title: G-G_Case13_0W

description: Library name: G-G_Case13_0W


title: G-G_Case11_12W

status: Public on Sep 01 2025

type: SRA

city: Nagoya

first: Yoshifumi

last: Kanayama

address: 1 kawasumi, Mizuho-cho, Mizuho-ku

country: Japan

institute: Nagoya City University Graduate school of Medical Sciences

description: Library name: G-G_Case11_12W

library_source: transcriptomic

data_processing:
Fastq files were processed using an RNA-seq integrative pipeline, ikra (v2.0.1).
Assembly: GRCh38
Supplementary files format and content: CSV files include scaledTPM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: periheral blood

extract_protocol:
Total RNA extraction using Trizol reagent
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit, Nextera XT DNA Library Prep Kit.

treatment_protocol: Guselkumab 100 mg is given subcutaneously at Week 0 and again at Week 4, followed by a maintenance phase where 100 mg is administered subcutaneously every 8 weeks. Peripheral blood sampling was performed before treatment and at Weeks 4 and 12.

tag: tissue

value: periheral blood

tag: cell line

tag: cell type

value: Lymphocyte

tag: treatment

value: Guselkumab


title: G-G_Case12_0W

description: Library name: G-G_Case12_0W


title: G-G_Case12_12W

description: Library name: G-G_Case12_12W


title: mouse perfusion isolated hepatocyte,G0,snRNA-seq

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

description:
Library name: M_G0_perfusion_hepatocyte_Nuclei_001-184
Smart-seq3xpress

library_source: transcriptomic single cell

data_processing:
We used Trimmomatic (v0.39) to remove index, primer, and adapter sequences from the paired-end reads. The trimmed reads were then aligned to the Mus musculus reference genome (GRCm38/mm10) using Hisat2 (v2.1.0) with default parameters. For snRNA-seq, transcript quantification for both sets of nuclei was performed using featureCounts (v1.5.3) with the parameter -t transcript to comprehensively include intronic reads, ensuring robust detection of nuclear transcripts. Gene expression values were calculated as transcripts per 0.1 million (TP0.1M) and log-transformed. To prevent transcriptome perturbations by extremely highly expressed genes, the genes Apoa2, Alb, and Fabp1 were excluded from the total transcript calculations.
Please note that each processed data column header corresponds to the fastq file from which the data was generated from. The fastq files associated with each sample records and their computed md5 checksums are listed in the 'sample_to_processed_data_readme.txt'.
Assembly: mm10
Supplementary files format and content: Smart-seq3xpress output files: Comma-separated expression value matrix files

organism: Mus musculus

source_name: liver

extract_protocol:
Mouse hepatocytes isolation was performed as previously reported. Mice were anesthetized by intraperitoneal injection of 2,2,2-tribromoethanol and then perfused through the inferior vena cava with 10 mL of pre-warmed (37°C) phosphate-buffered saline (PBS) containing 1 mM EGTA. The portal vein was cut at the start of perfusion to allow blood clearance. The liver was then perfused and digested with 10 mL of pre-warmed 1 mg/mL collagenase IV (Sigma-Aldrich, C5138) in RPMI 1640 medium (Gibco, 21870076). The digested liver tissue was collected into PBS and filtered through a 70 μm cell strainer. The cell suspension was centrifuged at 50 × g for 2 minutes at 4°C, and the cell pellets were resuspended in RPMI 1640 medium supplemented with 1% fetal bovine serum (FBS). To enrich for viable hepatocytes, Percoll (GE, 17-0891-09) diluted in PBS was added to the cell suspension, followed by centrifugation at 50 × g for 2 minutes. The cell pellets were then collected, washed once, and resuspended in RPMI 1640 medium supplemented with 1% FBS. Smart-seq3xpress scRNA-seq experiments was performed according to the published procedure(Hagemann-Jensen et al., 2022). Briefly, purified single hepatocytes were manually picked with a microcapillary pipette under a microscope and transferred into the 384-well PCR plates containing 0.3 μL of lysis buffer and 3 μL of silicone oil (Merck, 317667). The mRNA was reverse transcribed into cDNA using 0.2 μL of dispensed RT mix. The cDNA was then amplified using 0.6 μL PCR mix. The library of each cell was constructed separately using the TruePrep DNA Library Prep Kit (Vazyme, TD501)
Smart-seq3xpress scRNA-seq experiments was performed according to the published procedure(Hagemann-Jensen et al., 2022). Briefly, purified single hepatocytes were manually picked with a microcapillary pipette under a microscope and transferred into the 384-well PCR plates containing 0.3 μL of lysis buffer and 3 μL of silicone oil (Merck, 317667). The mRNA was reverse transcribed into cDNA using 0.2 μL of dispensed RT mix. The cDNA was then amplified using 0.6 μL PCR mix. The library of each cell was constructed separately using the TruePrep DNA Library Prep Kit (Vazyme, TD501)

value: liver

value: hepatocyte

tag: strain

tag: genotype

value: WT

tag: Stage

tag: Sex

value: female


title: G-G_Case11_4W

description: Library name: G-G_Case11_4W


title: mouse liver tissue isolated hepatocyte,G0,snRNA-seq

description:
Library name: M_G0_liver_tissue_hepatocyte_Nuclei_001-252
Smart-seq3xpress


title: mouse hepatocyte, P4L, Acss2HMKO, scRNA-seq

description:
Library name: M_P4L_Acss2_HMKO_001-336
Smart-seq3xpress

data_processing:
We used Trimmomatic (v0.39) to remove index, primer, and adapter sequences from the paired-end reads. The trimmed reads were then aligned to the Mus musculus reference genome (GRCm38/mm10) using Hisat2 (v2.1.0) with default parameters. FeatureCounts (v1.5.3) was employed with default settings to assign reads to genes for scRNA-seq. Gene expression values were calculated as transcripts per 0.1 million (TP0.1M) and log-transformed. To prevent transcriptome perturbations by extremely highly expressed genes, the genes Apoa2, Alb, and Fabp1 were excluded from the total transcript calculations.
Please note that each processed data column header corresponds to the fastq file from which the data was generated from. The fastq files associated with each sample records and their computed md5 checksums are listed in the 'sample_to_processed_data_readme.txt'.
Assembly: mm10
Supplementary files format and content: Smart-seq3xpress output files: Comma-separated expression value matrix files


title: mouse hepatocyte, P4L, WT, scRNA-seq

description:
Library name: M_P4L_Acss2_WT_001-498
Smart-seq3xpress


title: G-G_Case11_0W

description: Library name: G-G_Case11_0W


title: G-G_Case10_12W

description: Library name: G-G_Case10_12W


title: G-G_Case10_4W

description: Library name: G-G_Case10_4W


title: mouse perfusion isolated hepatocyte,P7-L,snRNA-seq

description:
Library name: M_P7L_perfusion_hepatocyte_Nuclei_001-298
Smart-seq3xpress


title: mouse hepatocyte, P7-L+d7-NL, scRNA-seq

description:
Library name: M_P7L+d7NL_001_409
Smart-seq3xpress


title: G-G_Case10_0W

description: Library name: G-G_Case10_0W


title: G-G_Case7_12W

description: Library name: G-G_Case7_12W


title: mouse hepatocyte, P7-L+d4-NL, scRNA-seq

description:
Library name: M_P7L+d4NL_001_425
Smart-seq3xpress


title: mouse liver tissue isolated hepatocyte,G14.5,snRNA-seq

description:
Library name: M_G14.5_liver_tissue_hepatocyte_Nuclei_001-224
Smart-seq3xpress


title: G-G_Case7_0W

description: Library name: G-G_Case7_0W


title: mouse hepatocyte, P7-L+d1-NL, scRNA-seq

description:
Library name: M_P7L+d1NL_001_472
Smart-seq3xpress


title: G-G_Case6_12W

description: Library name: G-G_Case6_12W


title: G-G_Case6_0W

description: Library name: G-G_Case6_0W


title: mouse hepatocyte, G0, WT, scRNA-seq

description:
Library name: M_G0_Il6st_WT_001-150
Smart-seq3xpress


title: G-G_Case6_4W

description: Library name: G-G_Case6_4W


title: mouse hepatocyte, G14.5, WT, scRNA-seq

description:
Library name: M_G14.5_Il6st_WT_001-422
Smart-seq3xpress


title: mouse hepatocyte, G0, Il6stHMKO, scRNA-seq

description:
Library name: M_G0_Il6st_HMKO_001-277
Smart-seq3xpress


title: G-G_Case5_12W

description: Library name: G-G_Case5_12W


title: G-G_Case5_4W

description: Library name: G-G_Case5_4W


title: mouse hepatocyte, P14-NL, scRNA-seq

description:
Library name: M_P14NL_001_297
Smart-seq3xpress


title: mouse hepatocyte, P7-NL, scRNA-seq

description:
Library name: M_P7NL_001_297
Smart-seq3xpress


title: mouse hepatocyte, P2-NL, scRNA-seq

description:
Library name: M_P2NL_001_310
Smart-seq3xpress


title: G-G_Case5_0W

description: Library name: G-G_Case5_0W


title: G-G_Case4_12W

description: Library name: G-G_Case4_12W


title: G-G_Case4_4W

description: Library name: G-G_Case4_4W


title: mouse hepatocyte, P1-NL, scRNA-seq

description:
Library name: M_P1NL_001_282
Smart-seq3xpress


title: G-G_Case4_0W

description: Library name: G-G_Case4_0W


title: mouse hepatocyte, P14-L, scRNA-seq

description:
Library name: M_P14L_001_332
Smart-seq3xpress


title: G-G_Case3_12W

description: Library name: G-G_Case3_12W


title: mouse hepatocyte, P7-L, scRNA-seq

description:
Library name: M_P7L_001_501
Smart-seq3xpress


title: G-G_Case7_4W

description: Library name: G-G_Case7_4W


title: G-G_Case3_4W

description: Library name: G-G_Case3_4W


title: G-G_Case3_0W

description: Library name: G-G_Case3_0W


title: G-G_Case2_12W

description: Library name: G-G_Case2_12W


title: mouse hepatocyte, G14.5, Il6stHMKO, scRNA-seq

description:
Library name: M_G14.5_Il6st_HMKO_001-602
Smart-seq3xpress


title: G-G_Case2_4W

description: Library name: G-G_Case2_4W


title: G-G_Case2_0W

description: Library name: G-G_Case2_0W


title: mouse hepatocyte, G18.5, scRNA-seq

description:
Library name: M_G18.5_001_333
Smart-seq3xpress


title: mouse hepatocyte, P4-L, scRNA-seq

description:
Library name: M_P4L_001_329
Smart-seq3xpress


title: mouse hepatocyte, P1-L, scRNA-seq

description:
Library name: M_P1L_001_395
Smart-seq3xpress


title: mouse hepatocyte, G14.5, scRNA-seq

description:
Library name: M_G14.5_001_348
Smart-seq3xpress


title: mouse hepatocyte, G16.5, scRNA-seq

description:
Library name: M_G16.5_001_324
Smart-seq3xpress


title: G-G_Case1_12W

description: Library name: G-G_Case1_12W


title: mouse hepatocyte, P2-L, scRNA-seq

description:
Library name: M_P2L_001_429
Smart-seq3xpress


title: G-G_Case1_4W

description: Library name: G-G_Case1_4W


title: mouse hepatocyte, P21-L, scRNA-seq

description:
Library name: M_P21L_001_313
Smart-seq3xpress


title: mouse hepatocyte, G10.5, scRNA-seq

description:
Library name: M_G10.5_001_366
Smart-seq3xpress


title: TGFb3

city: NEW HAVEN

first: Rongmo

last: Zhang

state: CT

address: 300 George street

country: USA

institute: Yale

description: Library name: TGFb3

data_processing:
PartekFlow platform
Strict paired-end compatibility was applied for gene expression quantification. Read counts were normalized using the trimmed mean of M-values method.
Assembly: human genome (Hg19)
Supplementary files format and content: normalized Counts per millions generated from raw fastq files

molecule: polyA RNA

source_name: aorta

growth_protocol: Primary Human Aortic smooth muscle cells (HASMCs) from two donors were purchased from Promocell (C-12533) and Lonza (CC-2571) respectively. The HASMCs were cultured in Smooth Muscle Cell Growth Medium-2 (SmGM-2, CC-3181, Lonza), supplemented with BulletKit (CC-4149, Lonza), 100 µg/mL penicillin and 100 µg/mL streptomycin. Cell culture dishes were maintained in a humidified 37 °C incubator with 5% CO2.

extract_protocol:
Extraction of total RNA was performed using the RNeasy Mini Kit (14734, Qiagen), according to the manufacturer’s instructions.
Novaseq sequencings with 25 million reads per sample were performed to detect the whole transcriptome. RNA-seq data was aligned to the reference human genome (Hg19) using STAR aligner on PartekFlow platform

treatment_protocol: For TGFβ treatments, 10 ng/ml TGFβ2 or PBS were added into the complete SmGM-2 growth media for 7 days with media changes every other day.

value: aorta

value: primary cells

value: aortic smooth muscle cells

value: 12 ng/mL TGFb2


title: mouse hepatocyte, P7-L+d2-NL, scRNA-seq

description:
Library name: M_P7L+d2NL_001_428
Smart-seq3xpress


title: mouse hepatocyte, G8.5, scRNA-seq

description:
Library name: M_G8.5_001_438
Smart-seq3xpress


title: TGFb2

description: Library name: TGFb2

value: 11 ng/mL TGFb2


title: mouse hepatocyte, G5.5, scRNA-seq

description:
Library name: M_G5.5_001_366
Smart-seq3xpress


title: Control3

description: Library name: Control3

value: PBS


title: mouse hepatocyte, G1.5, scRNA-seq

description:
Library name: M_G1.5_001-308
Smart-seq3xpress


title: mouse hepatocyte, G3.5, scRNA-seq

description:
Library name: M_G3.5_001_354
Smart-seq3xpress


title: Control2

description: Library name: Control2


title: Control1

description: Library name: Control1


title: mouse hepatocyte, G0, scRNA-seq

description:
Library name: M_G0_001-378
Smart-seq3xpress


title: mouse hepatocyte, P0, scRNA-seq

description:
Library name: M_P0_001_327
Smart-seq3xpress


title: C04

city: Atlanta

first: Edwin

last: Horwitz

state: Georgia

address: 1570 Haygood Drive NE

institute: Emory University

description:
Library name: C04
10x Genomics

data_processing:
Data were processed with Cell Ranger v7.0.1
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab delimited barcode and features, counts matrix

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (MNCs) were isolated from EDTA-anticoagulated whole blood for scRNAseq by layering over Ficoll and density centrifugation
10x Chromium libraries were prepared by the Emory Integrated Genomics Core using Chromium Next GEM Single Cell 3' kit v3.1. 10,000 cells were encapsulated and barcoded per sample.

value: Blood

value: Mononuclear cell

value: Healthy


title: G-G_Case1_0W

description: Library name: G-G_Case1_0W


title: C03

description:
Library name: C03
10x Genomics


title: EBs, METTL3-KO#2-dox+_rep2, RNA-seq

city: WuHan

first: Jie

last: Yang

state: Hubei Province

address: Donghu Road, No. 115

department: Medical Research Insitiute

institute: WuHan university

description:
Library name: Sample 18
RNA-seq

data_processing:
Illumina bcl2fastq v2.20software used for basecalling.
Sequenced reads were trimmed for adaptor sequence by trim_glore version 0.6.6, the clean data were mapped to GRCh38 whole genome using HISAT2 version 2.1.0.
Raw RNAseq reads were performed with FeatureCounts (V2.0.1) using gencode v29 human gene annotation.
Raw counts were normalized to Transcripts Per Million (TPM).
Gene expression difference was analyzed by Bioconductor R package DESeq2. m6Aseq peaks were analyzed by MeTPeak and differentially binding m6A peaks were identified using MeTDiff.
Assembly: GRCh38
Supplementary files format and content: TPM for RNAseq

source_name: cell line

growth_protocol: The human ESC line H9 was cultured with mTeSR1 (STEMCELL, cat#85850) on Matrigel-coated plates.

extract_protocol:
RNA was extracted with HiPure Total RNA Mini Kit (Magen, Cat#R4111-03).
mRNA libraries were prepared for sequencing using standard DNBSEQ-T7 protocols, whereas m6A-seq libraries were prepared following Illumina protocols.

treatment_protocol: METTL3 depletion was achieved by supplementing mTeSR1 medium with 2 μg/mL doxycycline for a 4-day culture period.

value: cell line

value: EBs derived from differentiated hESCs

value: dox+


title: EBs, METTL3-KO#2-dox+_rep1, RNA-seq

description:
Library name: Sample 17
RNA-seq


title: EBs, METTL3-KO#1-dox+_rep2, RNA-seq

description:
Library name: Sample 16
RNA-seq


title: C02

description:
Library name: C02
10x Genomics


title: EBs, METTL3-KO#1-dox+_rep1, RNA-seq

description:
Library name: Sample 15
RNA-seq


title: mouse hepatocyte, G12.5, scRNA-seq

description:
Library name: M_G12.5_001_442
Smart-seq3xpress


title: EBs, WT-DOX+_rep2, RNA-seq

description:
Library name: Sample 14
RNA-seq


title: B04

description:
Library name: B04
10x Genomics

value: Severe asthma


title: B03

description:
Library name: B03
10x Genomics


title: B05

description:
Library name: B05
10x Genomics


title: B02

description:
Library name: B02
10x Genomics


title: TGFb1

description: Library name: TGFb1

value: 10 ng/mL TGFb2


title: A06

description:
Library name: A06
10x Genomics

value: Mild asthma


title: EBs, WT-DOX+_rep1, RNA-seq

description:
Library name: Sample 13
RNA-seq

value: WT


title: EBs, METTL3-KO#2-dox-_rep1, RNA-seq

description:
Library name: Sample 11
RNA-seq

value: dox-


title: A05

description:
Library name: A05
10x Genomics


title: EBs, METTL3-KO#1-dox-_rep2, RNA-seq

description:
Library name: Sample 10
RNA-seq


title: A04

description:
Library name: A04
10x Genomics


title: EBs, METTL3-KO#1-dox-_rep1, RNA-seq

description:
Library name: Sample 9
RNA-seq


title: EBs, WT-DOX-_rep2, RNA-seq

description:
Library name: Sample 8
RNA-seq


title: EBs, WT-DOX-_rep1, RNA-seq

description:
Library name: Sample 7
RNA-seq


title: A02

description:
Library name: A02
10x Genomics


title: EBs, METTL3-KO#2-dox-_rep2, RNA-seq

description:
Library name: Sample 12
RNA-seq


title: A03

description:
Library name: A03
10x Genomics


title: A01

description:
Library name: A01
10x Genomics


title: EBs, HDAC2-KO#2-rep2, RNA-seq

description:
Library name: Sample 6
RNA-seq


title: EBs, HDAC2-KO#2-rep1, RNA-seq

description:
Library name: Sample 5
RNA-seq


title: EBs, HDAC2-KO#1-rep2, RNA-seq

description:
Library name: Sample 4
RNA-seq


title: Mononuclear cells, 15 days post gMSC infusion

description:
Library name: gMSC-D15-MNC
10x Genomics

value: gMSC post-infusion (15 days)


title: Mononuclear cells, 35 days post gMSC infusion

description:
Library name: gMSC-D35-MNC
10x Genomics

value: gMSC post-infusion (35 days)


title: EBs, HDAC2-KO#1-rep1, RNA-seq

description:
Library name: Sample 3
RNA-seq


title: EBs, WT-rep2, RNA-seq

description:
Library name: Sample 2
RNA-seq


title: hESCs, METTL3-KO#1-dox+, H3K27ac_ChIP-seq

description:
Library name: Sample 55
ChIP-seq

library_source: genomic

data_processing:
Illumina bcl2fastq v2.20software used for basecalling.
Sequenced reads were trimmed for adaptor sequence by trim_glore version 0.6.6, the clean data were mapped to GRCh38 whole genome using HISAT2 version 2.1.0.
Raw RNAseq reads were performed with FeatureCounts (V2.0.1) using gencode v29 human gene annotation.
Raw counts were normalized to Transcripts Per Million (TPM).
Gene expression difference was analyzed by Bioconductor R package DESeq2. m6Aseq peaks were analyzed by MeTPeak and differentially binding m6A peaks were identified using MeTDiff.
Assembly: GRCh38
Supplementary files format and content: TPM for RNAseq
Supplementary files format and content: bigwig files for m6A-seq
Supplementary files format and content: bigwig files for CUT&Tag
Supplementary files format and content: bigwig files for ChIPseq

molecule: genomic DNA

value: hESCs


title: hESCs, METTL3-KO#2-dox+, H3K27ac_ChIP-seq

description:
Library name: Sample 56
ChIP-seq


title: hESCs, METTL3-KO#2-dox-, H3K27ac_ChIP-seq

description:
Library name: Sample 54
ChIP-seq


title: hESCs, HDAC2-KO#2, polysome, RNA-seq

description:
Library name: Sample 42
polysome bound RNA, RNA-seq
H9_HDAC2-KO_RNA_polysome_tpm.csv
C99-P


title: hESCs, METTL3-KO#1-dox-, H3K27ac_ChIP-seq

description:
Library name: Sample 53
ChIP-seq


title: hESCs, HDAC2-KO#1, polysome, RNA-seq

description:
Library name: Sample 41
polysome bound RNA, RNA-seq
H9_HDAC2-KO_RNA_polysome_tpm.csv
C90-P


title: hESCs, WT-rep2, polysome, RNA-seq

description:
Library name: Sample 40
polysome bound RNA, RNA-seq
H9_HDAC2-KO_RNA_polysome_tpm.csv
H9-2-P


title: EBs, WT-rep1, RNA-seq

description:
Library name: Sample 1
RNA-seq


title: hESCs, METTL3-KO#2-dox+, HDAC2_ChIP-seq

description:
Library name: Sample 52
ChIP-seq


title: hESCs, METTL3-KO#1-dox+ HDAC2_ChIP-seq

description:
Library name: Sample 51
ChIP-seq


title: hESCs, HDAC2-KO#2, 4h, RNA-seq

description:
Library name: Sample 38
Actinomycin D treatment, RNA-seq
H9_HDAC2-KO_RNA_stability_tpm.csv
B-4-1


title: Mononuclear cells, pre-infusion

description:
Library name: gMSC-MNC-Pre
10x Genomics

value: Pre-infusion


title: hESCs, METTL3-KO#2-dox-, HDAC2_ChIP-seq

description:
Library name: Sample 50
ChIP-seq


title: hESCs, METTL3-KO#1-dox-, HDAC2_ChIP-seq

description:
Library name: Sample 49
ChIP-seq


title: hESCs, METTL3-KO#2-dox-, ChIP-seq (Input)

description:
Library name: Sample 48
ChIP-seq


title: hESCs, HDAC2-KO#2, 2h, RNA-seq

description:
Library name: Sample 36
Actinomycin D treatment, RNA-seq
H9_HDAC2-KO_RNA_stability_tpm.csv
B-2-1


title: hESCs, HDAC2-KO#1, 2h, RNA-seq

description:
Library name: Sample 35
Actinomycin D treatment, RNA-seq
H9_HDAC2-KO_RNA_stability_tpm.csv
A-2-3


title: hESCs, METTL3-KO#1-dox-, ChIP-seq (Input)

description:
Library name: Sample 47
ChIP-seq


title: hESCs, HDAC2-KO#2, METTL3_CUT&tag

description:
Library name: Sample 46
CUT&Tag

data_processing:
Illumina bcl2fastq v2.20software used for basecalling.
Sequenced reads were trimmed for adaptor sequence by trim_glore version 0.6.6, the clean data were mapped to GRCh38 whole genome using HISAT2 version 2.1.0.
Raw RNAseq reads were performed with FeatureCounts (V2.0.1) using gencode v29 human gene annotation.
Raw counts were normalized to Transcripts Per Million (TPM).
Gene expression difference was analyzed by Bioconductor R package DESeq2. m6Aseq peaks were analyzed by MeTPeak and differentially binding m6A peaks were identified using MeTDiff.
Assembly: GRCh38
Supplementary files format and content: TPM for RNAseq
Supplementary files format and content: bigwig files for m6A-seq
Supplementary files format and content: bigwig files for CUT&Tag
Supplementary files format and content: bigwig files for ChIPseq
Library strategy: CUT&Tag


title: hESCs, HDAC2-KO#2, 0h, RNA-seq

description:
Library name: Sample 34
Actinomycin D treatment, RNA-seq
H9_HDAC2-KO_RNA_stability_tpm.csv
B-0-1


title: hESCs, HDAC2-KO#1, METTL3_CUT&tag

description:
Library name: Sample 45
CUT&Tag


title: hESCs, METTL3-KO#1-dox+, m6A, IP

description:
Library name: Sample 26
m6A-seq


title: hESCs, WT-rep1, 2h, RNA-seq

description:
Library name: Sample 29
Actinomycin D treatment, RNA-seq
H9_HDAC2-KO_RNA_stability_tpm.csv
H9-2-1


title: hESCs, WT-rep2, 2h, RNA-seq

description:
Library name: Sample 30
Actinomycin D treatment, RNA-seq
H9_HDAC2-KO_RNA_stability_tpm.csv
H9-2-2


title: hESCs, METTL3-KO#1-dox-, m6A, Input

description:
Library name: Sample 23
m6A-seq


title: hESCs, WT-rep1, 4h, RNA-seq

description:
Library name: Sample 31
Actinomycin D treatment, RNA-seq
H9_HDAC2-KO_RNA_stability_tpm.csv
H9-4-1


title: hESCs, HDAC2-KO#1, 0h, RNA-seq

description:
Library name: Sample 33
Actinomycin D treatment, RNA-seq
H9_HDAC2-KO_RNA_stability_tpm.csv
A-0-1


title: hESCs, WT-rep1, METTL3_CUT&tag

description:
Library name: Sample 43
CUT&Tag


title: hESCs, METTL3-KO#2-dox+_rep2, RNA-seq

description:
Library name: Sample 14
RNA-seq
H9_METTL3-KO_tpm.csv
5_13_M71_dox2


title: hESCs, METTL3-KO#2-dox+_rep1, RNA-seq

description:
Library name: Sample 13
RNA-seq
H9_METTL3-KO_tpm.csv
5_13_M71_dox1


title: hESCs, WT-rep1, 0h, RNA-seq

description:
Library name: Sample 27
Actinomycin D treatment, RNA-seq
H9_HDAC2-KO_RNA_stability_tpm.csv
H9-0-1


title: hESCs, WT-rep2, 4h, RNA-seq

description:
Library name: Sample 32
Actinomycin D treatment, RNA-seq
H9_HDAC2-KO_RNA_stability_tpm.csv
H9-4-2


title: hESCs, HDAC2-KO#2, m6A-seq, Input

description:
Library name: Sample 20
m6A-seq


title: hESCs, WT-rep2, METTL3_CUT&tag

description:
Library name: Sample 44
CUT&Tag


title: hESCs, METTL3-KO#2-dox-_rep2, RNA-seq

description:
Library name: Sample 10
RNA-seq
H9_METTL3-KO_tpm.csv
5_13_M71_WT2


title: hESCs, HDAC2-KO#2, m6A-seq, IP

description:
Library name: Sample 22
m6A-seq


title: hESCs, HDAC2-KO#1, 4h, RNA-seq

description:
Library name: Sample 37
Actinomycin D treatment, RNA-seq
H9_HDAC2-KO_RNA_stability_tpm.csv
A-4-1


title: hESCs, METTL3-KO#1-dox+_rep2, RNA-seq

description:
Library name: Sample 12
RNA-seq
H9_METTL3-KO_tpm.csv
5_13_A59_dox2


title: hESCs, HDAC2-KO#1, m6A-seq, IP

description:
Library name: Sample 21
m6A-seq


title: hESCs, WT-rep1, polysome, RNA-seq

description:
Library name: Sample 39
polysome bound RNA, RNA-seq
H9_HDAC2-KO_RNA_polysome_tpm.csv
H9-1-P


title: hESCs, METTL3-KO#2-dox-_rep1, RNA-seq

description:
Library name: Sample 9
RNA-seq
H9_METTL3-KO_tpm.csv
5_13_M71_WT1


title: hESCs, WT-rep2, m6A-seq, Input

description:
Library name: Sample 16
m6A-seq


title: hESCs, METTL3-KO#1-dox-, m6A, IP

description:
Library name: Sample 24
m6A-seq


title: hESCs, WT-rep1, m6A-seq, IP

description:
Library name: Sample 17
m6A-seq


title: hESCs, METTL3-KO#1-dox+_rep1, RNA-seq

description:
Library name: Sample 11
RNA-seq
H9_METTL3-KO_tpm.csv
5_13_A59_dox1


title: hESCs, WT-rep2, m6A-seq, IP

description:
Library name: Sample 18
m6A-seq


title: hESCs, HDAC2-KO#1, m6A-seq, Input

description:
Library name: Sample 19
m6A-seq


title: hESCs, METTL3-KO#1-dox+, m6A, Input

description:
Library name: Sample 25
m6A-seq


title: hESCs, WT-rep2, 0h, RNA-seq

description:
Library name: Sample 28
Actinomycin D treatment, RNA-seq
H9_HDAC2-KO_RNA_stability_tpm.csv
H9-0-2


title: root nodule, WT_10dpi_rep3

first: Yufang

last: Tian

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Sequence raw reads were filtered by OAPnuke. Align clean reads to genome sequences HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) using Bowtie2 v2.2.5.
Assembly: Lotusjaponicus_Gifu_v1.3
Supplementary files format and content: tab-delimited text file include FPKM values for each samples

organism: Lotus japonicus

source_name: root nodule

growth_protocol: The L. japonicus seedlings were inoculated with rhizobia M. loti MAFF 303099 strain three days after transferring to vermiculite.

extract_protocol:
RNA samples was extracted from L. japonicus or soybean tissues using the RNeasy® Plant Mini Kit (QIAGEN, 74904)
DNBSEQ Transcriptome

value: root nodule

tag: time

value: 10 dpi


title: hESCs, HDAC2-KO#2-rep1, RNA-seq

description:
Library name: Sample 5
RNA-seq
H9_HDAC2-KO_tpm.csv
C99_1


title: hESCs, METTL3-KO#1-dox-_rep1, RNA-seq

description:
Library name: Sample 7
RNA-seq
H9_METTL3-KO_tpm.csv
5_13_A59_WT1


title: hESCs, HDAC2-KO#1-rep2, RNA-seq

description:
Library name: Sample 4
RNA-seq
H9_HDAC2-KO_tpm.csv
C90_2


title: MCF7, siFOXA1, rep2

city: San Juan

first: Hector

last: Franco

state: Puerto Rico

address: 2nd Floor Centro Medico- Office #275

institute: University of Puerto Rico Comprehensive Cancer Center

description: Library name: siFOXA1_B

data_processing:
Reads mapped to the genome using BWA v.0.7.12
Only reads with less than 2 mismatches are kept, and PCR duplicates were removed
Aligned reads that were unmapped, not primary alignments, failed platform QC, or had MAPQ<30 were removed
Alignments were filtered to remove those found in the ENCODE hg38 blacklist v.2 (accession 14 June 2023)
MACS v.2.2.6 was used to pool replicates during peak-calling and determine fold-enrichment over a pooled input background sample
Assembly: hg38
Supplementary files format and content: Bigwig of blacklist-filtered ("no_blacklists*.bw") pooled-replicate fragment density across the genome, represented as fold-enrichment relative to a pooled input sample as background
Supplementary files format and content: Narrow peak file of blacklist-filtered ("no_blacklists*.narrowPeak") pooled-replicate pileup and fold-enrichment relative to a pooled input sample as background, as called by MACS

growth_protocol: MCF7 cell lines were maintained in DMEM (Gibco 11995065) + 10% FBS (SERADIGM 97068-085) + 1% penicillin/streptomycin (Corning MT3002CI)

extract_protocol:
Extraction performed by Active Motif
ChIP-seq for NR2C2 was performed by Active Motif using Abcam antibody 109301

treatment_protocol: MCF7 cells were either untreated (control) or treated with 40 nM siRNA targeting FOXA1 for 48 hours and then fixed with 11% formaldehyde following Active Motif’s Epigenetic Services ChIP Fixation Protocol

value: breast adenocarcinoma

value: NR2C2, Abcam ab109301

value: siRNA


title: hESCs, HDAC2-KO#2-rep2, RNA-seq

description:
Library name: Sample 6
RNA-seq
H9_HDAC2-KO_tpm.csv
C99_2


title: MCF7, siFOXA1, rep1

description: Library name: siFOXA1_A


title: MCF7, control, rep2

description: Library name: control_B


title: hESCs, METTL3-KO#1-dox-_rep2, RNA-seq

description:
Library name: Sample 8
RNA-seq
H9_METTL3-KO_tpm.csv
5_13_A59_WT2


title: hESCs, HDAC2-KO#1-rep1, RNA-seq

description:
Library name: Sample 3
RNA-seq
H9_HDAC2-KO_tpm.csv
C90_1


title: R661P-2_03

city: L'Hospitalet de Llobregat

first: Jacopo

last: Boni

state: Barcelona

address: Avinguda de la Granvia de l’Hospitalet, 199

department: Hereditary Cancer

country: Spain

institute: IDIBELL

description: Library name: ABA33337

data_processing:
Libraries were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files), which underwent quality control analysis using FastQC.
To avoid low-quality data negatively influencing downstream analysis, we trimmed the reads on the 3′-end and only used the first 51 bp from the 5′-end of each read for further analysis.
Assembly: bwa.hsapiens.hs37d5
Supplementary files format and content: Table with all samples’ log CPM counts per gene

source_name: HOG

extract_protocol:
RNA samples were collected in triplicates using the RNeasy kit (QIAGEN) and integrity was evaluated using RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent).
Libraries were generated using the TruSeq® Stranded mRNA LT Sample Prep Kit (Illumina Inc., Rev.E, October 2013).

value: HOG

value: Oligodendroglioma

value: FGFR1 R661P


title: MCF7, control, rep1

description: Library name: control_A


title: hESCs, WT-rep1, m6A-seq, Input

description:
Library name: Sample 15
m6A-seq


title: hESCs, WT-rep2, RNA-seq

description:
Library name: Sample 2
RNA-seq
H9_HDAC2-KO_tpm.csv
H9_2


title: R661P-1_03

description: Library name: ABA33334


title: R661P-1_01

description: Library name: ABA33332


title: MCF7, Input

description: Library name: Input_pooled


title: R661P-1_02

description: Library name: ABA33333


title: MFC7, NC 4

city: Wuhan

first: Zilun

last: RUAN

state: Hubei

address: Donghu Road, No. 115, Wuchang District

department: Department of Infectious Diseases, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University

institute: Wuhan University

data_processing:
FASTQ files were first trimmed using Trim_galore (v0.6.9) to remove sequencing adapters and low-quality reads (Q<15). Trimmed sequencing reads were aligned to the human Hg38 reference genome (GENCODE, GRCh37.p13) using STAR (v2.7.10a). SAM files were subsequently converted to BAM files, sorted, and indexed using samtools (v1.15). BAM files were used to generate bigwig files using bamCoverage (part of the Deeptools package; v3.5.1). Read counting across genomic features was performed using featureCounts (part of the subread package; v2.0.1).
Assembly: hg38
Supplementary files format and content: txt file includes raw counts for each sample

source_name: Human breast tissue

extract_protocol:
RNA-seq experiment and high through-put sequencing were conducted by Seqhealth Technology Co., LTD (Wuhan, China). Approximately 1×107 cells were used for RNA extraction, and DNA digestion was carried out by DNaseI after RNA extraction. The quality of RNA was determined by examining A260/A280 and 1.5% agarose gel electrophoresis.
Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies). Total RNAs (2 mg) were used for stranded RNA sequencing library preparation, PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

value: Human breast tissue

value: Breast Epithelial cancer cells (ER Pos)

value: NC

value: CRISPR-Cas9 knockout, Control


title: MFC7, NC 3


title: MFC7, PIP5K1A knockout 3

value: PIP5K1A knockout

value: CRISPR-Cas9 knockout


title: MFC7, NC 2


title: MFC7, PIP5K1A knockout 2


title: K656E-R661P-2_03

description: Library name: ABA33331

value: FGFR1 K656E R661P


title: R661P-2_01

description: Library name: ABA33335


title: hESCs, WT-rep1, RNA-seq

description:
Library name: Sample 1
RNA-seq
H9_HDAC2-KO_tpm.csv
H9_1

value: hESCs

value: WT


title: R661P-2_02

description: Library name: ABA33336


title: K656E-R661P-2_02

description: Library name: ABA33330


title: K656E-R661P-2_01

description: Library name: ABA33329


title: MFC7, NCKAP1 knockout 3

value: NCKAP1 knockout


title: MFC7, NCKAP1 knockout 2


title: MFC7, CYFIP1 knockout 3

value: CYFIP1 knockout


title: MFC7, NCKAP1 knockout 1


title: K656E-2_01

description: Library name: ABA33326

value: FGFR1 K656E


title: K656E-2_02

description: Library name: ABA33327


title: MFC7, CYFIP1 knockout 1


title: MFC7, PIP5K1A knockout 1


title: K656E-R661P-1_02

description: Library name: ABA33324


title: K656E-R661P-1_03

description: Library name: ABA33325


title: K656E-1_01

description: Library name: ABA33320


title: Parental_xen, bio rep 1

city: Lexington

first: Yekaterina

last: Zaytseva

state: KY

address: 760 Press ave

department: Toxicology and Cancer Biology

institute: University of Kentucky

data_processing:
BGI used DNBSEQ platform, averagely generating about 4.43G Gb bases per sample. The average mapping ratio with reference genome is 91.97%, the average mapping ratio with gene is 75.21%; 18826 genes were identified
Data fitering
HISAT was used to align the clean reads to the reference genome; Bowtie2 was used to align the clean reads to the reference genes
Assembly: Homo sapiens: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: Processed gene expression data file is in xls format and contains the following contents: st_gene_id, gene_id, gene_symbol, FPKM, TPM, read count for each sample, and the average of FPKM, TPM, read count within each group
Supplementary files format and content: Processed RNA expression data file is in xls format and contains the following contents: st_rna_id, rna_id, gene_id, FPKM, TPM, read count for each sample, and the average of FPKM, TPM, read count within each group

growth_protocol: PT130  (Parental and PLX8394 resistant) cells were maintained in DMEM supplementaed with 10% Fetal Bovine Serum (FBS) and antibiotic in humidified atmosphere with 5% CO2 at 37C. Xenografts were established with PT130 parental and PLX8394 resistant cells and differences in growth was assessed. Tumors were collected, weighted, and a small part of the tumor was used for RNA extraction.

extract_protocol:
RNA was collected using RNeasy mini plus kit (Qiagen)
the library construction protocal follows the BGISEQ-500 (DNBSEQ-G50)  library construction steps

treatment_protocol: Resistant cells were treated with 1uM PLX8394 everytime cells were split or media was changed.

value: Colorectal Cancer Cells

value: BRAFV600E, KRAS, FGFR


title: Resistant_xen, bio rep 1


title: P2_xen2, bio rep 2


title: K656E-1_03

description: Library name: ABA33322

value: HOG


title: R1_xen1, bio rep 1


title: K656E-2_03

description: Library name: ABA33328

value: Oligodendroglioma


title: K656E-1_02

description: Library name: ABA33321


title: R2_4m, bio rep 2


title: R1_4m, bio rep 1


title: N546K-R661P-2_01

description: Library name: ABA33317

value: FGFR1 N546K R661P


title: R2_xen2, bio rep 2


title: N546K-R661P-2_03

description: Library name: ABA33319


title: N546K-R661P-2_02

description: Library name: ABA33318


title: P2_4m,  bio rep 2


title: P1_4m, bio rep 1


title: MFC7, CYFIP1 knockout 2

value: Human breast tissue


title: N546K-2_03

description: Library name: ABA33316

value: FGFR1 N546K


title: K656E-R661P-1_01

description: Library name: ABA33323


title: N546K-2_01

description: Library name: ABA33314


title: N546K-2_02

description: Library name: ABA33315


title: N546K-R661P-1_03

description: Library name: ABA33313


title: N546K-R661P-1_02

description: Library name: ABA33312


title: R_2m, bio rep 1


title: P_2m, bio rep 1


title: P1_xen1, bio rep 1


title: N546K-R661P-1_01

description: Library name: ABA33311


title: N546K-1_03

description: Library name: ABA33309


title: KO_ACC_2

city: Shenzhen

first: Xidan

last: Zhou

state: Guangdong

address: No. 1068 Xueyuan Avenue, Shenzhen University Town

institute: Chinese Academy of Sciences Shenzhen Institutes of Advanced Technology

description: Library name: sample 5

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Ensembl 112
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: anterior cingulate cortex (ACC)

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

value: anterior cingulate cortex (ACC)

value: KO


title: KO_ACC_3

description: Library name: sample 6


title: N546K-1_02

description: Library name: ABA33308


title: N546K-1_01

description: Library name: ABA33307


title: WT_ACC_3

description: Library name: sample 3


title: Parental_03

description: Library name: ABA33303

value: FGFR1 WT


title: KO_ACC_1

description: Library name: sample 4


title: Parental_02

description: Library name: ABA33302


title: WT_ACC_2

description: Library name: sample 2


title: Parental_01

description: Library name: ABA33301


title: Sample_WT3_ACC_IP

description: Library name: sample 18

data_processing:
Raw data of fastq format were first processed using fastp software (v 0.20.1). Clean data were obtained for downstream analyses by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. The ribosomal RNAs were removed using SortMeRNA software (v 2.1). After ribosomal RNA removing, the clean reads were mapped to the genome using hisat2 (v 2.1.0). IGV software was used to visualize called peaks from RIP-seq samples. Peak calling and differential peaks analysis were both performed using R package exomePeak2 (v 1.4.0). Called peaks were then annotated using BEDTools (v 2.29.2). HOMER (v 4.11.1) was used to find de novo and known motif. Then StringTie (v 1.3.3b) was used to perform expression level for all mRNAs. Differential expression analysis was performed using R package DESeq (v 1.38.0). q value < 0.05 and fold change ≥ 1.5 was set as the threshold for the identification of significantly differential peaks.
Assembly: Ensembl 112
Supplementary files format and content: WT_IPVSWT_input_peak.xlsx contained YTHDF1-bound site information.

extract_protocol:
tissues were homogenized with polysome lysis buffer (100 mM KCl, 5 mM MgCl2, 10 mM HEPES (pH 7.2), 0.5% NP40, 1 mM DTT, supplemented with RNase inhibitors and protease inhibitors), and incubated on ice for 5 minutes. After centrifugation at 15,000 g for 15 minutes at 4 ℃, 40μL of supernatant was collected for RNA extraction as input sample and another 40uL was collected for Western blotting analysis. The remaining supernatant was incubated with YTHDF1 antibody-coupled protein A/G beads at 4 °C for 4 h on a rotator. The beads were then washed with ice-cold NT2 buffer (50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1 mM MgCl2 and 0.05% NP-40). TRIzol was added to input and IP samples to extract total RNA. RNA quality control was measured on a Qubit.
Sample libraries were prepared with SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio, 63488). Libraries were sequenced on a NoveSeq 6000 (Illumina).


title: Xenograft D458 tumor No RT_161

city: Aurora

first: Bethany

last: Veo

state: CO

department: Pediatrics-Heme/Onc

institute: University of Colorado Anschutz Medical Campus

description:
Library name: 161
10x Genomics

data_processing:
Data was processed using nf-core/scrnaseq v2.4.0 (doi: 10.5281/zenodo.3568187) of the nf-core collection of workflows44, utilizing reproducible software environments from the Bioconda45 and Biocontainers46 projects
Assembly: GRCh38 2020
Supplementary files format and content: gz

source_name: brain

growth_protocol: D458 tumor cells were cultured in Dulbecco’s modified eagle’s medium (DMEM) supplemented with 10% FBS (Sigma-Aldrich), 1 mM sodium pyruvate (Gibco), 1× penicillin/streptomycin solution (Cellgro), and with 1× L-glutamine (Cellgro). Cells were collected and a suspension of 20,000 cells/3uL was made in DMEM. Cells were injected in the cerebellum of nude mice.

extract_protocol:
D458 xenograft tumors were harvested from the cerebellum of mice. Tumors were chopped with razor blades and dissociated in RPMI media. Live cell suspensions were flow sorted based on green fluorescent protein (GFP) expression on a MoFlo XDP-Flex (Beckman Coulter) and 2,000/mL GFP+ cells were submitted to the University of Colorado Genomics core for scRNA sequencing with the Chromium X. N=6
10x Genomics Library preparation protocol

treatment_protocol: Mice were irradiated at 0.5 Gy/ Day for 5 days. Tumors were allowed to grow until endpoint, and mice were euthanized.

value: brain

value: medulloblastoma

value: NT


title: Sample_RIP_seq_2_IP

description: Library name: sample 16

value: WT


title: Xenograft D458 tumor No RT_160

description:
Library name: 160
10x Genomics


title: Sample_WT1_ACC_Input

description: Library name: sample 13


title: Sample_RIP_seq_2_Input

description: Library name: sample 15


title: Xenograft D458 tumor +RT_60

description:
Library name: 60
10x Genomics

value: Radiation 2.5Gy


title: Xenograft D458 tumor +RT_57

description:
Library name: 57
10x Genomics


title: Sample_WT1_ACC_IP

description: Library name: sample 14


title: Xenograft D458 tumor +RT_59

description:
Library name: 59
10x Genomics


title: Xenograft D458 tumor +RT_56

description:
Library name: 56
10x Genomics


title: WT3_ACC_IP

description: Library name: sample 12

data_processing:
Base calling software: BCL convert
Data filter: fastp(0.19.4)，remove adapters, repeat sequences and low quality sequences
reads alignment : HISAT2(2.0.4)
Peak calling diffpeak : R package: exomePeak (1.5.0)
Peak annotation : ANNOVAR
Transcript assembly and quantification : StringTie (2.1.2)
Differential Expression Analysis :R package: edgeR(4.1)
Motif: HOMER(4.10)
Assembly: GRCH38
Supplementary files format and content: WT_IPVSWT_input_peak.xlsx contained methylation site information of m6A

extract_protocol:
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.
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(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol


title: 2_1433X_ATAC4

description: Library name: 2_1433X_ATAC4

data_processing:
The feature-barcode matrix was generated using cellranger-arc (10x Genomics, v2.0.2), aligning the sequenced reads to the human reference genome (10x Cell Ranger reference GRCh38 2020-A-2.0.0) followed by standard procedure using Seurat R package (v4.4.0). Cells with fewer than 200 genes detected were filtered from the scMultiome dataset. Low-quality cells with mapped reads in the mitochondrial genes >10% were removed. Doublets were identified using scDblFinder (v1.16.0). To address the issue of technical differences across samples, the cell count matrix was individually normalized by the total read count and log-transformed, and the top 2000 variable genes were selected for each sample using option “vst” in Seurat’s FindVariableFeatures function. Principal components analysis (PCA) was conducted on the scaled expression matrix. The top 15 principal components (PCs) were used to compute SharedNearestNeighbors (SNNs) in Seurat R package, and for UMAP embedding. Nucleosome signal was computed with Signac’s Nucleosome Signal function. Low-quality cells were removed from the scMultiome dataset based on the following criteria: < 2000 or > 100,000 fragments mapped to peak regions, nucleosome signal > 2, and TSS enrichment <1. MACS2 was employed to recall peaks for each sample. LSI was performed by Signac (v1.10.0). A joint neighbor graph that represents both gene expression and DNA accessibility measurements was done by FindMultiModalNeighbors function in Signac. UMAP was generated PCA dimensional reduction for gene expression and LSI indexing for DNA accessibility.
10x Cell Ranger reference GRCh38 2020-A-2.0.0
Seurat R package (v4.4.0).
Assembly: GRCh38 2020
Supplementary files format and content: gz, csv

extract_protocol:
Human MB samples were collected and viably banked at the time of surgery at Children’s Colorado with consent (COM-IRB 95-500) over a 10-year period. Samples were processed to obtain single nuclei for single-cell Multiome sequencing according to the 10X Genomics (Pleasanton, CA) protocol. Briefly, a rice grain size of cyropreserved tumor tissue was homogenized in chilled 0.1X Lysis Buffer with a pellet pestle.  Lysis buffer(10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2, 0.1%Tween-20, 0.1% NP-40, 0.01% Digitonin, 1% BSA, 1mM DTT, 1U/mL RNase Inhibitor) and Lysis Dilution buffer(10mM Tris-HCl(pH7.4), 10mM NaCl, 3mM MgCl2, 1%BSA, 1mM DTT, 1U/mL RNAse inhibitor).  Samples were incubated on ice for 5 min, mixed, then iced again 10 min. Samples are washed with 500mL of chilled wash buffer (10mM Tris-HCl(pH7.4), 10mM NaCl, 3mM MgCl2, 1%BSA, 0.1% Tween-20, 1mM DTT, 1U/mL RNase inhibitor) and passed through a 40mM strainer twice. The samples were centrifuged at 500 rcf for 5 min at 4°C. The nuclei pellet was then washed twice with 1 mL of chilled wash buffer. Nuclei were counted on the Countess II FL automated cell counter, and nuclei were diluted in nuclei buffer and submitted for sequencing. The Chromium Next GEM Chip J Single Cell Kit (10xGenomics), Dual Index Kit TT set A, and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle were used for sample preparation and library sequencing on the Chromium
Library construction followed the 10x genomics Chromium Next GEM Single Cell Multiome. ATAC + Gene Expression user guide. ATAC LibraryConstruction Action Item 10x PN Preparation & Handling Storage Equilibrate to Room Temperature Sample Index 3000427- −20°C Plate N, Set A Place on Ice SI-PCR Primer B 2000128 Vortex, centrifuge briefly. −20°C Amp Mix 2000047/2000103 Vortex, centrifuge briefly. −20°C KAPA Library Quantification Kit for Illumina® Prepare 80% Ethanol Prepare 10 ml for 8 reactions Step 5 ATAC Library Construction 5.1 Sample Index PCR Choose the appropriate sample index sets to ensure that no sample indices overlap in a multiplexed sequencing run. a. Prepare Sample Index PCR Mix. Sample Index PCR Mix Add reagents in the order listed PN 1X (μl) 4X +10% (μl) 8X +10% (μl) Amp Mix 2000047/2000103 50 220 440 SI- PCR Primer B 2000128 7.5 33 66 Total - 57.5 253 506 b. Transfer 40 µl pre-amplified sample from step 4.3p to a new tube strip (35 µl of the remaining sample volume will be used for cDNA Amplification and the rest can be stored at −20°C long term for generating additional libraries). Add 57.5 µl Sample Index PCR Mix to the sample. Pipette mix and centrifuge briefly. c. Add 2.5 µl of an individual Sample Index N, Set A to each well. Record assignment. Pipette mix and centrifuge briefly. d. Incubate in a thermal cycler with the following protocol. Lid Temperature Reaction Volume Run Time hh:mm:ss 105°C 100 µl ~30 min Step Temperature Time 1 98°C 00:00:45 2 98°C 00:00:20 3 67°C 00:00:30 4 72°C 00:00:20 Go to step 2, see table below for # cycles 5 72°C 00:01:00 6 4°C Hold Cycle Number Optimization Table Targeted Nuclei Recovery Total Cycles ≤2,000 9 2,001-6,000 8 STOP e. Store at 4°C for up to 72 h or proceed to the next step.  A Single Cell Gene Expression library is generated using a fixed proportion (10 µl, 25%) of the total cDNA (40 µl) obtained at step 6.2n. The complexity of this library will be comparable to one generated using a higher proportion (>25%) of the cDNA. The remaining proportion (30 µl, 75%) of the cDNA may be stored at 4°C for up to 72 h or at −20°C for longer-term storage (up to 4 weeks). Correlation: cDNA input & Library Complexity Library Complexity (Median genes/UMI’s) cDNA Volume (µl) (% total cDNA) Recommended 10 µl (25%) 20 µl (50%) 30 µl (75%) 40 µl (100%) Note that irrespective of the total cDNA yield (ng), which may vary based on cell type, targeted nuclei recovery etc., this protocol has been optimized for a broad range of input mass (ng), as shown in the example below. The total number of SI PCR cycles (step 7.5d) should be optimized based on carrying forward a fixed proportion (10 µl, 25%) of the total cDNA yield calculated during Post cDNA Amplification QC & Quantification (step 6.3). Example: Library Construction Input Mass & SI PCR Cycles Cell Type Targeted Nuclei Recovery Total cDNA Yield (ng) cDNA Input into Fragmentation SI PCR Cycle Number Volume (µl) Mass (ng) Low High RNA Content 150 ng 10 µl 37.5 ng 14 High 400 ng 10 µl 100 ng 13 Low RNA Content Low High 1 ng 10 µl 0.25 ng 16 100 ng 10 µl 25 ng 14 Click to TOC Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide • Rev F 60Step 7 7.1 Fragmentation, End Repair & A-tailing Click to TOC ! Gene Expression Library Construction a. Prepare a thermal cycler with the following incubation protocol. Lid Temperature Reaction Volume Run Time hh:mm:ss 65°C 50 µl ~35 min Step Temperature Time Pre-cool block Pre-cool block prior to preparing the Fragmentation Mix 4°C Hold Fragmentation 32°C 00:05:00 End Repair & A-tailing 65°C 00:30:00 Hold 4°C Hold b. Vortex Fragmentation Buffer. Verify there is no precipitate. c. Prepare Fragmentation Mix on ice. Pipette mix and centrifuge briefly. Fragmentation Mix Add reagents in the order listed PN 1X (μl) 4X + 10% (μl) 8X + 10% (μl) Fragmentation Buffer 2000091 5 22 44 Fragmentation Enzyme 2000090/ 2000104 10 44 88 Total - 15 66 132 d. Transfer ONLY 10 µl purified cDNA sample from cDNA Cleanup (step 6.2n) to a tube strip. Note that only 10 µl (25%) cDNA sample is sufficient for generating 3ʹ Gene Expression library. The remaining 30 µl (75%) cDNA sample can be stored at 4°C for up to 72 h or at −20°C for up to 4 weeks for generating additional Gene Expression libraries. e. Add 25 µl Buffer EB to each sample. f. Add 15 µl Fragmentation Mix to each sample. g. Pipette mix 15x (pipette set to 35 µl) on ice. Centrifuge briefly. h. Transfer into the pre-cooled thermal cycler (4°C) and press “SKIP” to initiate the

value: Grp 3 recurrent MB

value: patient tumor

value: mixed


title: WT3_ACC_Input

description: Library name: sample 11


title: WT1_ACC_IP

description: Library name: sample 8


title: 2_1433X_ATAC3

description: Library name: 2_1433X_ATAC3


title: WT2_ACC_Input

description: Library name: sample 9


title: WT_ACC_1

description: Library name: sample 1


title: WT1_ACC_Input

description: Library name: sample 7


title: 2_1433X_ATAC2

description: Library name: 2_1433X_ATAC2


title: WT2_ACC_IP

description: Library name: sample 10


title: 1_1433_ATAC4

description: Library name: 1_1433_ATAC4

value: Grp 3 MB


title: Sample_WT3_ACC_Input

description: Library name: sample 17


title: WW,striatum tissue,wild-type

city: Shiyan prefecture level city in Hubei

first: Jingjing

last: Weng

address: Shiyan City, Hubei Province

institute: Hubei University of Medicine

description: Library name: Sample 6

data_processing:
Raw reads were processed to generate gene expression profiles using an internal pipeline. Briefly, after filtering read one without poly T tails, cell barcode and UMI was extracted. Adapters and poly A tails were trimmed (fastp V1) before aligning read two to GRCh38 with ensemble version 92 gene annotation (fastp 2.5.3a and featureCounts 1.6.2). Reads with the same cell barcode, UMI and gene were grouped together to calculate the number of UMIs per gene per cell. The UMI count tables of each cellular barcode were used for further analysis. Cell type identification and clustering analysis using Seurat program). The Seurat program (http://satijalab.org/seurat/, R package,v.3.0.1) was applied for analysis of RNA-Sequencing data. UMI count tables were loaded into R using read.table function. Then we set the parameter resolution to 0.6 for FindClusters function to clustering analyses.
Assembly: mus musculus ensembl 92
Supplementary files format and content: matrix files

source_name: striatum

extract_protocol:
Mouse midbrain and striatum sites were taken, washed three times with pre-chilled Hanks Balanced Salt Solution (HBSS), and then cut into 2-3 mm blocks. After digestion, the tissue blocks were spin-digested with GEXSCOPE® Tissue Dissociation Solution (Singleron) at 37°C for 2.5 hours; they were then filtered through 70 μm and 40 μm sterile filters and centrifuged at 360 × g for 5 minutes. Subsequently, the supernatant was discarded, and the cell pellet was suspended in 600 µL of phosphate-buffered saline (PBS, HyClone). Samples were stained with Tissue Blue (Biorad, USA) and cell viability was estimated using a phase contrast light microscope (Nikon, Japan).Single-cell suspensions with 1×105 cells/mL in concentration in PBS (HyClone) were prepared.
Single-cell suspensions were then loaded onto microfluidic devices and scRNA-seq libraries were constructed according to Singleron GEXSCOPER protocol by GEXSCOPER Single-Cell RNA Library Kit(Singleron Biotechnologies) .Individual libraries were diluted to 4nM and pooled for sequencing. Pools were sequenced on Illumina HiSeq X with 150 bp paired end reads.

value: striatum

value: wild-type


title: 1_1433_ATAC2

description: Library name: 1_1433_ATAC2


title: AW,striatum tissue,A53T

description: Library name: Sample 5


title: 1_1433_ATAC3

description: Library name: 1_1433_ATAC3


title: 2_1433X_ATAC1

description: Library name: 2_1433X_ATAC1


title: WMM,midbrain tissue,wild-type

description: Library name: Sample 4

source_name: midbrain

value: midbrain


title: WMF,midbrain tissue,wild-type

description: Library name: Sample 3


title: AMM,midbrain tissue,A53T

description: Library name: Sample 2


title: Vibhakar_655_two_3

description: Library name: Vibhakar_655_two_3

value: Grp 4 recurrent MB


title: AMF,midbrain tissue,A53T

description: Library name: Sample 1


title: Vibhakar_655_two_2

description: Library name: Vibhakar_655_two_2


title: Vibhakar_655_two_1

description: Library name: Vibhakar_655_two_1


title: Vibhakar_655_4

description: Library name: Vibhakar_655_4

value: Grp 4 MB


title: heart, Mertk knockdown, TAC, 8week, rep3

city: shanghai

first: yikai

last: cui

address: xietu street 180

institute: fudan university

description:
Library name: KO3
Column name in1_genes_fpkm_expression.txt:count.K_3 and FPKM.K_3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: heart

value: heart

value: Mertk knockdown

value: transverse aortic constriction


title: heart, Mertk knockdown, TAC, 8week, rep1

description:
Library name: KO1
Column name in1_genes_fpkm_expression.txt:count.K_1 and FPKM.K_1


title: heart, Mertk knockdown, TAC, 8week, rep2

description:
Library name: KO2
Column name in1_genes_fpkm_expression.txt:count.K_2 and FPKM.K_2


title: Vibhakar_655_1

description: Library name: Vibhakar_655_1

value: brain


title: Vibhakar_655_3

description: Library name: Vibhakar_655_3


title: heart, wildtype, TAC, 8week, rep3

description:
Library name: WT3
Column name in1_genes_fpkm_expression.txt:count.W_3 and FPKM.W_3


title: heart, Mertk knockdown, TAC, 8week, rep4

description:
Library name: KO4
Column name in1_genes_fpkm_expression.txt:count.K_4 and FPKM.K_4


title: heart, wildtype, TAC, 8week, rep2

description:
Library name: WT2
Column name in1_genes_fpkm_expression.txt:count.W_2  and FPKM.W_2


title: heart, wildtype, TAC, 8week, rep4

description:
Library name: WT4
Column name in1_genes_fpkm_expression.txt:count.W_4 and FPKM.W_4


title: 1_1433_ATAC1

description: Library name: 1_1433_ATAC1


title: Vibhakar_1520_two_3

description: Library name: Vibhakar_1520_two_3


title: Colon, Mouse Myh11-CreERT2;WT, Rep 2

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 2720 S. Moody Avenue

institute: OREGON HEALTH & SCIENCE UNIVERSITY

description: Library name: TC-58630

data_processing:
Sequence reads were mapped to mm10 and hg38 using STAR_2.7.10b.
Read counts extraction and normalization were performed using RSEM_v1.3.1.
Assembly: GENCODE vM25, GENCODE 41
Supplementary files format and content: .txt (Raw counts)

source_name: Colon

extract_protocol:
Mouse tissues were harvested 54 days from the last tamoxifen injection. RNA was isolated from mouse and human samples using RNeasy Fibrous Tissue Mini Kit (QIAGEN, cat# 74104). 250ng of RNA was used to prepare sequencing libraries
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA library preparation kit and following manufacturers' protocol

treatment_protocol: Mice were injected daily with 70uL of 20mg/mL Tamoxifen for eight consecutive days

value: Colon

value: Cre-Control (Myh11-CreERT2;WT)

value: 20mg/mL Tamoxifen


title: MPMEC (Input)

city: Shanghai

first: Jian

address: 180 Fenglin Road

institute: Zhongshan hospital

description: Library name: MPMEC1_INPUT_1

data_processing:
For ChIP-seq, raw data were processed with fastp, aligned to the reference genome using BWA, and peaks were called with MACS2. motif analysis was performed with Homer, and peak annotation and functional enrichment (GO and KEGG) were carried out using ChIPseeker, GOseq, and KOBAS. Differential peak analysis was conducted with DiffBind or edgeR.
Assembly: mm39
Supplementary files format and content: For ChIP-seq, bw files were provided.

source_name: mouse pulmonary microcirculation endothelial cells (MPMEC)

extract_protocol:
For ChIP-seq, cells were fixed with 1% formaldehyde, and nuclear genomes were extracted and subjected to immunoprecipitation (IP) according to the instructions of the kit (CST #9003).
For ChIP-seq, library preparation was proceeded as follows: (1) The DNA fragments were end-repaired and A-tailed. (2) The DNA fragments with A tail were ligated with sequencing adaptors. (3) The final DNA library was obtained after size selection and PCR amplification. Libraries were analyzed for size distribution by Agilent 5400 system (Agilent, USA) and quantified by QPCR (1.5nM)


title: Vibhakar_655_two_4

description: Library name: Vibhakar_655_two_4


title: MPMEC, H3K14la (IP)

description: Library name: MPMEC1_IP_1

value: mouse pulmonary microcirculation endothelial cells (MPMEC)


title: Colon, Mouse Myh11-CreERT2;WT, Rep 1

description: Library name: TC-58629


title: Vibhakar_1520_two_4

description: Library name: Vibhakar_1520_two_4

value: Grp 3 recurrent MB


title: Vibhakar_1520_1

description: Library name: Vibhakar_1520_1

value: patient tumor


title: 2_1433X_GEX

description: Library name: 2_1433X_GEX

molecule: nuclear RNA

value: mixed


title: Colon, Mouse Mbnl1flox/flox;Mbnl2flox/null, Rep 3

description: Library name: TC-58628


title: Vibhakar_1520_4

description: Library name: Vibhakar_1520_4

value: Grp 3 MB


title: Colon, Mouse Mbnl1flox/flox;Mbnl2flox/null, Rep 2

description: Library name: TC-58627


title: Vibhakar_655_2

description: Library name: Vibhakar_655_2


title: Colon, Mouse Mbnl1flox/flox;Mbnl2flox/null, Rep 1

description: Library name: TC-58626


title: 1_1433_GEX

description: Library name: 1_1433_GEX


title: Colon, Mouse Myh11-CreERT2;Mbnl1flox/flox;Mbnl2flox/null, Rep 1

description: Library name: TC-58623

value: conditional double knockout (Myh11-CreERT2;Mbnl1flox/flox;Mbnl2flox/null)


title: Vibhakar_655_two_GEX

description: Library name: Vibhakar_655_two


title: Vibhakar_1520_two_2

description: Library name: Vibhakar_1520_two_2


title: Vibhakar_1520_GEX

description: Library name: Vibhakar_1520


title: Colon, Mouse Myh11-CreERT2;Mbnl1flox/flox;Mbnl2flox/null, Rep 3

description: Library name: TC-58625


title: Vibhakar_1520_3

description: Library name: Vibhakar_1520_3


title: Vibhakar_655_GEX

description: Library name: Vibhakar_655


title: Colon, Mouse Myh11-CreERT2;Mbnl1flox/flox;Mbnl2flox/null, Rep 2

description: Library name: TC-58624


title: Jejunum, Mouse Myh11-CreERT2;WT, Rep 2

description: Library name: TC-58621

source_name: Jejunum

value: Jejunum


title: PDX411_915_RT ATAC

description:
Library name: 915 ATAC
10 x genomics

data_processing:
These data were merged with the GEX single nuclei gene expression data from mouse PDX samples 914 – 918, which were derived from MED411. Data were log-normalized, and SCTransform (v2) was performed in Seurat using percent mitochondrial gene expression as the regression variable. Harmony integration47 was applied but deemed unnecessary, presumably because all samples originated from a single patient. Dataset integration was validated by comparing Uniform Manifold and Projection (UMAP) plots of the patient sample and the untreated PDX control. To generate the clustering analysis, a principal component analysis (PCA) with 30 dimensions was used to generate the UMAP projection. FindClusters was run in Seurat with resolution of 0.6. Differential expression analysis was performed on the SCT assay using FindAllMarkers with min.pct and logfc threshold set to 0.25.
10x Cell Ranger reference GRCh38 2020-A-2.0.0
Data integration, clustering analysis, and plotting were performed in Seurat (5.0.0), running under R version 4.3.1. Single-sample gene set enrichment analysis (ssGSEA, version 10.1.0) was performed using GenePattern (Broad Institute). Integration and analysis of scRNA-seq data: The gene expression matrix file for scRNA-Seq performed on MED411 patient samples was obtained from Gene Expression Omnibus archive GSE11992614. These data were merged with the GEX single nuclei gene expression data from mouse PDX samples 914 – 918, which were derived from MED411. Data were log-normalized, and SCTransform (v2) was performed in Seurat using percent mitochondrial gene expression as the regression variable.
Assembly: GRCh38 2020
Supplementary files format and content: gz

extract_protocol:
MED411 cell isolation from mouse xenograft was conducted with NeuroCultÔ Enzymatic Dissociation Kit (STEMCELL Technologies). Mouse cells were depleted from the single cell suspension with the Mouse Cell Depletion Kit on LS Columns (Miltenyi Biotec). Isolated human cells were then processed according to 10X Genomics nuclei isolation protocol for single-cell Multiome sequencing as described. Briefly, a rice grain size of cyropreserved tumor tissue was homogenized in chilled 0.1X Lysis Buffer with a pellet pestle.  Lysis buffer(10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2, 0.1%Tween-20, 0.1% NP-40, 0.01% Digitonin, 1% BSA, 1mM DTT, 1U/L RNase Inhibitor) and Lysis Dilution buffer(10mM Tris-HCl(pH7.4), 10mM NaCl, 3mM MgCl2, 1%BSA, 1mM DTT, 1U/L RNAse inhibitor).  Samples were incubated on ice for 5 min, mixed, then iced again 10 min. Samples are washed with 500L of chilled wash buffer (10mM Tris-HCl(pH7.4), 10mM NaCl, 3mM MgCl2, 1%BSA, 0.1% Tween-20, 1mM DTT, 1U/L RNase inhibitor) and passed through a 40M strainer twice. The samples were centrifuged at 500 rcf for 5 min at 4C. The nuclei pellet was then washed twice with 1 mL of chilled wash buffer. Nuclei were counted on the Countess II FL automated cell counter, and nuclei were diluted in nuclei buffer and submitted for sequencing.
Library construction followed the 10x genomics Chromium Next GEM Single Cell Multiome. ATAC + Gene Expression user guide. ATAC LibraryConstruction Action Item 10x PN Preparation & Handling Storage Equilibrate to Room Temperature Sample Index 3000427- −20°C Plate N, Set A Place on Ice SI-PCR Primer B 2000128 Vortex, centrifuge briefly. −20°C Amp Mix 2000047/2000103 Vortex, centrifuge briefly. −20°C KAPA Library Quantification Kit for Illumina® Prepare 80% Ethanol Prepare 10 ml for 8 reactions Step 5 ATAC Library Construction 5.1 Sample Index PCR Choose the appropriate sample index sets to ensure that no sample indices overlap in a multiplexed sequencing run. a. Prepare Sample Index PCR Mix. Sample Index PCR Mix Add reagents in the order listed PN 1X (μl) 4X +10% (μl) 8X +10% (μl) Amp Mix 2000047/2000103 50 220 440 SI- PCR Primer B 2000128 7.5 33 66 Total - 57.5 253 506 b. Transfer 40 µl pre-amplified sample from step 4.3p to a new tube strip (35 µl of the remaining sample volume will be used for cDNA Amplification and the rest can be stored at −20°C long term for generating additional libraries). Add 57.5 µl Sample Index PCR Mix to the sample. Pipette mix and centrifuge briefly. c. Add 2.5 µl of an individual Sample Index N, Set A to each well. Record assignment. Pipette mix and centrifuge briefly. d. Incubate in a thermal cycler with the following protocol. Lid Temperature Reaction Volume Run Time hh:mm:ss 105°C 100 µl ~30 min Step Temperature Time 1 98°C 00:00:45 2 98°C 00:00:20 3 67°C 00:00:30 4 72°C 00:00:20 Go to step 2, see table below for # cycles 5 72°C 00:01:00 6 4°C Hold Cycle Number Optimization Table Targeted Nuclei Recovery Total Cycles ≤2,000 9 2,001-6,000 8 STOP e. Store at 4°C for up to 72 h or proceed to the next step.  A Single Cell Gene Expression library is generated using a fixed proportion (10 µl, 25%) of the total cDNA (40 µl) obtained at step 6.2n. The complexity of this library will be comparable to one generated using a higher proportion (>25%) of the cDNA. The remaining proportion (30 µl, 75%) of the cDNA may be stored at 4°C for up to 72 h or at −20°C for longer-term storage (up to 4 weeks). Correlation: cDNA input & Library Complexity Library Complexity (Median genes/UMI’s) cDNA Volume (µl) (% total cDNA) Recommended 10 µl (25%) 20 µl (50%) 30 µl (75%) 40 µl (100%) Note that irrespective of the total cDNA yield (ng), which may vary based on cell type, targeted nuclei recovery etc., this protocol has been optimized for a broad range of input mass (ng), as shown in the example below. The total number of SI PCR cycles (step 7.5d) should be optimized based on carrying forward a fixed proportion (10 µl, 25%) of the total cDNA yield calculated during Post cDNA Amplification QC & Quantification (step 6.3). Example: Library Construction Input Mass & SI PCR Cycles Cell Type Targeted Nuclei Recovery Total cDNA Yield (ng) cDNA Input into Fragmentation SI PCR Cycle Number Volume (µl) Mass (ng) Low High RNA Content 150 ng 10 µl 37.5 ng 14 High 400 ng 10 µl 100 ng 13 Low RNA Content Low High 1 ng 10 µl 0.25 ng 16 100 ng 10 µl 25 ng 14 Click to TOC Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide • Rev F 60Step 7 7.1 Fragmentation, End Repair & A-tailing Click to TOC ! Gene Expression Library Construction a. Prepare a thermal cycler with the following incubation protocol. Lid Temperature Reaction Volume Run Time hh:mm:ss 65°C 50 µl ~35 min Step Temperature Time Pre-cool block Pre-cool block prior to preparing the Fragmentation Mix 4°C Hold Fragmentation 32°C 00:05:00 End Repair & A-tailing 65°C 00:30:00 Hold 4°C Hold b. Vortex Fragmentation Buffer. Verify there is no precipitate. c. Prepare Fragmentation Mix on ice. Pipette mix and centrifuge briefly. Fragmentation Mix Add reagents in the order listed PN 1X (μl) 4X + 10% (μl) 8X + 10% (μl) Fragmentation Buffer 2000091 5 22 44 Fragmentation Enzyme 2000090/ 2000104 10 44 88 Total - 15 66 132 d. Transfer ONLY 10 µl purified cDNA sample from cDNA Cleanup (step 6.2n) to a tube strip. Note that only 10 µl (25%) cDNA sample is sufficient for generating 3ʹ Gene Expression library. The remaining 30 µl (75%) cDNA sample can be stored at 4°C for up to 72 h or at −20°C for up to 4 weeks for generating additional Gene Expression libraries. e. Add 25 µl Buffer EB to each sample. f. Add 15 µl Fragmentation Mix to each sample. g. Pipette mix 15x (pipette set to 35 µl) on ice. Centrifuge briefly. h. Transfer into the pre-cooled thermal cycler (4°C) and press “SKIP” to initiate the

value: Medulloblastoma


title: Jejunum, Mouse Myh11-CreERT2;WT, Rep 1

description: Library name: TC-58620


title: Vibhakar_1520_two_1

description: Library name: Vibhakar_1520_two_1


title: PDX411_914_RT ATAC

description:
Library name: 914 ATAC
10 x genomics


title: Vibhakar_1520_two_GEX

description: Library name: Vibhakar_1520_two


title: Colon, Mouse Myh11-CreERT2;WT, Rep 3

description: Library name: TC-58631


title: Vibhakar_1520_2

description: Library name: Vibhakar_1520_2


title: Jejunum, Mouse Myh11-CreERT2;WT, Rep 3

description: Library name: TC-58622


title: PDX411_916_RT ATAC

description:
Library name: 916 ATAC
10 x genomics


title: Jejunum, Mouse Mbnl1flox/flox;Mbnl2flox/null, Rep 3

description: Library name: TC-58619


title: PDX411_918_NT ATAC

description:
Library name: 918 ATAC
10 x genomics

value: NT


title: Jejunum, Mouse Mbnl1flox/flox;Mbnl2flox/null, Rep 2

description: Library name: TC-58618


title: PDX411_915_RT

description:
Library name: 915 GEX
10 x genomics


title: Jejunum, Mouse Mbnl1flox/flox;Mbnl2flox/null, Rep 1

description: Library name: TC-58617


title: PDX411_916_RT

description:
Library name: 916 GEX
10 x genomics


title: Jejunun, Mouse Myh11-CreERT2;Mbnl1flox/flox;Mbnl2flox/null, Rep 2

description: Library name: TC-58615

value: conditional double knockout


title: Jejunun, Mouse Myh11-CreERT2;Mbnl1flox/flox;Mbnl2flox/null, Rep 3

description: Library name: TC-58616


title: PDX411_918_NT

description:
Library name: 918 GEX
10 x genomics


title: 458IR H3K27me3 GSK321_2

description:
Library name: irradiated_wtIDHi_2_H3k27me3
epicypher

data_processing:
Sequencing was performed on a Novaseq 6000. CUT&RUN-seq reads were aligned to the reference human genome hg38 using BOWTIE (v.2.3.4.1). Aligned reads were stripped of duplicate reads using Sambamba (v.0.6.8). Peaks were called using the program MACS (v2.1.2), with the narrow peak mode using matched input controls and a q-value of 0.00001. Peaks in the blacklisted genomic regions identified by the ENCODE consortium were excluded using bedtools. For downstream analysis and visualization, bamCoverage was used to generate bigwig files and density maps were produced using IGV tools. Group 3 MB enhancers were defined based on H3K27ac signals. Regions within 1kb of RefSeq TSS locations and peaks with strong H3K4me3 signals typical of active promoters were subtracted from these signals. Annotation and visualization of the peaks were conducted using ChIPseeker (v3.18). Differentially marked genes were calculated using DiffBind and DESeq2, based on the threshold of FDR < 0.05 and FC  ≥ 2.
Assembly: GRCh38 2020
Supplementary files format and content: bw, bed
Library strategy: CUT&RUN

growth_protocol: D425 (RRID:CVCL_1275; male) and D458 (RRID:CVCL_1161; male) cell lines were kindly provided by Dr. Darell D. Bigner (Duke University Medical Center, NC). Cells were cultured in Dulbecco’s modified eagle’s medium (DMEM) supplemented with 10% FBS (Sigma-Aldrich), 1 mM sodium pyruvate (Gibco), 1× penicillin/streptomycin solution (Cellgro), and with 1× L-glutamine (Cellgro). NHA cells were provided by Cynthia Hawkins (University of Toronto Hospital for Sick Children). MED411FH was originally harvested from a large cell anaplastic MB that was molecularly characterized as a Group 3 tumor. All cell lines were cultured at 37 °C with 95% air and 5% CO2.

extract_protocol:
5x105 cells were collected for analysis by CUT&RUN EpiCypher, CUTANA, CUT&RUN Kit Version 4 #14-1048) . Briefly, cells washed in wash buffer,  and resuspended in wah buffer plus activated beads.  The cells absorb the beads and are centrifuged and resuspended in antibody buffer. Antibody binds overnight at 4 degrees. Antibodies against, a-H3K4me3 and IgG controls were validated antibodies from EpiCypher. a-H3K27me3 (Cell Signaling technologies, #9733) and a-H3K27ac (Cell signaling technologies, #8173).
CUT&RUN library prep was performed with the NEBNextâUltraII DNA Library Prep Kit for Illuminaâ (NEB #E7645L) and NEBNext Multiplex Oligos for Illumina (NEB#E7350).

treatment_protocol: D458 and D458IR were exposed to 10mM 1DH305, or 1mM GSK321 for 48hrs

value: D458IR resistant

tag: cut&run antibody


title: 458IR H3K27me3 GSK321_1

description:
Library name: irradiated_wtIDHi_1_H3k27me3
epicypher


title: 458IR H3K27me3 IDH305_2

description:
Library name: irradiated_IDH305_2_H3k27me3
epicypher


title: 458IR H3K27me3

description:
Library name: irradiated_1_H3K27me3
epicypher

value: DMSO


title: 458IR H3K27me3 2

description:
Library name: irradiated_2_h3k27me3
epicypher


title: H3K27me3 2 458

description:
Library name: Control_2_H3K27me3
epicypher


title: Chronic_Colon_Metformin_rep1

city: Kobe

first: Kenji

last: Sugawara

state: Please Select

address: 7-5-1 Kusunoki-cho, Chuo-ku

institute: Kobe university graduate school of medicine

description:
Library name: Chronic_Colon_Metformin_rep1
Chronic_Colon_rawcount.txt

data_processing:
RNA-seq: Total RNA was extracted from mouse samples and used for stranded mRNA library preparation. Paired-end sequencing was performed on the NovaSeq 6000 platform. Raw reads were assessed with FastQC and trimmed using Trimmomatic to remove adapter sequences and low-quality bases. The resulting high-quality reads were aligned to the Mus musculus reference genome (mm10) using HISAT2, and transcript assembly was performed with StringTie. Gene-level raw read counts were subsequently generated using StringTie.
scRNA-seq: Cell Ranger was used to process raw FASTQ files. Reads were aligned to the Mus musculus reference genome (GRCm39, refdata-gex-GRCm39-2024-A, 10x Genomics).
Assembly: RNA-seq: mm10
Assembly: scRNA-seq: GRCm39
Supplementary files format and content: RNA-seq: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: scRNA-seq: Tag-separated values files and matrix files.

extract_protocol:
RNA-seq: Total RNA was extracted from intestinal tissue using the RNeasy Mini Kit (Qiagen), following the manufacturer’s instructions.
scRNA-seq: Mouse colon tissues were fixed with formaldehyde and dissociated using gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec). Tissue processing was performed following the protocol "Tissue Fixation & Dissociation for Chromium Fixed RNA Profiling" (CG000553 Rev.B, 10x Genomics).
RNA-seq: RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s instructions.
scRNA-seq: Single-cell libraries were prepared using the Chromium Fixed RNA Profiling kit (10x Genomics) following the manufacturer’s protocol (CG000527 Rev.D). Fixed cells were hybridized with probe sets, pooled, barcoded using Chromium X, and amplified with dual-indexed primers. Libraries were sequenced on an Illumina NovaSeq 6000.

value: male

value: Metformin

tag: batch


title: Chronic_Colon_Control_rep3

description:
Library name: Chronic_Colon_Control_rep3
Chronic_Colon_rawcount.txt

value: Colon

value: Control


title: 458IR H3K27ac GSK321_2

description:
Library name: irradiated_wtIDHi_2_H3K27ac
epicypher

value: brain


title: Chronic_Colon_Imeglimin_rep3

description:
Library name: Chronic_Colon_Imeglimin_rep3
Chronic_Colon_rawcount.txt

value: Imeglimin


title: Chronic_Colon_Imeglimin_rep1

description:
Library name: Chronic_Colon_Imeglimin_rep1
Chronic_Colon_rawcount.txt


title: H3K27me3 458

description:
Library name: Control_1_H3K27me3
epicypher


title: Chronic_Colon_Control_rep2

description:
Library name: Chronic_Colon_Control_rep2
Chronic_Colon_rawcount.txt


title: 458IR H3K27me3 IDH305_1

description:
Library name: irradiated_IDH305_1_H3K27me3
epicypher


title: Chronic_Colon_Metformin_rep2

description:
Library name: Chronic_Colon_Metformin_rep2
Chronic_Colon_rawcount.txt


title: Chronic_Colon_Control_sc

description: Library name: Chronic_Colon_Control_sc

value: Control/Metformin/Imeglimin


title: PDX411_914_RT

description:
Library name: 914 GEX
10 x genomics


title: 458IR H3K27ac GSK321_1

description:
Library name: irradiated_wtIDHi_1_H3K27ac
epicypher


title: heart, wildtype, TAC, 8week, rep1

description:
Library name: WT1
Column name in1_genes_fpkm_expression.txt: count.W_1 and FPKM.W_1

value: heart

value: WT

value: transverse aortic constriction


title: Chronic_Colon_Imeglimin_rep2

description:
Library name: Chronic_Colon_Imeglimin_rep2
Chronic_Colon_rawcount.txt


title: Chronic_DistalSI_Metformin_rep3

description:
Library name: Chronic_DistalSI_Metformin_rep3
Chronic_DistalSI_rawcount.txt


title: Jejunun, Mouse Myh11-CreERT2;Mbnl1flox/flox;Mbnl2flox/null, Rep 1

description: Library name: TC-58614

value: 20mg/mL Tamoxifen


title: 458IR H3K27ac 2 IDH305

description:
Library name: irradiated_IDH305_2_H3k27ac
epicypher


title: 458Ir H3K27ac IDH305

description:
Library name: irradiated_IDH305_1_H3K27ac
epicypher


title: Chronic_DistalSI_Metformin_rep1

description:
Library name: Chronic_DistalSI_Metformin_rep1
Chronic_DistalSI_rawcount.txt


title: 458IR H3K27ac 2

description:
Library name: irradiated_2_458IR_H3k27ac
epicypher


title: 458IR H3K27ac

description:
Library name: irradiated_1_458IR H3K27ac
epicypher


title: Chronic_DistalSI_Metformin_rep2

description:
Library name: Chronic_DistalSI_Metformin_rep2
Chronic_DistalSI_rawcount.txt


title: Chronic_Colon_Metformin_rep3

description:
Library name: Chronic_Colon_Metformin_rep3
Chronic_Colon_rawcount.txt


title: 458 H3K27ac 2

description:
Library name: Control_2_458_H3K27ac
epicypher


title: Chronic_DistalSI_Imeglimin_rep3

description:
Library name: Chronic_DistalSI_Imeglimin_rep3
Chronic_DistalSI_rawcount.txt


title: Chronic_DistalSI_Imeglimin_rep2

description:
Library name: Chronic_DistalSI_Imeglimin_rep2
Chronic_DistalSI_rawcount.txt


title: Chronic_DistalSI_Imeglimin_rep1

description:
Library name: Chronic_DistalSI_Imeglimin_rep1
Chronic_DistalSI_rawcount.txt


title: 458IR IDH305 H3K4me3 2

description:
Library name: irradiated_IDH305_2_H3K4me3
epicypher

value: H3K4me3 (epicypher, 13-0041K)


title: Chronic_DistalSI_Control_rep3

description:
Library name: Chronic_DistalSI_Control_rep3
Chronic_DistalSI_rawcount.txt


title: 458 H3K27ac

description:
Library name: Control_1_458 H3K27ac
epicypher

value: Medulloblastoma


title: 458IR H3K4me3 2

description:
Library name: irradiated_2_458IR H3K4me3
epicypher


title: Chronic_DistalSI_Control_rep1

description:
Library name: Chronic_DistalSI_Control_rep1
Chronic_DistalSI_rawcount.txt


title: 458IR IDH305 H3K4me3

description:
Library name: irradiated_IDH305_1_H3K4me3
epicypher


title: Chronic_Colon_Control_rep1

description:
Library name: Chronic_Colon_Control_rep1
Chronic_Colon_rawcount.txt


title: 458IR_GSK321 H3K4me3

description:
Library name: irradiated_GSK_1_458IR
epicypher


title: Chronic_MidleSI_Metformin_rep3

description:
Library name: Chronic_MidleSI_Metformin_rep3
Chronic_MiddleSI_rawcount.txt


title: 458IR, H3K4me3

description:
Library name: irradiated_1_458 H3K4me3
epicypher


title: Chronic_MidleSI_Metformin_rep1

description:
Library name: Chronic_MidleSI_Metformin_rep1
Chronic_MiddleSI_rawcount.txt


title: 458, H3K4me3_2

description:
Library name: Control_2_458_H3K4me3
epicypher


title: 458, H3K4me3

description:
Library name: Control_1_458 H3K4me3
epicypher


title: 458IR, GSK321 H3K4me3 2

description:
Library name: irradiated_GSK_2_458IR
epicypher


title: Chronic_MidleSI_Imeglimin_rep2

description:
Library name: Chronic_MidleSI_Imeglimin_rep2
Chronic_MiddleSI_rawcount.txt


title: IgG 458Ir 2

description:
Library name: igg_irradiated_1
epicypher

value: IgG (epicypher, #13-0042k)


title: Chronic_MidleSI_Control_rep2

description:
Library name: Chronic_MidleSI_Control_rep2
Chronic_MiddleSI_rawcount.txt


title: Chronic_MidleSI_Control_rep1

description:
Library name: Chronic_MidleSI_Control_rep1
Chronic_MiddleSI_rawcount.txt


title: Chronic_MidleSI_Imeglimin_rep1

description:
Library name: Chronic_MidleSI_Imeglimin_rep1
Chronic_MiddleSI_rawcount.txt


title: Chronic_MidleSI_Metformin_rep2

description:
Library name: Chronic_MidleSI_Metformin_rep2
Chronic_MiddleSI_rawcount.txt


title: Chronic_MidleSI_Control_rep3

description:
Library name: Chronic_MidleSI_Control_rep3
Chronic_MiddleSI_rawcount.txt


title: IgG 458

description:
Library name: igg_control_1
epicypher


title: Chronic_ProximalSI_Metformin_rep3

description:
Library name: Chronic_ProximalSI_Metformin_rep3
Chronic_proximalSI_rawcount.txt


title: IgG 458IR IDH305

description:
Library name: igg_irradiated_IDH305
epicypher


title: Chronic_DistalSI_Control_rep2

description:
Library name: Chronic_DistalSI_Control_rep2
Chronic_DistalSI_rawcount.txt


title: 458IR, H3k4me3_2

description:
Library name: irradiated_2_458 H3K4me3
epicypher


title: Chronic_ProximalSI_Imeglimin_rep3

description:
Library name: Chronic_ProximalSI_Imeglimin_rep3
Chronic_proximalSI_rawcount.txt


title: Chronic_ProximalSI_Metformin_rep1

description:
Library name: Chronic_ProximalSI_Metformin_rep1
Chronic_proximalSI_rawcount.txt


title: 458IR_wt_IDHi ATAC

description: Library name: 458IR_wt_IDHi

data_processing:
Peaks were called using the program MACS (v2.1.2), with the narrow peak mode using matched input controls and a q-value of 0.00001. Peaks in the blacklisted genomic regions identified by the ENCODE consortium were excluded using bedtools
Assembly: GRCh38 2020
Supplementary files format and content: bw, peaks.narrowpeaks

extract_protocol:
Cell pellets were resuspended in 450mL of cold hypotonic buffer (10mM Tris-HCL, pH7.4, 10mM NaCl, 3mM MgCl2). Next, 50mL of 1% IGEPAL CA-630 was added and inverted to mix. Samples were iced for 10min, centrifuged for 10mins at 4°C. Cells pellets were resuspended in transposition reaction mix and incubated at 37°C for 60min. Following transposition, the DNA was isolated, purified, and prepped for sequencing.
amplify transposed DNA fragments with Ad1.noMX and AD2.barcode* primers. High-fidelifty 2x PCR master mix. Purify PCR reaction with Ampure XP beads.

treatment_protocol: D458 and D458IR cells were exposed to IDH305 or GSK321 at IC50 for 48h. 50,000 cells were collected and washed in cold 1x PBS.  The sequencing library is purified with AMpure XP beads (Millipore). ATAC assay kit (Cell BiologicsÔ ATAC-Seq Kit (Cat# CB6936)).

value: D458 IR

value: medulloblastoma


title: Chronic_MidleSI_Imeglimin_rep3

description:
Library name: Chronic_MidleSI_Imeglimin_rep3
Chronic_MiddleSI_rawcount.txt


title: 458IR_IDH305 ATAC

description: Library name: 458IR_IDH305


title: Chronic_ProximalSI_Imeglimin_rep2

description:
Library name: Chronic_ProximalSI_Imeglimin_rep2
Chronic_proximalSI_rawcount.txt


title: Chronic_ProximalSI_Imeglimin_rep1

description:
Library name: Chronic_ProximalSI_Imeglimin_rep1
Chronic_proximalSI_rawcount.txt


title: 458IR_DMSO _2 ATAC

description: Library name: 458IR_DMSO _2

value: NT


title: Chronic_ProximalSI_Control_rep3

description:
Library name: Chronic_ProximalSI_Control_rep3
Chronic_proximalSI_rawcount.txt

value: male


title: 458IR_DMSO  ATAC

description: Library name: 458IR_DMSO


title: Gag PABPΔZF cytosolic fraction_ISBM-036

city: Munich

first: Gil

middle: Gregor

last: Westmeyer

address: Arcisstrasse 21

country: Germany

institute: Technical University Munich

description:
Library name: 23L010014
Stable exporter line without zinc finger domains in the export system, cytosolic fraction from subcellular fractionation

data_processing:
Deduplication via czid-dedup (paired-end mode)
featurecounts_harmonized.csv: Paired-end reads were aligned to the combined human-murine index via STAR  (star --readFilesCommand zcat --genomeDir {COMBINED_INDEX_STAR} --readFilesIn {R1} {R2} --runThreadN 8 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix {OUTPUT_NAME} --quantMode GeneCounts TranscriptomeSAM))
featurecounts_harmonized.csv: Gene level feature counting via featurecounts (featureCounts -a {COMBINED_INDEX_GTF} -o {OUTPUT_FILE}  -g gene_id -t exon -s 2 -p)
Quant files (*.sf.gz): Quantification via salmon (salmon quant -i {COMBINED_INDEX_SALMON} -l A -1 {R1} -2 {R2} --validateMappings -p 8 -o {OUT_PATH}")
Assembly: hg38, mm39, ARS-UCDI1.2
Supplementary files format and content: featurecounts_harmonized.csv: comma seperated plaintext file containing the raw counts mapping to features and metadata for all samples
Supplementary files format and content: Quant files (*.sf.gz): comma seperated plaintext file containing the TPMs and estimated number of reads for a specific sample, including metadata

growth_protocol: HEK293T cells were cultured in advanced DMEM supplemented wih 10% FCS and passaged by using Accutase at confluency

extract_protocol:
RNA from cell lysate was harvested using the NEB Monarch® Total RNA Miniprep Kit (T2010S). NTVE derived RNA was extracted from the supernatant using the Zymo Research Quick-RNA Viral Kit (R1040).
Libraries were constructed according to the protocols using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus for total RNA runs and Illumina Stranded mRNA Prep for polyA enriched runs

treatment_protocol: 500 ng/ml doycycline for NTVE induction; 50 ng/ml interferon-gamma or ASCL1 transactivation for pertubation.

value: immortalised cell line

value: NTVE Gag:PABP; Pgk-TetON3g  (ISBM-036)

tag: rna origin

value: Cell Lysate (fractionated)

tag: spike-in

value: doxycycline 500ng/ul


title: IgG 458_2

description:
Library name: igg_control_2
epicypher

value: brain

value: DMSO


title: Chronic_ProximalSI_Control_rep2

description:
Library name: Chronic_ProximalSI_Control_rep2
Chronic_proximalSI_rawcount.txt

value: Control


title: Gag PABP lysate_ISBM-036

description:
Library name: 23L010011
Stable exporter line without zinc finger domains in the export system

value: Cell Lysate


title: Acute_Colon_Metformin_rep3

description:
Library name: Acute_Colon_Metformin_rep3
Acute_Colon_rawcount.txt

value: Colon

value: Metformin


title: Gag(ZF) lysate_ISBM-038

description:
Library name: 23L010008
Stable exporter line without poly-A binding protein in the export system

value: Gag (ZF); Pgk-TetON3g  (ISBM-038)


title: Gag PABP(ZF) lysate_ISBM-014

description:
Library name: 23L010009
Stable NTVE line

value: NTVE Gag:PABP(ZF); Pgk-TetON3g (ISBM-014)


title: 458IR_wt_IDHi_2 ATAC

description: Library name: 458IR_wt_IDHi_2


title: Acute_Colon_Metformin_rep2

description:
Library name: Acute_Colon_Metformin_rep2
Acute_Colon_rawcount.txt


title: Chronic_ProximalSI_Control_rep1

description:
Library name: Chronic_ProximalSI_Control_rep1
Chronic_proximalSI_rawcount.txt


title: NTVE (ASCL1 transactivated)-2_ISBM-015

description:
Library name: SN-ASCL1-2
Stable NTVE line, ASCL1 transactivation

value: NTVE Gag:PABP(ZF); Pgk-TetON3g + transactivation (ISBM-015)

value: Supernatant


title: Acute_Colon_Metformin_rep1

description:
Library name: Acute_Colon_Metformin_rep1
Acute_Colon_rawcount.txt


title: Acute_Colon_Imeglimin_rep3

description:
Library name: Acute_Colon_Imeglimin_rep3
Acute_Colon_rawcount.txt

value: Imeglimin


title: NTVE (ASCL1 transactivated)-3_ISBM-015

description:
Library name: SN-ASCL1-3
Stable NTVE line, ASCL1 transactivation


title: Chronic_ProximalSI_Metformin_rep2

description:
Library name: Chronic_ProximalSI_Metformin_rep2
Chronic_proximalSI_rawcount.txt


title: Acute_Colon_Imeglimin_rep2

description:
Library name: Acute_Colon_Imeglimin_rep2
Acute_Colon_rawcount.txt


title: NTVE (ASCL1 transactivated)-1_ISBM-015

description:
Library name: SN-ASCL1-1
Stable NTVE line, ASCL1 transactivation


title: 458IR_IDH305_2 ATAC

description: Library name: 458IR_IDH305_2

value: D458 IR

value: medulloblastoma


title: Acute_Colon_Imeglimin_rep1

description:
Library name: Acute_Colon_Imeglimin_rep1
Acute_Colon_rawcount.txt

value: male


title: NTVE -6_ISBM-014

description:
Library name: SN6
Stable NTVE line

value: immortalised cell line


title: NTVE -5_ISBM-014

description:
Library name: SN5
Stable NTVE line


title: NTVE -4_ISBM-014

description:
Library name: SN4
Stable NTVE line


title: Acute_Colon_Control_rep3

description:
Library name: Acute_Colon_Control_rep3
Acute_Colon_rawcount.txt


title: NTVE -3_ISBM-014

description:
Library name: SN3
Stable NTVE line


title: NTVE -1_ISBM-014

description:
Library name: SN1
Stable NTVE line


title: NTVE -2_ISBM-014

description:
Library name: SN2
Stable NTVE line


title: Acute_Colon_Control_rep2

description:
Library name: Acute_Colon_Control_rep2
Acute_Colon_rawcount.txt


title: Acute_Colon_Control_rep1

description:
Library name: Acute_Colon_Control_rep1
Acute_Colon_rawcount.txt


title: Tsc2-/-/sgGSK3α&β/NRas_4

city: San Francisco

first: Guofei

last: Cui

state: CALIFORNIA

institute: UCSF

description: Library name: Samples 20

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house Perl scripts (Novogene). 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.
Paired-end reads were mapped to mouse reference genome (mm10) by Hisat2 v2.0.5.
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.
Differential expression analysis was performed using the DESeq2 R package (version 1.24.0).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files includes raw counts for each sample

source_name: liver tumor tissue

extract_protocol:
Total RNA was extracted from frozen mouse liver specimens (Akt/NRas 5-6 weeks post-injection (w.p.i.), sgGSK3a&b/NRas 9.4w.p.i., Tsc2-/-/sgGSK3α&β/NRas 6-9w.p.i., Tsc2-/-/NRas 20-24w.p.i., and normal liver -14.9 weeks) using the Quick-RNA™ Miniprep Kit (Cat# R1055, Zymo Research, Irvine, CA, USA). >6 µg of total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

value: liver tumor tissue

value: Tsc2 KO GSK3 KO plus overexpression of acvtivated NRas

value: 9.1 weeks post-injection

value: M

tag: tumor stage

value: late stage


title: Tsc2-/-/sgGSK3α&β/NRas_3

description: Library name: Samples 19

value: 8.4 weeks post-injection


title: NTVE (ASCL1 transactivated) lysate-2_ISBM-015

description:
Library name: L-ASCL1-2
Stable NTVE line, ASCL1 transactivation

value: Cell Lysate

value: doxycycline 500ng/ul


title: NTVE (ASCL1 transactivated) lysate-3_ISBM-015

description:
Library name: L-ASCL1-3
Stable NTVE line, ASCL1 transactivation


title: Tsc2-/-/sgGSK3α&β/NRas_2

description: Library name: Samples 18

value: 8 weeks post-injection


title: Tsc2-/-/sgGSK3α&β/NRas_1

description: Library name: Samples 17

value: 6.1 weeks post-injection


title: NTVE lysate-4_ISBM-014

description:
Library name: L4
Stable NTVE line

value: NTVE Gag:PABP(ZF); Pgk-TetON3g (ISBM-014)


title: sgGSK3α&β/NRas_2

description: Library name: Samples 14

value: GSK3 KO plus overexpression of acvtivated NRas

value: 9.4 weeks post-injection


title: sgGSK3α&β/NRas_3

description: Library name: Samples 15


title: NTVE lysate-6_ISBM-014

description:
Library name: L6
Stable NTVE line


title: NTVE (ASCL1 transactivated) lysate-1_ISBM-015

description:
Library name: L-ASCL1-1
Stable NTVE line, ASCL1 transactivation

value: NTVE Gag:PABP(ZF); Pgk-TetON3g + transactivation (ISBM-015)


title: NTVE lysate-5_ISBM-014

description:
Library name: L5
Stable NTVE line


title: sgGSK3α&β/NRas_4

description: Library name: Samples 16


title: sgGSK3α&β/NRas_1

description: Library name: Samples 13


title: NTVE lysate-3_ISBM-014

description:
Library name: L3
Stable NTVE line