuspend in PBS and immediately dilvered for GEM preparation.
Gel-Bead in Emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) and QuBit (ThermoFisher) analyses

value: brain tumor


title: Dox,rep1


title: HepG2, CLIP-seq, FUBP1 CLIP, siCtrl, rep3

description: Library name: CLIP_FUBP1CLIP_siCtrl_rep3

value: siCtrl


title: HepG2, CLIP-seq, FUBP1 CLIP, siFBL, rep1

description: Library name: CLIP_FUBP1CLIP_siFBL_rep1


title: 5709-TVA-B

description: 10x Genomics


title: HepG2, CLIP-seq, FUBP1 CLIP, siCtrl, rep2

description: Library name: CLIP_FUBP1CLIP_siCtrl_rep2


title: BV2_WT_LPS2-input

value: WT


title: Control,rep2


title: 5310-WT-B-p53

description: 10x Genomics


title: 5830-WT-NF1

description: 10x Genomics


title: BV2_WT_LPS3-input


title: HepG2, CLIP-seq, input, siFBL, rep3

description: Library name: CLIP_input_siFBL_rep3


title: Control,rep1


title: BV2_WT_LPS1-input


title: BV2_WT_LPS3-IP


title: 5179-WT-HF1

description: 10x Genomics


title: HepG2, CLIP-seq, input, siFBL, rep2

description: Library name: CLIP_input_siFBL_rep2


title: 3920-19

description: 10x Genomics


title: MES28 cells,NC-3

city: Nanjing

first: Hui

last: Huang

address: Longmian Avenue No.101

institute: Nanjing Medical University

description: Library name: Sample12

data_processing:
Raw sequencing data were filtered using SOAPnuke to remove reads containing adaptor contamination, reads with more than 0.1% unknown bases (N), and low-quality reads, defined as those where over 20% of bases have a quality score below 15. The filtered data were used as clean data.
Assembly: GRCh38
Supplementary files format and content: FPKM,TPM and raw count values for each Sample

extract_protocol:
Total RNA was extracted from GSCs preconditioned with 5 Gy irradiation and 72-hour culture using RNAiso Plus (Takara, 9109).
Total RNA was processed using mRNA enrichment with Oligo(dT) magnetic beads to isolate polyA-tailed mRNA. The RNA was fragmented using a fragmentation buffer, followed by reverse transcription with random N6 primers. cDNA was synthesized and converted into double-stranded DNA. The synthesized double-stranded DNA was end-polished, 5' phosphorylated, and 3' adenylated. A 'T' overhang adaptor was ligated to the 3' end. The ligation product was amplified by PCR using specific primers. The PCR product was denatured and circularized into single-stranded DNA using a bridging primer to obtain a circular single-stranded DNA library. The constructed library was quality checked and sequenced upon passing QC.

value: NC


title: MES28 cells,NC-1

description: Library name: Sample10


title: MES28 cells,NC-2

description: Library name: Sample11


title: HepG2, CLIP-seq, input, siFBL, rep1

description: Library name: CLIP_input_siFBL_rep1


title: 5783-TVA-B

description: 10x Genomics


title: MES28 cells,IR-2

description: Library name: Sample8

value: IR


title: 7484-EGFR

description: 10x Genomics


title: MES28 cells,IR-3

description: Library name: Sample9


title: BV2_WT_LPS1-IP


title: 6791-EGFR

description: 10x Genomics


title: HepG2, CLIP-seq, input, siCtrl, rep3

description: Library name: CLIP_input_siCtrl_rep3


title: MouseOvary2

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

description: 10x Genomics Chromium Single Cell Gene Expression data

data_processing:
The data was analyzed using the 10x Genomics Chromium Single Cell software suite (cellranger-6.0.1).
The demultiplexing and conversion of Illumina base call files (BCL) to raw FASTQ files was done using "cellranger mkfastq" with default parameters.
The sequencing reads were aligned to the mouse reference (refdata-gex-mm10-2020-A) and analyzed using "cellranger count".
Assembly: mm10
Supplementary files format and content: cellranger generated unfiltered feature-barcode matrix file.

source_name: Single cells obtained from aging mouse ovary

extract_protocol:
Single cells were obtained from enzymatic digestion of aging mouse ovary. Cell viability and concentration were measured by Countess II FL Automated Cell Counter (Life Technologies) targeting ≥90% cell viability. The cell emulsification is performed with the 10X Chromium Controller using the Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 (10X Genomics 1000092) and Chromium Chip B Single Cell Kit (10X Genomics 1000074).
The RT reaction to generate 10X barcoded single stranded cDNA, in the single cell containing GEMs, is performed using an Eppendorf MasterCycler Pro thermal cycler. Post GEM-RT Cleanup is conducted by breaking the GEMS with 10X Recovery Agent to separate the aqueous phase from the Recovery Agent and Partitioning oil. A cleanup of the sscDNA containing aqueous phase is completed using Dynabeads MyOne Silane beads (Life Technologies 37002D). The second strand cDNA amplification is performed using the cDNA Amplification Mix on the Eppendorf MasterCycler Pro. The 3’ gene expression library construction is initiated with fragmentation, end repair and A-tailing of the dscDNA followed by adapter ligation and a sample index PCR using the Illumina compatible indexed adapters in the Chromium i7 Multiplex kit (10X Genomics 120262). Validation of the single cell library is conducted using the Agilent Tapestation 4200 ScreenTape assay (Agilent 5067-5576).

value: Ovary


title: HepG2, CLIP-seq, input, siCtrl, rep2

description: Library name: CLIP_input_siCtrl_rep2


title: MouseOvary1


title: MES28 cells,IR-1

description: Library name: Sample7


title: 6739-EGFR

description: 10x Genomics


title: HepG2, CLIP-seq, input, siCtrl, rep1

description: Library name: CLIP_input_siCtrl_rep1


title: HepG2, CLIP-seq, FUBP1 CLIP, siCtrl, rep1

description: Library name: CLIP_FUBP1CLIP_siCtrl_rep1


title: GSC387 cells,NC-3

description: Library name: Sample6


title: MbovP202_3

city: Wuhan

first: Doukun

last: Lu

address: Huazhong Agricultural University

institute: National Key Laboratory of Agricultural Microbiology

description: Library name: Sample6

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.
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.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus
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: fa:https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/263/795/GCF_002263795.2_ARS-UCD1.3/GCF_002263795.2_ARS-UCD1.3_genomic.fna.gz
Supplementary files format and content: Tab-delimited text files includes RPKM values for each sample

organism: Bos taurus

source_name: Bovine peritoneal macrophages

growth_protocol: The BoMac and BoMacMbovP202 cells were grown in RPIM 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.

extract_protocol:
Cells RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions.
NEBNext® Ultra™ II RNA Library Prep Kit for Illumina

value: Bovine peritoneal macrophages

value: BoMacMbovP202 cells

value: Macrophage cells

value: stable monoclonal cell lines expressing MbovP202


title: GSC387 cells,NC-2

description: Library name: Sample5


title: HepG2, caRNA, Nm-mut-seq, Treat, rep3

description:
Library name: Nm-mut-seq-Treat3
caRNA.treat.mut.txt

data_processing:
*library strategy: Nm-mut-seq
The raw sequencing data were uploaded without adapter trimming. In analysis, reads were first trimmed by cutadapt with parameter "-m 20 -g GTTCAGAGTTCTACAGTCCGACGATC -a ATCACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", then duplicates were removed by bbmap/clumpify.sh, again trimmed by cutadapt with paramter "-m 20 -u -5". Samples were mapped with tophat2 with paramter "-g 4 -N 3 --read-edit-dist 3", and mutations were identified by JACUSA with parameter "call-1 -P FR-SECONDSTRAND -c 5" and further filtered for sequencing depth ≥ 10, mutated read depth ≥ 3 in all three replicates and mutation ratios > 3-fold of input mutation ratios, > 1.5-fold of background mutation ratios.
the processed data column header information is in the 'processed_data_readme.txt'
Assembly: hg38
Supplementary files format and content: txt file of JACUSA identified base number at each site

molecule: nuclear RNA

extract_protocol:
For purification of chromatin-associated RNA, 10 million HepG2 cells were washed in PBS and harvested at 500g for 3 mins. Cells were lysed by 200 μL cold NP-40 lysis buffer (10 mM Tris pH 7.5, 0.15% NP-40, 150 mM NaCl) and suspended by flicking the tube without pipetting. After lysing on ice for 5 mins, The lysate was layered over 200 μL cold sucrose cushion (10 mM Tris pH 7.5, 0.15% NP-40, 150 mM NaCl, 24% sucrose) and centrifuged at 15,000g for 10 mins at 4°C. The pellet was wash with PBS and suspended by 100 μL cold glycerol buffer (20 mM Tris pH 8.0, 75 mM NaCl, 0.5 mM EDTA, 50% Glycerol) by flicking the tube without pipetting, followed by mixing with 100 μL cold nuclei lysis buffer (10 mM HEPES pH 7.6, 7.5mM MgCl2, 0.2 mM EDTA, 300 mM NaCl, 1M Urea, 1% NP40) and vortexing at highest speed for 6 times of 10 sec each. The lysate was incubated on ice for 2 mins followed by centrifugation at 15,000 g for 10 mins at 4°C. The pellet was further washed with PBS and digested with TURBO DNase followed by proteinase K. RNA was purified by TRIzol.
rRNA was removed by RiboMinus™ Eukaryote System v2, and the residual RNA was cleaned up by RNA Clean & Concentrator™-5 (Zymo Research, R1014) with removal of short RNA < 200 nt. RNA was fragmented by RNA Fragmentation Reagent (Invitrogen, AM8740), end repaired and ligated with 3′ linker 5'rApp-NNNNNATCACGAGATCGGAAGAGCACACGTCT-3SpC3. The residual adapter was removed with 5'-deadenylase and RecJf, purified and ligated with 5′ SR adapter supplied in the NEBNext® Small RNA Library Prep Set. The ligated product was separated in halves and used to perform RT reaction with balanced (1 mM dNTP each, named Ctrl) or biased (2  μM dG/C/TTP and 1 mM dATP, named Treat), followed by RNaseH digetion and PCR amplification. Sequencing by Illumina NovaSeq X was conducted with single-end 100 bp.

value: Biased dNTP in RT step


title: Al_WT_2

city: Beijing

first: lei

last: zhang

address: Yuanmingyuan West Rd. No.2, Beijing, China

department: College of Horticulture

institute: China Agricultural University

data_processing:
NovaSeq 6000
fastx_toolkit_0.0.14/SeqPrep/Sickle were used for estimating sequencing quality to gain clean reads.
TopHat2 / HISAT2 were used to analysis the mapped data quality.
The mapped reads were spliced using StringTie or Cufflinks software
FPKM （Fragments Per Kilobases per Millionreads）values were used to show gene expression level.
Assembly: SL 3.0; https://solgenomics.net/organism/Solanum_lycopersicum/genome
Supplementary files format and content: xlsx file includes FPKM values for each Sample

organism: Solanum lycopersicum

source_name: root

extract_protocol: Total RNA was extracted from 20 days old wild-type tomato and slszp1 mutant plants treated with 60 μM Al solutions (pH 4.7). Three biological replicated samples were collected form each treatment and sequenced.

value: root

tag: age

value: 20 days after germination

value: wild type


title: BV2_WT_LPS2-IP


title: GSC387 cells,NC-1

description: Library name: Sample4


title: HepG2, caRNA, Nm-mut-seq, Treat, rep2

description:
Library name: Nm-mut-seq-Treat2
caRNA.treat.mut.txt


title: MbovP202_2

description: Library name: Sample5


title: Al_WT_1


title: MbovP202_1

description: Library name: Sample4


title: szp1_3Al

value: slszp1 mutant


title: HepG2, caRNA, Nm-mut-seq, Ctrl, rep3

description:
Library name: Nm-mut-seq-Ctrl3
caRNA.ctrl.mut.txt

value: Normal dNTP in RT step


title: GSC387 cells,IR-3

description: Library name: Sample3


title: Control_3

description: Library name: Sample3

value: BoMac cells

value: empty vector control


title: Control_2

description: Library name: Sample2


title: GSC387 cells,IR-2

description: Library name: Sample2


title: HepG2, caRNA, Nm-mut-seq, Ctrl, rep2

description:
Library name: Nm-mut-seq-Ctrl2
caRNA.ctrl.mut.txt


title: Control_1

description: Library name: Sample1


title: GSC387 cells,IR-1

description: Library name: Sample1


title: szp1_1Al


title: HepG2, caRNA, Nm-mut-seq, Ctrl, rep1

description:
Library name: Nm-mut-seq-Ctrl1
caRNA.ctrl.mut.txt


title: Control_Brain2

status: Public on Apr 19 2025

city: 武汉WuHan

first: 澄

last: 华

state: 湖北Hubei

institute: Wuhan University of Technology

description: Library name: Control_Brain2

data_processing:
SOAPnuke(v2.1.0); fastqc(v0.11.8)
The sequencing results were processed using the fastp software to remove low-quality and adapter-containing reads. The clean data were analyzed with FastQC and in-house software to calculate the number of sequencing reads, data yield, sequencing error rate, Q20 content, Q30 content, and GC content.
Assembly: Mouse mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Mouse Naive2

extract_protocol:
Total RNA was extracted from cortical tissues using TRIzol Reagent followed by purification with the RNeasy Mini Kit , including on-column DNase I digestion to remove genomic DNA. RNA purity was assessed by NanoDrop 2000 with A260/A280 = 1.9-2.1 and A260/A230 >1.8. RNA integrity (RIN ≥7) was confirmed using an Agilent 2100 Bioanalyzer RNA Nano Chip. Genomic DNA contamination was excluded by PCR amplification of GAPDH intronic regions.
After total RNA extraction, eukaryotic mRNA was enriched using Oligo(dT) magnetic beads. The mRNA was fragmented into short segments using fragmentation buffer. First-strand cDNA was synthesized from the mRNA template with random hexamer primers, followed by second-strand cDNA synthesis using buffer, dNTPs, RNase H, and DNA polymerase I. The double-stranded cDNA was purified with the QiaQuick PCR Purification Kit and eluted in EB buffer. End repair, poly(A) tailing, and sequencing adapter ligation were performed. Size selection was conducted via agarose gel electrophoresis. The libraries were amplified by PCR and sequenced on an Illumina HiSeq platform.

value: brain


title: Control_Brain1

description: Library name: Control_Brain1

source_name: Mouse Naive1


title: Control_Brain3

description: Library name: Control_Brain3

source_name: Mouse Naive3


title: EAE_Brain2

description: Library name: EAE_Brain2

source_name: Mouse EAE2


title: EAE_Brain1

description: Library name: EAE_Brain1

source_name: Mouse EAE1


title: Al_WT_3


title: EAE+Drug_Brain1

description: Library name: EAE+Drug_Brain1

source_name: Mouse Drug1

value: Au18(L-NIBC)14  treatment


title: HepG2, caRNA, Nm-mut-seq, Treat, rep1

description:
Library name: Nm-mut-seq-Treat1
caRNA.treat.mut.txt


title: RIBO_seq_PP2_rep3

city: WuHan

first: chenchao

last: yan

state: Hubei Province

address: Donghu Road, No. 115

institute: WuHan university

description: ribosome bound total RNA

data_processing:
Adapters were trimmed using Cutadapt (v1.18)
RIBO-seq reads aligning to mitochondrial, ribosomal RNA, and tRNA sequences were filtered using Bowtie (v1.2)
Next, mRNA-seq and RIBO-seq reads were aligned to the human genome (hg38) with STAR (v2.7.1a)
Raw reads were counted using FeatureCounts (v1.6.4)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw gene counts for each Sample
Library strategy: RIBO-seq

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: differentiated hESCs

tag: developmental stage

value: Late pancreatic progenitor

value: WT


title: RIBO_seq_PP2_rep2

description: ribosome bound total RNA


title: RIBO_seq_PP1_rep2

description: ribosome bound total RNA

value: Early pancreatic progenitor


title: RIBO_seq_PP2_rep1

description: ribosome bound total RNA


title: szp1_2Al


title: RIBO_seq_PP1_rep1

description: ribosome bound total RNA


title: RIBO_seq_DE_rep1

description: ribosome bound total RNA

value: Definitive endoderm


title: RIBO_seq_DE_rep2

description: ribosome bound total RNA


title: LPS/IFN-γ-primed BMDM of PKM2FL/FL mice 1

city: Guangzhou

last: Junli

state: Guangdong

address: Guangzhou, Jinan university

country: Singapore

institute: jinan university

description:
Library name: Sample 1
Bone marrow-derived macrphages of PKM2FL/FL mice were primed with LPS/IFN-γ for 16h and subjected to RNA-seq analysis

data_processing:
Assess data quality using FastQC(version=0.12.1 ), evaluating metrics such as base quality distribution, GC content, and sequence duplication rates.
Subsequently, use Trim-Galore(version=0.6.10) to remove sequencing adapters and low-quality bases, enhancing alignment accuracy.
Align the resulting clean reads to the reference genome using Hisat2(version=2.2.1).
After alignment, use Samtools(version=1.19.2) to organize the results, filter out low-quality alignments, and convert them into standardized BAM format files for downstream analysis.
Quantify gene expression using subread(version= 2.0.6), calculating expression levels based on the number of reads.
Assembly: mm10
Supplementary files format and content: Raw sequencing data in FASTQ.gz format, containing raw reads and quality scores.
Supplementary files format and content: Processed gene expression counts matrix in CSV format, generated after alignment and quantification.

source_name: Bone marrow

growth_protocol: 1%P/S and 10% FBS-containing DMEM

extract_protocol:
Centrifuge the femural and tibia to get the bone marrow of mice and then cultured in M-CSF containing DMEM for 7 day for BMDM differentiation
RNA library were prepared using SMARTER RNA-seq library Prep Kit  following manufacture's protocols

treatment_protocol: 10 ng/mL LPS plus 25 ng/mL IFN-γ for 16 h

value: Bone marrow

value: bone marrow-derived macrophages

value: LPS/IFN-γ


title: RNA_seq_PP2_rep3

description: rRNA depleted total RNA

data_processing:
Adapters were trimmed using Cutadapt (v1.18)
RIBO-seq reads aligning to mitochondrial, ribosomal RNA, and tRNA sequences were filtered using Bowtie (v1.2)
Next, mRNA-seq and RIBO-seq reads were aligned to the human genome (hg38) with STAR (v2.7.1a)
Raw reads were counted using FeatureCounts (v1.6.4)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw gene counts for each Sample


title: LPS/IFN-γ-primed BMDM of PKM2ΔMAC mice 2

description:
Library name: Sample 5
Bone marrow-derived macrphages of PKM2ΔMAC mice were primed with LPS/IFN-γ for 16h and subjected to RNA-seq analysis


title: LPS/IFN-γ-primed BMDM of PKM2FL/FL mice 3

description:
Library name: Sample 3
Bone marrow-derived macrphages of PKM2FL/FL mice were primed with LPS/IFN-γ for 16h and subjected to RNA-seq analysis


title: LPS/IFN-γ-primed BMDM of PKM2FL/FL mice 2

description:
Library name: Sample 2
Bone marrow-derived macrphages of PKM2FL/FL mice were primed with LPS/IFN-γ for 16h and subjected to RNA-seq analysis


title: LPS/IFN-γ-primed BMDM of PKM2ΔMAC mice 1

description:
Library name: Sample 4
Bone marrow-derived macrphages of PKM2ΔMAC mice were primed with LPS/IFN-γ for 16h and subjected to RNA-seq analysis


title: LPS/IFN-γ-primed BMDM of PKM2ΔMAC mice 3

description:
Library name: Sample 6
Bone marrow-derived macrphages of PKM2ΔMAC mice were primed with LPS/IFN-γ for 16h and subjected to RNA-seq analysis


title: EAE_Brain3

description: Library name: EAE_Brain3

source_name: Mouse EAE3


title: RNA_seq_PP2_rep1

description: rRNA depleted total RNA


title: MLL-AF9 Ube2n C87S-4OHT rep 2

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: KIFL-4OHT-2
AML oncogene MLL-AF9 is retorvirally transduced

data_processing:
FastQC (v0.11.2) was used to test read quality.
Paired-end reads were aligned against mm10 genome using HISAT (v2.0.5). Stranded (RF)
Gene counts were summarized using featureCounts (v1.5.2)
Assembly: mm10
Supplementary files format and content: iGEAK__rawCounts.tsv
Supplementary files format and content: Tab-delimted raw gene counts, sample info, and gene annotation matrices

source_name: bone marrow

growth_protocol: MLL-AF9 transduced murine BM cells were cultured in Iscove’s Modified Dulbecco’s Medium supplemented with 10% FBS and 1% penicillin/ streptomycin and 10ng/ml of each murine IL-3, human IL-6, and murine SCF.

extract_protocol:
The cells were collected, and RNA was extracted using ZYMO RESEARCH Quick-RNA Miniprep kit (#R1055).
After the confirmation of the RNA quality using Agilent 2100 Bioanalyzer, the libraries were prepared with polyA selection using the Truseq RNA Library Prep Kit, and the libraries were sequenced at an average depth of 30M paired-end 100bp nucleotide reads. After the quality of reads was examined using FastQC (v0.11.7, https://www.bioinformatics.babraham.ac.uk/projects/fastqc), paired-end reads were aligned against mouse mm10 genome (iGenome,https://support.illumina.com/sequencing/sequencing_software/igenome.html) using HISAT2 (v2.0.5,http://daehwankimlab.github.io/hisat2).

treatment_protocol: MLL-AF9 transduced Ube2nWT or Ube2nC87S cells were treated in either 100% ethanol control or 50nM 4OHT for 48 hours in same density in triplicates.

value: bone marrow

value: Hematopoietic stem and progenitor cells

value: Ube2n C87S


title: MLL-AF9 Ube2n C87S-control rep 3

description:
Library name: KIFL-vehicle-3
AML oncogene MLL-AF9 is retorvirally transduced

value: control


title: MLL-AF9 Ube2n C87S-4OHT rep 1

description:
Library name: KIFL-4OHT-1
AML oncogene MLL-AF9 is retorvirally transduced


title: MLL-AF9 Ube2n C87S-4OHT rep 3

description:
Library name: KIFL-4OHT-3
AML oncogene MLL-AF9 is retorvirally transduced


title: RNA_seq_PP1_rep2

description: rRNA depleted total RNA


title: EAE+Drug_Brain3

description: Library name: EAE+Drug_Brain3

source_name: Mouse Drug3


title: MLL-AF9 Ube2n C87S-control rep 2

description:
Library name: KIFL-vehicle-2
AML oncogene MLL-AF9 is retorvirally transduced


title: MLL-AF9 Ube2n C87S-control rep 1

description:
Library name: KIFL-vehicle-1
AML oncogene MLL-AF9 is retorvirally transduced


title: EAE+Drug_Brain2

description: Library name: EAE+Drug_Brain2

source_name: Mouse Drug2


title: RNA_seq_PP1_rep1

description: rRNA depleted total RNA


title: MLL-AF9 Ube2n WT-4OHT rep 3

description:
Library name: WTFL-4OHT-3
AML oncogene MLL-AF9 is retorvirally transduced

value: Ube2n WT


title: MLL-AF9 Ube2n WT-4OHT rep 2

description:
Library name: WTFL-4OHT-2
AML oncogene MLL-AF9 is retorvirally transduced


title: RNA_seq_DE_rep1

description: rRNA depleted total RNA


title: RNA_seq_DE_rep2

description: rRNA depleted total RNA


title: MLL-AF9 Ube2n WT-4OHT rep 1

description:
Library name: WTFL-4OHT-1
AML oncogene MLL-AF9 is retorvirally transduced


title: mouse-cortex-cKO-E18.5-rep3

first: Jian

last: Zhang

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

data_processing:
The raw data was filtered with SOAPnuke (v1.6.5) , afterwards clean reads were obtained and stored in FASTQ format.
The clean data were mapped to the reference genome GRCm38/mm10 by HISAT (v2.2.1)
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.4.5). The expression level of genes was calculated by RSEM (v1.3.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: brain

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen,15596026)
Optimal Dual-mode mRNA Library Prep Kit

value: cKO


title: mouse-cortex-cKO-E18.5-rep1


title: MLL-AF9 Ube2n WT-control rep 3

description:
Library name: WTFL-vehicle-3
AML oncogene MLL-AF9 is retorvirally transduced


title: MLL-AF9 Ube2n WT-control rep 2

description:
Library name: WTFL-vehicle-2
AML oncogene MLL-AF9 is retorvirally transduced


title: RNA_seq_PP2_rep2

description: rRNA depleted total RNA


title: mouse-cortex-WT-E18.5-rep3


title: mouse-cortex-WT-RIP-Ybx1-rep1

data_processing:
The filtered reads were aligned to the mouse reference genome (GRCm38) using BWA mem (v 0.7.12).
Then the MACS2 (version 2.1.0) peak calling software was used to identify regions of IP enrichment over background, followed by the motif detected by Homer.
Peak related genes are then confirmed by PeakAnnotator. Different peak analysis was based on the fold enrichment of peaks of different experiments.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
To identify the target mRNAs of the m5C reader protein Ybx1, we carired out anti Ybx1 RNA Immunoprecipitation (RIP) followed by RNA-sequencencing. Using EZ-Magna RIP  RNA-Binding Protein Immunoprecipitation Kit (Millipore), RNA from wild type mouse cortex was pulled down by rabbit polyclonal anti-Ybx1 (abcam).
The library was constructed by Novogene Corporation. Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: antibody

value: rabbit polyclonal anti-Ybx1 (abcam)


title: IMR-90-12h&24h

first: 白

last: 可

address: Huangpu Avenue 601

department: College of Life Science and Technology

institute: Jinan University

description:
IMR-90 cells , incubated with or without 18β-GA (50 μM) and IL6 (50 ng/ml) for 12h,24h，there are four treatment groups at each time point.:con;GA;IL6;IL6andGA
Each time point consists of 8 replicates

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.
RNA-seq data processing was carried out with a custom script. Briefly, 10-base well position barcodes and 10-base UMI information from read1 fastq are first incorporated into read2 fastq as part of sequence ID. STAR (version 2.4.2a) was used for alignment to the reference human genome (hg38 from the University of California, Santa Cruz Genome Browser;) using the annotation data from iGenomes (Illumina).
Normalization and removal of batch effects of count value and significant expression differences were detected using Seruat (version 4.3.0). We used GSVA (version 2.40.1) for feature score calculation.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: embryonic lung

extract_protocol:
Cells at different incubation time points attached to wells were lysed directly in wells with lysis buffer. Incubate at 72 °C for 5 min. After the cells are fully lysed, the released mRNA was immediately reverse transcribed into cDNA. Mix the cell lysate and the RT mix containing the barcoded RT primers and incubated at 42 °C for 2 h to obtain cDNA.
A total amount of 50ng cDNA per sample was used as input material for the sample preparations. Sequencing libraries were generated using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme)

value: embryonic lung

value: cell lines

value: Fibroblasts


title: MLL-AF9 Ube2n WT-control rep 1

description:
Library name: WTFL-vehicle-1
AML oncogene MLL-AF9 is retorvirally transduced


title: mouse-cortex-WT-E18.5-rep1

value: brain


title: mouse-cortex-cKO-E13.5-rep3


title: mouse-cortex-WT-E18.5-rep2

value: WT


title: mouse-cortex-WT-RIP-Ybx1-rep2


title: mouse-cortex-WT-E13.5-rep2


title: N3

first: Tao

last: Gui

state: Jiangsu

address: NO.100 Shizi Street, Hongshan Road

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using TopHat (http://ccb.jhu.edu/software/tophat/index.shtml) software.
The mapping criteria of bowtie was as follows: sequencing reads should be uniquely matched to the genome allowing up to 2 mismatches, without insertions or deletions.
Then the region of gene were expanded following depths of sites and the operon was obtained.
In addition, the whole genome was split into multiple 15kbp windows that share 5kbp. New transcribed regions were defined as more than 2 consecutive windows without overlapped region of gene, where at least 2 reads mapped per window in the same orientation.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: normal endometrium

growth_protocol: N-eMSCs and A-eMSCs were isolated from human endometrial tissues and maintained in DMEM/F12 supplemented with 10% fetal bovine serum and 100 µg/ml streptomycin and 100 IU/ml penicillin at 37˚C in a 5% CO2 incubator.

extract_protocol:
RNA was harvested using Trizol Reagent (Invitrogen, Carlsbad, CA). At least 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit following manufacturer's protocols.

value: normal endometrium

value: Endometrial mesenchymal stem cells (eMSCs)

value: Normal eutopic endometrial mesenchymal stem cells (N-eMSCs)


title: mouse-cortex-WT-RIP-Input-rep1


title: mouse-cortex-WT-RIP-Input-rep2


title: mouse-cortex-WT-E13.5-rep3


title: mouse-cortex-cKO-E13.5-rep1


title: mouse-cortex-KD-E13.5-RNA-seq-rep3

value: KD


title: IMR-90-4h&8h

description:
IMR-90 cells , incubated with or without 18β-GA (50 μM) and IL6 (50 ng/ml) for 4h,8h，there are four treatment groups at each time point.:con;GA;IL6;IL6andGA
Each time point consists of 8 replicates


title: mouse-cortex-WT-E13.5-rep1


title: mouse-cortex-cKO-E13.5-rep2


title: N2


title: IMR-90-0h&2h

description:
IMR-90 cells , incubated with or without 18β-GA (50 μM) and IL6 (50 ng/ml) for 0h,2h，there are four treatment groups at each time point.:con;GA;IL6;IL6andGA
Each time point consists of 8 replicates,


title: mouse-cortex-cKO-E18.5-rep2


title: mouse-cortex-KD-E13.5-RNA-seq-rep2


title: N1


title: mouse-cortex-KD-E13.5-RNA-seq-rep1


title: RNA-Seq of human skin: sample 5

first: Sida

last: Chen

address: 622W 168th Street

institute: Columbia University

description: Library name: AK5

data_processing:
Raw sequencing data were processed using the 10x Genomics spaceranger-2.1.0 pipelines to generate FASTQ files Sequences were aligned to Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A reference to obtain gene expression counts using Cell or Space Ranger's default settings
Assembly: GRCh38
Supplementary files format and content: Loupe Browser file (cloupe.cloupe) contains Loupe Browser visualization and analysis file
Supplementary files format and content: filtered feature-barcode (filtered_feature_bc_matrix) matrices contains only tissue-associated barcodes. For Visium probe-based assays, genes not in the filtered probe set are removed from the filtered matrix by default.
Supplementary files format and content: web_summary.html contains experimental metrics and automated secondary analysis results.

organism: human skin metagenome

source_name: skin

extract_protocol:
RNA was extracted according to the Visium v2 CytAssist Spatial Gene Expression protocol
Library was constructed according to the Visium v2 CytAssist Spatial Gene Expression protocol

value: skin

value: skin cells


title: RNA-Seq of human skin: sample 4

description: Library name: AK4


title: A3

source_name: Eutopic endometrium

value: Eutopic endometrium

value: Adenomyotic eutopic endometrial mesenchymal stem cells (A-eMSCs)


title: mouse-cortex-WT-E13.5-RNA-seq-rep2


title: mouse-cortex-WT-E13.5-RNA-seq-rep1


title: A2


title: MM.1R-addDrug_2

type: RNA

city: Zhengzhou

first: zhen

address: Dongming Road

institute: Henan Cancer Hospital

description: Gene expression in MM.1R cells after the addition of the drug Epirubicin Hydrochloride

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip primeview human PathArrayTM.

scan_protocol: Affymetrix human GeneChip PrimeView and the outcomes were scanned by Affymetrix Scanner 3000.

data_processing:
The first step is to remove background noise such as non-specific binding, which helps to detect fold differences at lower abundances. The second step is to eliminate non-experimental errors between measurements, allowing measurements under experimental conditions to be compared. Third, this step involves PM correction, specifically adjusting the fluorescence values of PM probes. Finally, the fluorescence intensity values are aggregated from the probe level to the probe set level.
The statistical significance of raw data was completed by a Welch t-test with Benjamini-Hochberg FDR.  |Fold Change| ≥ 1.3 and FDR < 0.05 as significant.
The datasets were analyzed using affy package in R software.

label: 3’ IVT Biotin Label

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MM.1R cells were cultured in 1640 medium containing 10% fetal bovine serum (FBS) in cell incubator with 5% CO2 at 37°C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol:
MM.1R cells in logarithmic growth phase were infected by adding 20 μL 1×108 TU/mL shCtrl or added drug, culturing in 1640 medium with 10% FBS in a 6-well dish with 2×10^5 cells per well.
drug treatment: Epirubicin Hydrochloride for Injection, produced by HISUM Pharmaceutical Co., Ltd (China). The purpose of adding the drug was to inhibit the proliferation of MM.1R cells.

value: Epirubicin Hydrochloride


title: RNA-Seq of human skin: sample 1

description: Library name: AK1


title: A1


title: LOC4013123

status: Public on Apr 18 2025

first: Zhengyue

last: Cao

address: No. 27 Taiping Road, Haidian District

institute: State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Radiation Medicine

description: Library name: LOC4013123

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Homo sapiens.GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

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

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung Carcinoma

value: LOC401314 overexpression


title: LOC4013121

description: Library name: LOC4013121

value: LOC401312 overexpression


title: vector3

description: Library name: vector3

value: Vector


title: LOC4013122

description: Library name: LOC4013122

value: LOC401313 overexpression


title: MM.1R-addDrug_3


title: vector1

description: Library name: vector1


title: vector2

description: Library name: vector2


title: 293XT cells, dCas12f-ABE-ZFP, biol rep3

city: Xihu District, Hangzhou

first: Xing

last: Chang

state: Zhejiang

address: No.18 Shilongshan Road Cloud Town

department: School of Life Sciences

institute: Westlake University

description:
Library name: Sample 9
Column name in raw_counts_All_Samples.txt: Z7-rep3

data_processing:
Adapter sequences were removed from reads using Trim Galore (v.0.6.10).
Reads were aligned to hg38 by STAR (v.2.7.10b).
Aligned BAMs were tag added and sorted by SAMtools (v.1.18). Duplication was removed by the Picard MarkDuplicates module (v.3.11) and unmapped reads were filtered with SAMtools. BAMs were converted to mpileup format using SAM- tools.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: 293XT cells were cultured in DMEM with 10% FBS and 1% P/S, maintained at 37 °C in a 5% CO2 incubator.

extract_protocol:
RNA was extracted by HP Total RNA Kit (Omega Bio-tek, USA)
After purified from total RNA, mRNA was fragmented by divalent cations. After cDNA synthesis, adaptor with hairpin loop structure was added to 3’ ends of DNA fragments. Then fragments were purified and were amplified by PCR. The library was purified again and the quality was evaluated using Agilent 2100 Bioanalyzer. Index-coded samples were clustered on a cBot Cluster Generation System with TruSeq PE Cluster Kit v3-cBot-HS (Illumina, USA) following manufacturer’s instructions.

treatment_protocol: 293XT cells were transfected with dCasMINI-ABE or zmBE, together with a corresponding sgRNA targeting PLXNB2. Unedited cells were included as mock.

value: renal epithelioid cells

value: Transfected with dCas12f-ABE-ZFP and an sgRNA


title: 293XT cells, dCas12f-ABE-ZFP, biol rep2

description:
Library name: Sample 8
Column name in raw_counts_All_Samples.txt: Z7-rep2

value: WT


title: MM.1R-addDrug_1


title: 293XT cells, dCas12f-ABE-ZFP, biol rep1

description:
Library name: Sample 7
Column name in raw_counts_All_Samples.txt: Z7-rep1


title: 293XT cells, dCas12f-ABE, biol rep2

description:
Library name: Sample 5
Column name in raw_counts_All_Samples.txt: C7-rep2

value: Transfected with dCas12f-ABE and an sgRNA


title: 293XT cells, dCas12f-ABE, biol rep3

description:
Library name: Sample 6
Column name in raw_counts_All_Samples.txt: C7-rep3


title: 293XT cells, dCas12f-ABE, biol rep1

description:
Library name: Sample 4
Column name in raw_counts_All_Samples.txt: C7-rep1


title: MM.1R-shCtrl_2

description: Gene expression from data MM.1R cells infected with shCtrl

value: shCtrl


title: 293XT cells, mock, biol rep2

description:
Library name: Sample 2
Column name in raw_counts_All_Samples.txt: WT-rep2


title: 293XT cells, mock, biol rep1

description:
Library name: Sample 1
Column name in raw_counts_All_Samples.txt: WT-rep1


title: RNA-Seq of human skin: sample 3

description: Library name: AK3


title: MM.1R-shCtrl_1


title: RNA-Seq of human skin: sample 2

description: Library name: AK2


title: ZBTB7B_C10180A_ChIP_2

city: Toronto

first: Arttu

last: Jolma

state: Ontario

address: 160 College Street, Room 1350

department: Donnelly Centre

country: Canada

institute: University of Toronto

description:
Library name: ZBTB7B_C10180A_ChIP_2
ZBTB7B, Thpok  K360N mutant  ChIP, replicate2. Protein expressed as an exogenous eGFP fusion using input chromatin ERR14748649

library_source: genomic

data_processing:
Constant flank derived bases were removed with Cutadapt (using the adapters AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT).
Reads were mapped into human genome build hg38 with bowtie2 (options: --very-sensitive, --no-unal). The mapped trimmed reads were filtered using samtools (options: -q 30, -F 1548, version 1.20)
Peak calling was performed with MACS2 using sample-specific backgrounds that are available at accession PRJEB87201 and ERP170421
Assembly: hg38
Supplementary files format and content: Bigwig files are based on Bowtie2 mapping followed by MACS3 peak calling.
Supplementary files format and content: Narrowpeak files have been derived following the custom Peak calling was performed with MACS2

molecule: genomic DNA

growth_protocol: HEK293 cells were grown and maintained in high glucose DMEM supplemented with 10% FBS. TF cell lines were established via transfection and selection of transfected cells in 200ug/ml of hygromycin in growth media.

extract_protocol:
20 million cells were cross-linked with 1% formaldehyde and palletted in cold PBS. Cell pallettes were lysed in a 3 step lysis procedure and chromatin was sonicated at the last step. Sonicated chromatin ws immunoprecipitated using anti-eGFP IgG (Rabbit polycclonal, abcam290) coated magnetic beads. For "input" control samples (ERR accession provided in the description), 10ul of pre-IP sample were collected. After de-cross linking and DNA purification, both ChIP and Input samples were eluted in 60ul of elution buffer.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® kit and protocol

treatment_protocol: Established TF cell lines were treated with 1ug/ml of doxycycline 24 hours prior to cross linking. The TF expressions were confirmed using fluorescent microscopy and observation of GFP.

tag: protein


title: ZBTB7B_WT_ChIP_2

description:
Library name: ZBTB7B_WT_ChIP_2
ZBTB7B, Thpok WT ChIP, replicate2. Protein expressed as an exogenous eGFP fusion using input chromatin ERR14748645

tag: cell line


title: ZBTB7B_WT_ChIP_1

description:
Library name: ZBTB7B_WT_ChIP_1
ZBTB7B, Thpok WT ChIP, replicate1. Protein expressed as an exogenous eGFP fusion using input chromatin ERR14748644


title: MM.1R-shCtrl_3

tag: treatment


title: SYO5A2

city: Salt Lake City

first: Li

last: Li

state: Utah

address: 201 PRESIDENTS CIRCLE

institute: University of Utah

description: Library name: 23793X15

data_processing:
NovaSeq X Series 10B Reagent Kit_150x150 bp Sequencing (1250 M read-pairs/lane). The quality of raw paired-end sequence reads was assessed using FastQC. Low-quality (< 20) bases and adapter sequences were trimmed using Trimmomatic software (version 0.38) with the following parameters ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36. The trimmed reads were aligned to the reference genome (mouse genome version mm10 and human genome version hg38) using the HISAT2 RNA-seq aligner (version 2.1.0).
Assembly: hg38, mm10
Supplementary files format and content: txt, raw counts

extract_protocol:
RNA was extracted from samples using TRIzol (Ambion, Inc., Life Technologies, Carlsbad, CA, USA; 15596018), followed by chloroform to 16.67% by volume. RNA was then purified from the suspended lysate and eluted in water using a kit (Zymo Research, Irvine, CA, USA; RNA Clean & Concentrator R1018).
NEBNext Ultra II Directional RNA Library Prep with rRNA Depletion Kit (human,mouse,rat)

value: Human synovial sarcoma cells

value: SS18-SSX fusion

value: 5nM AZA


title: SYOC2

description: Library name: 23793X19

value: DMSO


title: SYOC1

description: Library name: 23793X18


title: HSSYD2

description: Library name: 23793X11

source_name: HS-SY-II

value: HS-SY-II

value: 500nM Decitabine


title: SYOD1

description: Library name: 23793X16


title: HSSYC2

description: Library name: 23793X13


title: HSSYD1

description: Library name: 23793X10


title: 293XT cells, mock, biol rep3

description:
Library name: Sample 3
Column name in raw_counts_All_Samples.txt: WT-rep3


title: HSSY5A2

description: Library name: 23793X9


title: DMSO, SS18SSX, R3

description: Library name: HSSY_DMSO_SS18SSX_R3

data_processing:
Raw reads were trimmed for quality and Illumina adapter sequences using trim-galore, then aligned to the human genome assembly T2T-CHM13 using Bowtie 2 (with “--very-sensitive” option). The spike-in data was analysed by aligning it to mouse genome mm10.
The reads from the spike-in were used to normalise the reads. PCR duplicates were removed using Rmdup tool. Down-sampling of reads for each sample was done based on the formula from Fursova et al. 2019: Down-sampling factor: α × 1⁄(N(ChIP SpikeIn)) ×(N(Input SpikeIn))⁄(N(Input HSSY) ) Where α is a coefficient applied for all the files normalized together so the value of the largest down-sampling factor equals 1
N(ChIP SpikeIn) is the total number of reads aligned to the dm6 in the IP sample; N(Input SpikeIn) is the total number of reads aligned to mm10 in the corresponding Input; N(Input HSSY) is the total number of reads aligned to the T2T genome in the corresponding Input sample.
The down-sampled replicates were then combined using the pileup function from MACS2 (q-value 0.05) and bigWig files were generated with ucsc-wigtobigwig tool. To visualize ChIP-Seq tracks, normalized bigWig files were generated with ucsc-wigtobigwig tool.
Assembly: T2T
Supplementary files format and content: bigWig

growth_protocol: DMEM, 10% fetal bovine serum and cultured at 37C at 5% CO2.

extract_protocol:
Nuclei were isolated and sonicated using a Covaris ultrasonicator (M220). Each sample was sheared for 30 minutes at following conditions: Duty Factor = 10%, Peak Power = 75.0, Cycles/Burst = 200. Sheared chromatin was incubated with 5µg anti-HA (rabbit CST) per sample overnight at 4°C on a rotator, followed by immunoprecipitation using magnetic beads. After washing, DNA was purified using the Qiagen PCR purification kit (#28104).
DNA fragments obtained after ChIP were quantified using Qubit dsDNA HS Assay Kit (Invitrogen). 5ng of DNA was used for library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S), SPRIselect beads (Beckman Coulter, #B23317) and NEBNext Multiplex Oligos for Illumina (NEB, Set 1 #E7335S) following NEB’s guidelines (NEB, E7645S). All the libraries were done without size selection with an input of 5ng. ChIP libraries were sequenced as 50bp Paired-End reads on NovaSeq 6K SP.

treatment_protocol: HSSY-II cells with endogenously HA-tagged SS18-SSX and RAG-MEF cells overexpressing HA-SS18-SSX were cultured, with the latter used for spike-in controls. After 12 days of 500nM decitabine or DMSO treatment in triplicate, 10 million HSSY-II were harvested and fixed using EGS (Thermo Fisher Scientific, #21565) and 1% formaldehyde (Thermo Fisher Scientific, #28908).

value: endogeneous tag of oncofusion HA-SS18-SSX


title: DMSO, SS18SSX, R1

description: Library name: HSSY_DMSO_SS18SSX_R1


title: HSSY5A1

description: Library name: 23793X8


title: ZBTB7B_C10180A_ChIP_1

description:
Library name: ZBTB7B_C10180A_ChIP_1
ZBTB7B, Thpok K360N mutant ChIP, replicate1. Protein expressed as an exogenous eGFP fusion using input chromatin ERR14748648


title: DMSO, SS18SSX, R2

description: Library name: HSSY_DMSO_SS18SSX_R2


title: mouse-cortex-WT-E13.5-RNA-seq-rep3

city: Shenzhen

tag: tissue

value: brain


title: DMSO, KDM2B, R3

description: Library name: HSSY_DMSO_KDM2B_R3

tag: genotype


title: DMSO, KDM2B, R1

description: Library name: HSSY_DMSO_KDM2B_R1


title: SYO5A1

description: Library name: 23793X14


title: HSSYC1

description: Library name: 23793X12


title: DMSO, input, R1

description: Library name: HSSY_DMSO_input_R1


title: DMSO, KDM2B, R2

description: Library name: HSSY_DMSO_KDM2B_R2


title: Decitabine, SS18SSX, R3

description: Library name: HSSY_Decitabine_SS18SSX_R3

value: 500 nM Decitabine


title: Decitabine, SS18SSX, R2

description: Library name: HSSY_Decitabine_SS18SSX_R2


title: Decitabine, SS18SSX, R1

description: Library name: HSSY_Decitabine_SS18SSX_R1


title: SYOD2

description: Library name: 23793X17


title: Decitabine, KDM2B, R3

description: Library name: HSSY_Decitabine_KDM2B_R3


title: Decitabine, KDM2B, R2

description: Library name: HSSY_Decitabine_KDM2B_R2


title: Decitabine, KDM2B, R1

description: Library name: HSSY_Decitabine_KDM2B_R1


title: Decitabine, input, R1

description: Library name: HSSY_Decitabine_input_R1


title: HSSY, sgDNMT1-b, R2

description: Library name: HSSY_sgDNMT1-b_R2

data_processing:
The quality of raw paired-end sequence reads was assessed using FastQC. Low-quality (< 20) bases and adapter sequences were trimmed using Trimmomatic software (version 0.38) with the following parameters ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36. The trimmed reads were aligned to the reference genome (mouse genome version mm10 and human genome version hg38) using the HISAT2 RNA-seq aligner (version 2.1.0).
Assembly: hg19
Supplementary files format and content: tsv. Contains FPKM and TPM

extract_protocol:
RNA was prepared using RNeasy mini kit (QIAGEN) according to the manufacturer’s protocoland including the DNaseI (QIAGEN) treatment.
RNA libraries were prepared at the DKFZ Genomics and Proteomics Core Facility and wassequenced on a NovaSeq 6K Paired-End 100 S4.

treatment_protocol: HSSY-II cells with endogenously HA-tagged SS18-SSX  were cultured with either 500nM decitabine or DMSO for 12 days

value: Cas9, DNMT1 knockout


title: HSSY, sgDNMT1-b, R1

description: Library name: HSSY_sgDNMT1-b_R1


title: Decitabine, input, R2

description: Library name: HSSY_Decitabine_input_R2


title: HSSY, sgDNMT1-a, R2

description: Library name: HSSY_sgDNMT1-a_R2


title: HSSY, sgDNMT1-a, R1

description: Library name: HSSY_sgDNMT1-a_R1


title: HSSY, sgCTRL, R2

description: Library name: HSSY_sgCTRL_R2

value: Cas9, safe guide


title: HSSY, sgCTRL, R1

description: Library name: HSSY_sgCTRL_R1


title: HSSY, Decitabine, R1

description: Library name: HSSY_Decitabine_R1


title: HSSY, DMSO, R1

description: Library name: HSSY_DMSO_R1


title: Hindbrain DIV17

city: Geneva

first: Denis

last: Jabaudon

address: Rue Michel-Servet 1

institute: University of Geneva

description: Library name: H17

data_processing:
Read were mapped and counted with cellranger 6.1.1
Count matrix were processed with Seurat package using SCTransform
Assembly: hg38
Supplementary files format and content: RDS file contains Seurat object with expression matrices and metadata

source_name: hPSC differentiation

extract_protocol:
the cell suspension at a concentration of 2’000 cells/μl was encapsulated into Gel Emulsion Droplets using the Chromium Controller system (10x Genomics) targeting 10’000 cells for each sample.
3’ Gene Expression libraries were generated in accordance with the 10x Genomics Protocols (Chromium Single Cell 3' Reagent Kits, v3.1 Chemistry, Dual Index). Libraries were pooled at a ratio dependent on the 10x Genomics indication and loaded on the Novaseq6000 sequencer to achieve a minimum of 50’000 reads/cell for each library.

value: hPSC differentiation


title: Hindbrain DIV20

description: Library name: H20


title: DMSO, input, R3

description: Library name: HSSY_DMSO_input_R3


title: Neocortex DIV17

description: Library name: F17


title: HSSY, DMSO, R2

description: Library name: HSSY_DMSO_R2


title: HSSY, Decitabine, R2

description: Library name: HSSY_Decitabine_R2


title: Neocortex DIV20

description: Library name: F20


title: Neocortex DIV13

description: Library name: F13


title: Hindbrain DIV13

description: Library name: H13


title: Hindbrain DIV15

description: Library name: H15


title: Neocortex DIV10

description: Library name: F10


title: DMSO, input, R2

description: Library name: HSSY_DMSO_input_R2


title: Neocortex DIV15

description: Library name: F15


title: Hindbrain DIV5

description: Library name: H5


title: Decitabine, input, R3

description: Library name: HSSY_Decitabine_input_R3


title: COLO320DM shTOP2B END-seq

first: haiyun

last: gan

address: xueyuan lu 1068

institute: Shenzhen Institute of Advanced Technology

data_processing:
Sequence reads were mapped back to the human reference genome (hg38) using BWA-MEM (WGS) or Bowtie2 (END-seq) software. Only consistent pair-end reads were chosen for further analysis.
For END-seq, the sequence reads mapped to the Watson and Crick strands of the reference genome were separated by in-house Perl programs and then genome-wide reads coverage was calculated by BEDTools and in-house Perl  programs.
To calculate the genome-wide read coverage BEDTools and self-developed Perl programs was performed.
Bedtools was used to generate BigWig files and counting matrices in bins around peak summits, and bedGraphToBigWig was used for visualization.
Assembly: hg38
Supplementary files format and content: bigwig files were generated for Watson and Crick strand or merged, scores represent the normalization reads density.

growth_protocol: Both the human glioblastoma cell line U251 and the human embryonic kidney cell line 293T were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Procell, PM150210) containing 10% fetal bovine serum (FBS, Excell, FSP500), supplemented with 100 U ml-1 penicillin, 100 mg ml-1 streptomycin, and 2 mM L-glutamine, at 37 ℃ under 5% CO2. COLO320DM and COLO320HSR cells were maintained in RPMI-1640 (VivaCell, C3010-0500) with the same supplements as above. All cell lines tested negative for mycoplasma contamination.

extract_protocol:
For WGS, entirely digestion (2 hour) with proteinase K (0.5 mg/ml) and RNase A (0.2 mg/ml) in PBS at 65 ℃, genomic DNA was extracted from cells with phenol:chloroform:isoamyl alcohol (25:24:1, PH 7.8) and precipitated with ethanol. The genomic DNA was resuspended in TE buffer and sonicated (Covaris M220) in AFA milliTUBEs (Covaris. 520045) to obtain 200~500 bp fragments. Sonication parameters: PIP 50, duty factor 10%, cycles 200, processing time 170 s. Then, the DNA was purified using the DNA Clean & Concentrator™-5 (ZYMO, D4004) kit. For END-seq, plugs making, DSB end blunting, A-tailing, ligation of END-Seq adapter 1, DNA shearing and extractio and streptavidin capture of labeled DSB ends, blunting, and A-Tailing ligation of END-Seq adapter 2 were implemented in sequence.
The WGS libraries were prepared with the fragmented DNA (1 µg) using the VAHTS® Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607). The WGS libraries were sequenced for at least 50 G data with PE150 on NovaSeq 6000. The END-seq library PCR was performed using standard Illumina Nextera Dual Indexing primers. Samples were pooled and sequenced using paired-end (2×150 bp) sequencing on an Illumina Novaseq or HiSeq X Ten platform by Annoroad Gene Technology Co. Ltd.

value: DM


title: Neocortex DIV5

description: Library name: F5


title: COLO320DM ATMi END-seq

value: ATM inhibitor


title: COLO320DM shTOP1 END-seq


title: COLO320DM END-seq

value: WT


title: COLO320DM shLIG3 WGS


title: COLO320HSR WGS

value: HSR


title: COLO320HSR END-seq


title: U251ecDNA+ WGS

value: ecDNA+


title: COLO320DM shTOP2B WGS


title: U251ecDNA+ shTOP2B WGS


title: COLO320DM WGS


title: Hindbrain DIV10

description: Library name: H10