title: TC1_Tissue_WT2

status: Public on Aug 30 2024

city: Suzhou

first: Wancheng

last: Liu

state: jiangsu

address: 100 Chongwen Road, Industrial Park

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description: On day 8 after incubation

data_processing:
Fastqc software used for quality control.
Sequenced reads were trimmed by trim_galore software for adaptor sequence with parameters -q 25 --phred33 --length 36 -e 0.1 --stringency 5 --paired, then mapped to mm10 whole genome using bowtie2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using featureCounts software.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: tumor tissue

extract_protocol:
TC1 WT and sgNAT10 tumor tissue were harvested on day  8 post-implanted. Total RNA was extracted using RNeasy Mini Kit (QIAGEN, cat#74104). ProtoScript II Reverse Transcriptase (New England BioLabs, cat#E7420L) was used with 0.6 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MCA205 and TC1 wild type (WT) and sgNAT10 cells (2x10^6 cells in 100ul PBS per mouse) were subcutaneously implanted.

value: tumor tissue

value: mouse fibrosarcoma TC1  cells

value: wild type


title: TC1_Tissue_WT3

type: SRA

country: China

description: On day 8 after incubation

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: genotype


title: SH-SY5Y cells _BBEE pre-treatment 24h_No_LPS induction 24h_rep1

status: Public on Aug 31 2024

type: RNA

city: Tsukuba

first: sharmin

last: Aktar

state: Ibaraki Prefecture

department: Life and Environmental Science

country: Japan

institute: University of Tsukuba

description: Gene expression data from SH-SY5Y cells, pre-treated with BBEE for 24 h and then no LPS-induced for 24h

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, human; Thermofisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (Thermofisher Scientific).

data_processing:
The raw image data was normalized following the SST-RMA method using the Transcriptome Analysis Console (TAC) software (ver. 4.0, Thermofisher Scientific) (Summarization: SST-RMA, Anova Method: eBays, DABG <0.05, Pos/Neg AUC Threshold: 0.7).
Signal intensity of all the samples derived from Transcriptome analysis console software. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CHP files ).
RMA (SST-RMA, Transcriptome Analysis Console, version 4)

label: biotin

organism: Homo sapiens

source_name: SH-SY5Y cells were treated with 0.2 mg/mL BBEE for 24 h and then induced with LPS solution (0 ng/mL) for 24 h

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol from 100 ng/ uL total RNA

growth_protocol: SH-SY5Y cells  were purchased from RIKEN BioResource Center (RIKEN BRC, Tsukuba, Ibaraki, Japan). SH-SY5Y cells were cultured in Dulbecco’s modified Eagle medium (DMEM) (Merck KGaA, Darmstadt, Germany) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Bio West, Nuaillé, France) and 1penicillin-streptomycin solution (Merck KGaA) at 37ºC in a humidified incubator containing 5% CO2 using 75cm2 flask (BD FALCON, Corning, NY, USA)

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: BBEE was extracted with 70% Ethanol (1 mL) at room temperature under the dark for 2 weeks. After the extraction was completed, it was centrifuged at 1000 xg for 10 minutes and collected the supernatant. The supernatant of the extracted sample was filtered by using a 0.22 µm filter unit and stored at -20 ºC in the dark until use. Lipopolysaccharide (LPS; E. coli O111:B4) was purchased from EMD Millipore Co. (Billerica, MA USA). 5 mg of LPS was dissolved in 2 ml of PBS (-), and stored at -80 ℃ under the dark until use. SH-SY5Y cells were seeded into a 96-well plate at density of 2.0×105 cells/mL and incubated at 37 °C for 24 h. The cells were treated with or without BBEE at 37 °C for 24 h. After the BBEE treatment, the LPS solution (1 ng/ml) was added to each well and incubated for 24h and 24 h at 37 °C.

value: SH-SY5Y cells (Resource No. RCB0535, RIKEN BRC, Tsukuba, Ibaraki, Japan)


title: E16.5 whole mouse heart r3

city: Montreal

first: Florian

last: Wuennemann

address: 5000 Rue Bélanger

country: Canada

institute: Montreal Heart Institute

description: Drop-seq library. R1 files contain cell barcodes, R2 files contain cDNA sequences.

data_processing:
Base calls and demultiplexing was performed using bcl2fastq (v2.17).
Raw FASTQ files for each sample were processed using kallisto and bustools (kb-python, v0.24.4, https://www.kallistobus.tools) against the ensemble reference release 98 for Mus musculus (GRCm38, primary assembly).
We utilized emptyDrops from the DropletUtils package in R (v.1.4.3, https://doi.org/10.1186/s13059-019-1662-y) to call single-cells from the raw, unfiltered digital gene expression (DGE) matrices (FDR threshold <= 1%).
Potential cell doublets were identified using the scrublet package (v.0.2.1,https://github.com/AllonKleinLab/scrublet) on a per sample basis and cells with a predicted scrublet score >= 0.25 were removed from furhter analysis.
Cells with more than 10.000 UMIs, less than 500 genes and more than 15% mitochondrial genes expressed, were further filtered out.
Genes expressed in less than 5 cells were also excluded from final analysis.
We fruther excluded red blood cells, contaminating lung cells and a potential multiplet cell cluster from the final dataset.
Genome_build: GRCm38
Supplementary_files_format_and_content: perinatheart.raw_umi_counts.final_cells.tsv: Flat tab-serparated text file with raw UMI counts for 67264 cells and 23245 genes for 36 samples (including 6 samples for E14.5 from GSE109247) used for analysis in the manuscript. Cells were filtered as descripted in data processing to remove any potential cell doublets and low quality cells.
Supplementary_files_format_and_content: perinatheart.metadata.final_cells.tsv: Metadata for all cells in perinatheart.raw_umi_counts.final_cells.tsv.

molecule: polyA RNA

source_name: Heart

extract_protocol:
Hearts were extracted by cutting the abdominal aorta using scissors and subsequently utilizing fine tweezers and carefully pulling out the lungs together with the connected heart. Any remaining lung tissue, trachea, fat or non-cardiac tissue was carefully removed. The pulmonary veins and the inferior vena cava were cut as close to the base of the heart as possible and the pulmonary artery and aorta were cut close to the pulmonary valve and ascending aorta, respectively, to exclude the majority of these two large vessels from the tissue dissociation. Hearts were dissociated using gentleMACS C-tubes (Miltenyi Biotec, Cat-Nr:130-093-237) containing enzymatic digestion solution according to manufacturer’s protocol from the Neonatal Heart Dissociation Kit (Miltenyi Biotec, Cat-Nr: 130-098-373) using a gentleMACS Octo Dissociator (Miltenyi Biotec, Cat-Nr: 130-095-937). Single cells were co-encapsulated with barcoded microbeads to produce single cell transcriptomes attached to microparticles (STAMPS) according to the Drop-seq protocol. STAMPS were counted and PCR amplified for 13 cycles. Amplified cDNA was measured using Bioanalyzer and used for library preparation.
A modified Nextera-XT protocol as described in Macosko et al. 2015 was used to construct libraries. Illumina i7 primer were used in combination with a custom i5 primer.
scRNA-seq with Illumina i7 and custom i5 primer.

tag: strain

tag: developmental time point

tag: replicate

tag: Sex

value: F

tag: illumina flowcell

tag: litter id


title: TC1_cell_sgNAT10_3

description: cell total mRNA

source_name: cell line

value: cell line


title: TC1_cell_sgNAT10_1

description: cell total mRNA


title: SH-SY5Y cells_2-AB  pre-treatment_No LPS induction rep1

description: Gene expression data from SH-SY5Y cells, maintained in culture medium for 24 h and no LPS-induced for 24h

source_name: SH-SY5Y cells were maintained in culture medium for 24h and then induced with LPS solution (0 ng/mL) for 24 h


title: TC1_cell_WT2

description: cell total mRNA


title: TC1_cell_WT1

description: cell total mRNA


title: MCA205_cell_WT3

description: cell total mRNA

value: mouse fibrosarcoma MCA205 cells


title: SH-SY5Y cells_No pre-treatment_LPS induction 24h_rep1

description: Gene expression data from SH-SY5Y cells, maintained in culture medium for 24 h and then LPS-induced for 24h

source_name: SH-SY5Y cells were maintained in culture medium for 24h and then induced with LPS solution (1 ng/mL) for 24 h


title: SH-SY5Y cells_No pre-treatment_LPS induction 24h_rep2


title: TC1_Tissue_sgNAT10_2

description: On day 8 after incubation


title: SH-SY5Y cells_BBEE pre-treatment 24h_No_LPS induction 24h_rep2


title: TC1_Tissue_sgNAT10_1

description: On day 8 after incubation


title: TC1_Tissue_WT1

description: On day 8 after incubation


title: MDA-MB-231, DVL1, ChIP, 1

city: Chapel Hill

first: Dalia

last: Martinez-Marin

state: NC

address: 450 West Dr

department: Dept of Pharmacology

country: USA

institute: University of North Carolina

library_source: genomic

data_processing:
FASTQ files were analyzed using DNASTAR’s Laser Gene software
Sequenced reads were aligned against the human genome (GRCh38.p14)
MACS2 and SPP were used for peak calling
Assembly: hg38
Supplementary files format and content: narrowPeak

molecule: genomic DNA

source_name: Breast

growth_protocol: MDA-MB-231 cells were maintined in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were cross-linked with 1% (w/v) formaldehyde for 8 min at room temperature and quenched in 0.125 M of glycine for 5 minutes at room temperature. Cells were resuspended in SDS Lysis and sonicated in a Diagenode Biorupter. 100 μg of chromatin was immunoprecipitated
libraries for ChIP-seq were prepared by AZENTA-GENEWIZ

value: Breast

tag: cell type

value: triple-negative breast cancer

value: WT

tag: chip antibody

value: DVL1 (Sigma, D3570)


title: MDA-MB-231, Input, 2


title: MDA-MB-231, Input, 1


title: MDA-MB-231, IgG, ChIP, 2

value: IgG (Sigma, I5006)


title: TC1_cell_sgNAT10_2

description: cell total mRNA


title: MDA-MB-231, Input, 3


title: OE1 - Tumor

city: Salt Lake City

first: Gregory

last: Ducker

state: UT

address: 15 N Medical Drive East

department: Biochemistry

institute: University of Utah

description: Nude mouse injected with BHMT OE cells, total RNA extracted from tumor

data_processing:
Kallisto quant - used for alignment to transcriptome GRCh38 and to quantify abundances of RNA-Seq transcripts (Galaxy Version 0.46.0.4). PARAMETERS: Perform sequence based bias correction: Yes Number of bootstrap samples: 0 Seed for the bootstrap sampling: 42 Search for fusions: No Library strandness information: Unstranded
DeSeq2 - used to measure differential expression between groups. DeSeq2 version 1.33.1 was used on R version 4.1.0.
Genome_build: GRCh38 (Homo sapiens)
Supplementary_files_format_and_content: Matrix Table with DeSeq2 output - both normalized and raw counts

source_name: Mouse Xenograft Tumor

extract_protocol:
Tumors were harvested from the nude mouse. RNA was homogenized using a Cryomill and extracted using the Qiagen RNAeasy Fibrous Mini Kit.
Illumina Stranded Total RNA Library Prep with Ribo-Zero Plus

tag: mouse strain

value: Nude

value: Solid tumor

tag: cell strain

value: BHMT OE


title: E16.5 whole mouse heart r2


title: TC1_cell_WT3

description: cell total mRNA


title: Germ cells from 15-day C57BL/6 cKO mutant 1

city: Bronx

first: Deyou

last: Zheng

state: NY

address: 1301 Morris Park Avenue

department: Department of Genetics

institute: Albert Einstein College of Medicine

description: Sample E

data_processing:
Paired-end reads from RNA sequencing were aligned using the STAR aligner (version 2.7.9a) to the mouse reference genome (mm39).
The alignment data were then used by the RSEM software (v 1.3.3) to quantify expression levels of individual genes (both coding and non-coding) in the Ensembl annotation (v105), yielding estimated read counts and transcripts per million (TPMs).
Genes with a TPM >= 1 in at least one of the eight samples were retained for differential expression analysis by DEseq2 (v1.38.3).
Assembly: mm39
Supplementary files format and content: csv-format text file includes raw counts and TPMs for each sample

source_name: 15-day testis

growth_protocol: Mgat2[F/F] and Mgat2[F/F]:Stra8-iCre male pups were produced in a barrier facility and sacrificed at 15 days after birth.

extract_protocol:
Total RNA was extracted from germ cells using RNAzol (Sigma Aldrich), quantitated by Nanodrop ND 1000 spectrophotometer and the quality determind by RQN values using Bioanalyzer software on a Pico RNA Chip performed by the Genomics Core at Albert Einstein School of Medicine.. RQN values were all 10. The RNA was sent on dry ice to Novogene. All samples passed NovaSeq PE150 quality control, poly A+ RNA was prepared by Novogene, 8 non-stranded mRNA libraries were prepared and subjected to paired-end RNA-seq.
Non-stranded mRNA-Seq libraries (poly A enrichment) were prepared by Novogene for 150 base pair paired-end (PE) sequencing on an Illumina HiSeq platform.

treatment_protocol: Male pups of 15 days were sacrificed, weighed, testicles were isolated and weighed and germ cells were isolated as follows:  The method of Wang et al. (Nat Commun (2019) 10:5196) with slight modifications was used. After removal of tunica albuginea, testis tubules were placed in 5 ml of enzymatic solution 1, (0.5 mg/ml collagenase Type I (cat # C0130-1G, Sigma-Aldrich) and 200 µg/ml DNase I (cat # DN25-100, Sigma-Aldrich) in DMEM:F12 medium) followed by gentle agitation in a shaking water bath at 37°C for 20 min (75 oscillations per min with manual shaking every 6 min). Tubules were then permitted to settle, and the supernatant was removed. After a wash with 5 ml of fresh DMEM:F12,  tubules were resuspended in 5 ml fresh DMEM:F12 and transferred to a new tube containing 5 ml of enzyme solution II (200 µg/ml DNase I and 1.25 mg/ml trypsin from Sigma-Aldrich) in DMEM:F12). After 20 min gentle agitation in a 37°C shaking water bath at 75 oscillations per min with manual inversion every 5 min, 20% FBS (cat # A42C22A, GeminiBio, West Sacramento, CA) was added, and clumps were dissociated by resuspending the cells 20 times using a 5 ml pipette. The suspension was filtered through a 70 µm filter (pre-wet with 1 ml DMEM:F12 followed by centrifugation at 1000 x g for 10 min at 4°C. The cell pellet was resuspended in 1 ml of cold HBSS (Gibco) and counted by hemocytometer. After centrifugation at 800 g for 10 min at 4ºC, the germ cell pellet was stored at -80ºC.

value: 15-day testis

value: germ cells

value: Mgat2[F/F]:Stra8-iCre male


title: Germ cells from 15-day C57BL/6 Control 3

description: Sample C

value: Mgat2[F/F] male


title: MCA205_cell_sgNAT10_3

description: cell total mRNA


title: Germ cells from 15-day C57BL/6 Control 2

description: Sample B


title: MCA205_cell_sgNAT10_2

description: cell total mRNA


title: MCA205_cell_sgNAT10_1

description: cell total mRNA


title: MCA205_cell_WT2

description: cell total mRNA

value: wild type


title: MCA205_cell_WT1

description: cell total mRNA


title: MDA-MB-231, DVL1, ChIP, 3


title: MDA-MB-231, IgG, ChIP, 1


title: Germ cells from 15-day C57BL/6 cKO mutant 2

description: Sample F


title: AML1007.5 TSA

city: Boston

first: Livius

last: Penter

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
surface marker expression
Raw data available: dbGap phs003015.v3

library_source: other

data_processing:
Demultiplexing of llumina sequencer's base call files (BCLs) using cellranger-atac mkfastq.
Alignment of raw reads to hg38, extraction of cell barcodes and DNA fragments using cellranger-atac count.
Conversion of fastq files for TSA using ASAP to kite (https://github.com/caleblareau/asap_to_kite)
Pseudoalignment and quantification of TSA counts using kallisto | bustools (PMID 33795888).
Assembly: GRCh38
Supplementary files format and content: Feature count matrix and cell barcode list in tsv file format.
Supplementary files format and content: DNA fragments in tsv file format.
Library strategy: ASAP-seq (scATAC-seq and CITE-seq using Total-seq A oligotags)

molecule: protein

source_name: bone marrow

extract_protocol:
Single cell suspensions were stained with Total-seq A surface marker oligotags followed by fixation with 1% formaldehyde and lysis with NP-40 substitute to retain mitochondrial DNA as described by Lareau & Ludwig et al., Nature Biotechnology 2021 (PMID 32788668) and Mimitou et al., Nature Biotechnology 2021 (PMID 34083792).
Single Cell ATAC (Assay for Transposase Accessible Chromatin) using Chromium platform (10x Genomics) according to manufacturer's instructions.

value: bone marrow

tag: pool

tag: library type

value: ADT

tag: treatment

value: end of treatment


title: Germ cells from 15-day C57BL/6 cKO mutant 4

description: Sample H


title: AML1007.6 TSA

value: relapse after second haploidentical transplantation


title: Germ cells from 15-day C57BL/6 Control 4

description: Sample D


title: MDA-MB-231, DVL1, ChIP, 2

value: Breast


title: Multiplex experiment 3 - AML1012.4 and AML1026.3 - Total-seq D

data_processing:
Demultiplexing of llumina sequencer's base call files (BCLs).
Alignment of raw reads to hg38, extraction of cell barcodes, DNA amplicons and oligotags using Tapestri pipeline.
Extraction of called variants and surface marker expression using Tapestri Insights v3.0.2.
Demultiplexing of samples based on clustering of single nucleotide variants in Tapestri Insights v3.0.2
Assembly: GRCh38
Supplementary files format and content: Allele frequencies and surface marker expression in tsv file format.
Library strategy: Single cell DNA sequencing and CITE-seq using Total-seq D oligotags.

extract_protocol:
Single cell suspensions were multiplexed and stained with Total-seq D surface marker oligotags followed loading onto Tapestri cartridge.
Single cell DNA and oligotag sequencing according to manufacturer's instructions (Mission Bio) using custom panels for mitochondrial and somatic nuclear DNA mutations.


title: AML1007.1 TSA

value: screening


title: Germ cells from 15-day C57BL/6 Control 1

description: Sample A


title: MDA-MB-231, IgG, ChIP, 3

value: triple-negative breast cancer

value: WT


title: AML1011.A scATAC-seq

description:
single cell chromatin accessibility
Raw data available: dbGap phs003015.v3

value: ATAC

value: relapse before first transplantation


title: Multiplex experiment 2 - AML1010.1 and AML1026.1 - Total-seq D

value: screening (AML1010), screening (AML1026)


title: Multiplex experiment 3 - AML1012.4 and AML1026.3 - scDNA-seq

description:
Allele frequencies
Raw data available: dbGap phs003015.v3

value: amplicon


title: Multiplex experiment 2 - AML1010.1 and AML1026.1 - scDNA-seq


title: AML1012.A TSA


title: Germ cells from 15-day C57BL/6 cKO mutant 3

description: Sample G

value: 15-day testis


title: AML1011.A TSA


title: AML1011.1 TSA


title: AML1012.A scATAC-seq


title: AML1007.1 scATAC-seq


title: AML1011.2 scATAC-seq

value: C2 (Decitabine and ipilimumab)


title: DMM-2

city: shanghai

first: bo

last: wang

address: 130 Meilong Rd.

institute: East China University of Science and Technology

data_processing:
The qualified dsDNA samples were sequenced using Illumina Nova Seq 6000 platform (San Diego, USA)
Raw sequencing reads were mapped to GRCh38 assembly of the human genome using Tophat2, version 2.0.10
Fragments per kilobase of exon model per million mapped reads (FPKM) were computed using Stringtie and normalized with TMM.
Assembly: GRCh38
Supplementary files format and content: table delimit file includes FPKM values each sample

source_name: adipose

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
dsDNA library was constructed using VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme) and purified using VIHTS DNA Clean Beads (Vazyme) according to the manufacturer’s instructions

value: adipose

value: adipose-derived stem cells

value: mesenchymal stem cells


title: DMM-1


title: DMS-2


title: DMS-1


title: DMS-3


title: AML1007.5 scATAC-seq

value: bone marrow


title: AML1007.6 scATAC-seq


title: AML1011.B scATAC-seq

value: complete remission before first transplantation


title: TC1_Tissue_sgNAT10_3

description: On day 8 after incubation

value: tumor tissue

value: mouse fibrosarcoma TC1  cells


title: P12_TN_102_core

city: Stanford

first: Caren

middle: Yu-Ju

last: Wu

state: CALIFORNIA

address: 1201 Welch Rd, Stanford, CA 94305

department: Department of Neurosurgery

institute: Stanford University

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0
Assembly: hg38
Supplementary files format and content: Seurat object with gene matrix

source_name: Tumor core

extract_protocol:
Brain tissues were cut into pieces and dissociated using a papain dissociation kit (Miltenyi Biote, USA) and ACK RBC Lysing Buffer (Thermo, USA). Cells from the tumor core and periphery were sorted separately before sequencing.
The single-cell RNA library was then generated using a Chromium Next GEM Single Cell 3’GEM, Library & Gel Bead Kit (10x Genomics) following the manufacturer’s protocol. All samples were sequenced and performed at multiplex paired-end 150 bp on the Illumina NovaSeq 6000. The Cell Ranger software pipeline (version 4.0.0) provided by 10x Genomics was used to demultiplex cellular barcodes, map reads to the genome, align transcriptomes, and produce a matrix of gene counts versus cells. Advanced analytics and data visualization were processed using the Seurat package (version 4.0.4). For cell-type classification, the SingleR package (version 1.0.1) , a computational method for unbiased cell type recognition of scRNA-seq with a reference transcriptomic, was applied to identify cell types. The TMEM119+ TAM populations were selected using the subset function in Seurat, and differential gene expression analysis was performed using the FindMarkers function with Wilcox’s rank-sum test. Published scRNA-seq datasets were downloaded and analyzed using the same workflow.

value: Tumor core

value: myeloid cells


title: AML1011.2 TSA

value: ADT


title: P8_TN_74_core


title: AML1011.B TSA


title: Control-2


title: Control-1


title: Control-3


title: P7_TN_100_margin (paried with P13)

source_name: Tumor margin

value: Tumor margin


title: P13_TN_99_core


title: DMM-3


title: P11_TN_103_margin (Paired with P12)


title: P9_TN_75_margin (paired with P8)


title: P10_TN_67_margin


title: PANC-1 cells, RoF&Tr

city: Sapporo

first: Takako

last: OOshio

address: Kita-15, Nishi-7, Kita-Ku

institute: Hokkaido University

data_processing:
The reads were aligned to human hg38 using STAR (version 2.7.3a) .
Mapped reads were then counted using HTSEQ (version2.0.2) and the expression of each RNA was converted to transcripts per kilobase million (TPM).
Assembly: hg38
Supplementary files format and content: tab-delimited text file include transcripts per kilobase million (TPM) for each sample.

source_name: PANC-1 cells

growth_protocol: AsPC-1 and PANC-1 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Rneasy mini kit (Qigagen). 2 ug of total RNA was used for the construction of sequencing libraries.
Sequence libraries were constructed with TruSeq stranded mRNA library preparation kit(Illumina) according to the manufacture's instructions.

treatment_protocol: PDAC cells were treated with a vehicle, or 10 µM roseoflavin and/or 1 nM trametinib for 24 hours.

value: PANC-1 cells

value: Pancreatic cancer-derived cells

value: WT

value: roseoflavin&trametinib


title: PANC-1 cells, Tr

value: trametinib


title: AML1011.1 scATAC-seq

value: ATAC

value: screening


title: PANC-1 cells, RoF

value: roseoflavin


title: PANC-1 cells, Control

value: vehicle


title: sciMETv3, brain, 4 donors, Illumina NovaSeq

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

description: Cell-level methylation calls and amethyst analysis object for Illumina-sequenced sciMETv3 dataset

data_processing:
Reads were processed using Premethyst and aligned to hg38
Methylation calls were analyzed using Amethyst
Assembly: hg38
Supplementary files format and content: Methylation calls in h5 format or a tar file with multiple h5 files included
Supplementary files format and content: Methylaiton metadata in amethyst object format, integrated with sciMETv3-only dataset

source_name: Brain BA46

extract_protocol:
Nuclei were extracted using nuclei isolation buffer and gentle dounce homogenization
sciMETv3 libraries were prepared using 3-level single-cell combinatorial indexing workflows

value: Brain BA46


title: RSV infected WT BRD4 rep1

city: Madison

first: Allan

last: Brasier

state: WI

address: 715 Highland

department: ICTR

institute: university of Wissconsin

description: BRD4 IP

data_processing:
Fastqc files were analyzed for quality metrics (Phred Score, GC content, duplication) using fastQC.
Adapters were trimmed using TrimGalore.
Genome alignment was by MACS2 to the GRCh38.p13 (hg38) genome assembly (NCBI)
Peak calling was using SEACR with top 20% peaks cut-off
Differential peak occupancy was determined using DIFFBIND v 4.2 using DESEQ2 (
Assembly: hg38
Supplementary files format and content: Seacr Peak file using relaxed stringency
Library strategy: CUT&RUN

source_name: hSAEC

growth_protocol: Telomerase-immortalized primary human small airway epithelial (hSAECs) were grown in small airway epithelial cell growth medium (SAGM, Lonza, Walkersville, MD, USA) in 5% CO2.

extract_protocol:
Cells were trypsinized, quantitated and 4 x 106 cells were incubated on ice for 10 minutes in 1 ml of nuclear extraction buffer (20 mM HEPES, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 1x cOmplete proteinase inhibitor, 1x protein phosphatase inhibitor cocktail and 0.5 mM spermidine), the released nuclei were pelleted at 600x g, 5 min at 4 oC.  The nutated nuclei were resuspended in antibody buffer produced by diluting 5 g of anti-SMARCA4 Ab in 500 l of Triton X-100-free wash buffer (WB, 20 mM HEPES, pH7.5, 150 mM NaCl, 0.05% Triton X-100, 0.1% BSA, 1x cOmplete proteinase inhibitor, 1x protein phosphatase inhibitor cocktail and 0.5 mM spermidine), and incubated with nutation overnight at 4 oC.  The nuclei were washed and incubated at 4 oC for 1 h in 50 l of WB containing 2.5 l of EpiCypher pAG-MNase 20x stock (EpiCypher, NC). Chromatin cleavage was conducted by incubating the nuclei on ice for 1 h in 150 l of BSA-free WB containing 2 mM CaCl2. The cleavage was terminated by adding 150 l of stop buffer (300 mM NaCl, 20 mM EDTA, 4 mM EGTA and 0.5 ng of E. coli Spike-in DNA (EpiCypher, NC) per 150 l).  The samples nutated at 4 oC for 1 h, centrifuged at 16,000x g for 5 min at 4 oC and the supernatant was collected. The DNA fragments were phenol-chloroform extracted, glycogen precipitated, and dissolved in 20 l of 0.1x TE buffer. CUT&RUN DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, MA) per the manufacturer’s instruction, with modification in SPRI bead clearance of adaptor ligation and library amplification reactions to retain small-sized DNA fragments. The quality of the resultant DNA libraries was confirmed by Agilent TapeStation HS DNA assay (Agilent, Santa Clara, CA, USA), and paired-end Illumina NGS was carried out on NovaSeq 6000 with 5 million reads per sample.
CUT&RUN DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, MA) per the manufacturer’s instruction, with modification in SPRI bead clearance of adaptor ligation and library amplification reactions to retain small-sized DNA fragments. The quality of the resultant DNA libraries was confirmed by Agilent TapeStation HS DNA assay (Agilent, Santa Clara, CA, USA), and paired-end Illumina NGS was carried out on NovaSeq 6000 with 5 million reads per sample.

treatment_protocol: S ucrose cushion-purified RSV Long strain was used to infect hSAECs at an MOI of 1.0 .

value: hSAEC

value: epithelial

value: Wild type

value: RSV


title: Mock infected WT BRD4 rep2

description: BRD4 IP

value: Mock


title: Mock infected WT BRD4 rep1

description: BRD4 IP


title: Mock infected WT BRD4 rep3

description: BRD4 IP


title: Mock infected WT rep3

description: IgG IP


title: RSV-infected  SMARCAKD BRD4-Rep3

description: BRD4 IP

value: SMARCA4 KD


title: AsPC-1 cells, RoF&Tr

source_name: AsPC-1 cells

value: AsPC-1 cells


title: RSV infected WT BRD4 rep2

description: BRD4 IP


title: Mock infected WT rep1

description: IgG IP


title: AsPC-1 cells, Tr


title: AsPC-1 cells, RoF


title: PSN1,AM9747,rep4

city: Thousand Oaks

first: Paul

last: Hughes

state: CA

address: 1 Amgen Center Dr

institute: Amgen Inc

data_processing:
The raw RNA-seq reads were preprocessed with fastp (v 0.19.8) and quantified by SALMON (v 0.13.1) using Omicsoft-processed gene model Human.B38_OmicsoftGencode.V33 as reference. The transcript-level count matrix was imported to R (v4.0.2) with package tximport (v 1.22.0) and converted to gene-level count object through package DESeq2 (v 1.34.0). Differential expression analysis was performed by fitting generalized linear model GLM against treatment (AM-9747 vs. DMSO control) with cell line as co-variate (~ treatment + cell_line). The significantly differential expressed genes (DEGs) were defined as FDR < 0.05 and absolute fold change > 1.5. The treatment DEGs were further filtered to ensure maximum condition mean FPKQ > 1 for all cell lines. Finally, 1803 treatment DEGs were identified to be differentially expressed in response to IC50 AM-9747 in three pancreas cell lines. These DEGs ranked by log2FC were further used for gene set enrichment analysis (GSEA) in Gene Ontology (GO.db v3.14.0), Reactome (ReactomePA v1.38.0) and Wikipathway (20220710) with R package clusterProfiler (v4.2.2). The enrichment significance was defined as FDR < 0.1 and top 10 enriched pathways were plotted using ggplot2 (v 3.4.2).
Alternative splicing analysis were mainly performed by SplAdder (v3.0.3) First, the raw RNA-seq reads were aligned to human GRCh38 gene model gencode V38 using hisat2 (v 2.2.0) by suppressing discordant alignments for paired reads (--no-discordant). The alignment was passed to create an individual splicing graph per input sample (spladder build --merge-strat single --no-extract-ase). Then all individual graphs were merged into a joint graph representation (spladder build --merge-strat merge_graphs --no-extract-ase) and edges and nodes in joint graph were quantified for each individual input sample (spladder build --merge-strat merge_graphs --no-extract-ase --quantify-graph --qmode single). Six types of events (exon skipping, intron retention, alternative 3’ splice sites, alternative 5’ splice sites, mutual exclusive exons and multiple exon skips) are quantified from the previous graph quantification. To identify the AM-9747 associated alternative splicing events, we compare AM-9747 treated samples to DMSO control within each cell lines using test mode of SplAdder. Significant alternative splicing events in response to AM-9747 were defined as FDR < 0.05 and effect direction is determined by delta percent spliced in (PSI). The genes under significant alternative splicing in response to AM-9747 were further used for gene set over-representative analysis in Gene Ontology, Reactome and Wikipathway with R package clusterProfiler. The enrichment significance was defined as FDR < 0.1 and top 10 enriched pathways were plotted using ggplot2.
Assembly: hg38
Supplementary files format and content: pancreas_cell_lines.AM9747.count_matrix.csv.gz is the count matrix in which row is gene symbol and column are sample name
Supplementary files format and content: pancreas_cell_lines.AM9747.colData.csv is the experiment condition group for samples
Supplementary files format and content: pancreas_cell_lines.AM9747.rowData.csv provide ensemble ids for gene symbol.

growth_protocol: Cell lines were cultured in ATCC-recommended growth media containing 10% FBS. Cell line cultures were maintained at 37°C in an atmosphere of 5% CO2 and cultured for 1-2 weeks prior to use in experiments.

extract_protocol:
Cells were harvested and RNA was extracted using Rneasy mini plus kit following manufacturer's protocols.
Strand-specific RNA sequencing library is prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions

treatment_protocol: 6 days treatment with AM-9747 (100 nM for PSN1 and BxPC3, 150 nM for MIAPACA2).

value: Adenocarcinoma Pancreatic Cell Line

value: PRMT5 inhibitor AM-9747

tag: time

value: Day 6


title: PSN1,AM9747,rep3

value: WT


title: PSN1,AM9747,rep1


title: AsPC-1 cells, Control

value: Pancreatic cancer-derived cells


title: PSN1,vehicle,rep2

value: DMSO


title: RSV-infected  SMARCAKD BRD4-Rep2

description: BRD4 IP


title: RSV-infected  SMARCAKD BRD4-Rep1

description: BRD4 IP


title: Mock-infected  SMARCAKDBRD4-Rep3

description: BRD4 IP


title: Mock-infected  SMARCAKD BRD4-Rep2

description: BRD4 IP


title: PSN1,vehicle,rep1


title: RSV infected WT BRD4 rep3

description: BRD4 IP


title: Mock nfected SMARCA4 KD BRD4 rep1

description: BRD4 IP


title: MIAPACA2,AM9747,rep3


title: MIAPACA2,AM9747,rep2


title: MIAPACA2,AM9747,rep1


title: PSN1,AM9747,rep2


title: MIAPACA2,vehicle,rep2


title: BXPC3,AM9747,rep2


title: MIAPACA2,vehicle,rep1


title: BXPC3,vehicle,rep3


title: BXPC3,vehicle,rep1


title: BXPC3,AM9747,rep3


title: HuH-R-55nm-3

city: 开封

first: yiwei

last: zhao

address: 河南大学金明校区

institute: 河南大学抗体药物开发技术国家地方联合工程实验室

data_processing:
Hisat2（version:2.0.4)Genome mapping
Assembly: GRCh38
Supplementary files format and content: Each folder contains the raw file of each sample, and the excel table contains the processed data of each sample.

source_name: liver

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat# 74106, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA,US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set(Cat#79254, QIAGEN, GmBH, Germany).
According to the experimental instructions, the purified Total RNA was subjected to the steps of mRNA separation, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, terminal repair, 3' terminal A addition, linker connection, enrichment, etc., to complete the construction of sequencing sample library.

tag: tissue

value: liver

value: HuH


title: HuH-R-55nm-2

institute: 河南大学抗体药物开发技术国家地方联合工程实验室

tag: cell line


title: BXPC3,vehicle,rep4

tag: genotype


title: PSN1,vehicle,rep3


title: HuH-P-2

institute: 河南大学抗体药物开发技术国家地方联合工程实验室


title: MIAPACA2,AM9747,rep4


title: HepG2R-250nm-3

institute: 河南大学抗体药物开发技术国家地方联合工程实验室


title: Mock infected WT rep2

description: IgG IP


title: HuH-P-3

institute: 河南大学抗体药物开发技术国家地方联合工程实验室


title: MIAPACA2,vehicle,rep4


title: HepG2-P-3

institute: 河南大学抗体药物开发技术国家地方联合工程实验室


title: HepG2R-250nm-1

institute: 河南大学抗体药物开发技术国家地方联合工程实验室


title: MIAPACA2,vehicle,rep3


title: BXPC3,AM9747,rep4


title: PSN1,vehicle,rep4


title: HepG2-P-1

institute: 河南大学抗体药物开发技术国家地方联合工程实验室


title: BXPC3,AM9747,rep1


title: BXPC3,vehicle,rep2


title: HuH-R-55nm-1

institute: 河南大学抗体药物开发技术国家地方联合工程实验室


title: HuH-P-1

institute: 河南大学抗体药物开发技术国家地方联合工程实验室


title: HepG2R-250nm-2

institute: 河南大学抗体药物开发技术国家地方联合工程实验室


title: FFA treated hepatocyte of H20 rep2

city: Nuthetal

first: Pascal

last: Gottmann

address: Arthur-Scheunert-Allee 114-116

country: Germany

institute: Deutsches Institut für Ernährungsforschung

description:
Column in matrix: H20F2
gene_count.txt
gene_fpkm.txt

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. 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.
Assembly: hg38
Supplementary files format and content: fpkm matrix

source_name: Liver

extract_protocol:
For sequencing, RNA was isolated using RNeasy Plus Kit (QIAGEN) as described in For sequencing, RNA was isolated using RNeasy Plus Kit (QIAGEN) as described in  the product handbook (www.qiagen.com/HB-0405)
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. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for  quantification and bioanalyzer for size distribution detection.

tag: individual

value: Liver

value: Primary hepatocyte

value: FFA


title: FFA treated hepatocyte of H20 rep3

description:
Column in matrix: H20F3
gene_count.txt
gene_fpkm.txt


title: FFA treated hepatocyte of H20 rep1

description:
Column in matrix: H20F1
gene_count.txt
gene_fpkm.txt


title: HepG2-P-2

institute: 河南大学抗体药物开发技术国家地方联合工程实验室


title: FFA treated hepatocyte of H961 rep3

description:
Column in matrix: H961F3
gene_count.txt
gene_fpkm.txt


title: FFA treated hepatocyte of F95P rep3

description:
Column in matrix: F95PF3
gene_count.txt
gene_fpkm.txt


title: FFA treated hepatocyte of H961 rep1

description:
Column in matrix: H961F1
gene_count.txt
gene_fpkm.txt


title: FFA treated hepatocyte of H961 rep2

description:
Column in matrix: H961F2
gene_count.txt
gene_fpkm.txt


title: FFA treated hepatocyte of F95P rep1

description:
Column in matrix: F95PF1
gene_count.txt
gene_fpkm.txt


title: FFA treated hepatocyte of M95 rep1

description:
Column in matrix: M95F1
gene_count.txt
gene_fpkm.txt


title: FFA treated hepatocyte of M95 rep3

description:
Column in matrix: M95F3
gene_count.txt
gene_fpkm.txt


title: FFA treated hepatocyte of M95 rep2

description:
Column in matrix: M95F2
gene_count.txt
gene_fpkm.txt


title: FFA treated hepatocyte of F95 rep1

description:
Column in matrix: F95F1
gene_count.txt
gene_fpkm.txt


title: Control hepatocyte of H20 rep3

description:
Column in matrix: H20C3
gene_count.txt
gene_fpkm.txt

value: Control


title: FFA treated hepatocyte of F95P rep2

description:
Column in matrix: F95PF2
gene_count.txt
gene_fpkm.txt


title: Control hepatocyte of H20 rep2

description:
Column in matrix: H20C2
gene_count.txt
gene_fpkm.txt


title: FFA treated hepatocyte of F95 rep3

description:
Column in matrix: F95F3
gene_count.txt
gene_fpkm.txt


title: GEX_207AIM

city: Seoul

first: Min-Seok

last: Rha

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Otorhinolaryngology

country: South Korea

institute: Yonsei University College of Medicine

description: 10x Genomics

data_processing:
The sequenced data were demultiplexed using the mkfastq function (Cell Ranger, 10X Genomics, v7.1.0) to generate fastq files. Demultiplexed fastq files of gene and ADT expression were aligned to the reference human genome (GRCH38; 10X Cell Ranger reference GRCh38-2020-A) and the barcode sequence of each ADT, and filtering, barcode counting, and UMI counting were performed to generate feature-barcode matrices using the count function (Cell Ranger, v7.1.0).
Assembly: GRCH38
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, filtered_contig_annotations.csv

source_name: Nasal tissue

extract_protocol:
Nasal cells were stimulated with 1 μg/mL SARS-CoV-2 S OLP pools (PepTivator, SARS-CoV-2 Prot_S Complete; Miltenyi Biotec) and 1 μg/mL anti-human CD28 and CD49d mAbs (BD Biosciences) for 24 hours. Following stimulation, nasal cells were stained with PE-conjugated anti-CD3 antibody (BD Biosciences), APC-conjugated CD137 antibody (Miltenyi Biotec), and LIVE/DEAD near-IR fluorescent reactive dye (Invitrogen). And then live CD137+CD3+ T cells were sorted using an ARIA II instrument (BD Biosciences).
Single-cell CITE-seq library was generated using the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) following the manufacturer’s instructions. Libraries were constructed and sequenced at a depth of approximately 33,000 reads per cell for gene, antibody-derived tags (ADTs), and TCR sequence expression using the Novaseq 6000 platform (Illumina).

value: Nasal tissue

value: T cells

value: SARS-CoV-2 spike OLPs

value: mRNA


title: N276_GT

description: gDNA data for genotyping

value: Nasal cells

value: gDNA


title: FB_207AIM

description: 10x Genomics

value: ADT

tag: adt

value: anti-CD107a-TotalSeq-C (H4A3), anti-CD127-TotalSeq-C (A019D5), anti-CD134-TotalSeq-C (Ber-ACT35), anti-CD137-TotalSeq-C (4B4-1), anti-CD14-TotalSeq-C (63D3), anti-CD152-TotalSeq-C (BNI3), anti-CD154-TotalSeq-C (24-31), anti-CD185-TotalSeq-C (J252D4), anti-CCR7-TotalSeq-C (G043H7), anti-CD200-TotalSeq-C (OX-104), anti-CD223-TotalSeq-C (11C3C65), anti-CD25-TotalSeq-C (BC96), anti-ICOS-TotalSeq-C (C398.4A), anti-PD-1-TotalSeq-C (EH12.2H7), anti-CD366-TotalSeq-C (F38-2E2), anti-CD38-TotalSeq-C (HIT2), anti-CD39-TotalSeq-C (A1), anti-CD4-TotalSeq-C (RPA-T4), anti-CD45RA-TotalSeq-C (HI100), anti-CD57-TotalSeq-C (QA17A04), anti-CD69-TotalSeq-C (FN50), anti-CD8-TotalSeq-C (SK1), anti-CD95-TotalSeq-C (DX2), anti-HLA-DR-TotalSeq-C (L243), anti-KLRG1-TotalSeq-C (SA231A2), anti-TCR Vα24-Jα18-TotalSeq-C (6B11), anti-TCR TCR Vα7.2-TotalSeq-C (3C10), anti-TCR α/β -TotalSeq-C (IP26), anti-TCR γ/δ-TotalSeq-C (B1), anti-TIGIT-TotalSeq-C (A15153G)


title: GEX_188AIM

description: 10x Genomics


title: N202_GT

description: gDNA data for genotyping


title: N326_GT

description: gDNA data for genotyping


title: N197_GT

description: gDNA data for genotyping


title: Control hepatocyte of H961 rep2

description:
Column in matrix: H961C2
gene_count.txt
gene_fpkm.txt


title: N188_GT

description: gDNA data for genotyping


title: N207_GT

description: gDNA data for genotyping


title: N304_GT

description: gDNA data for genotyping


title: FB_188AIM

description: 10x Genomics


title: N315_GT

description: gDNA data for genotyping


title: N251_GT

description: gDNA data for genotyping


title: Control hepatocyte of H961 rep1

description:
Column in matrix: H961C1
gene_count.txt
gene_fpkm.txt


title: FFA treated hepatocyte of F95 rep2

description:
Column in matrix: F95F2
gene_count.txt
gene_fpkm.txt


title: Control hepatocyte of H961 rep3

description:
Column in matrix: H961C3
gene_count.txt
gene_fpkm.txt


title: Control hepatocyte of M95 rep2

description:
Column in matrix: M95C2
gene_count.txt
gene_fpkm.txt


title: Control hepatocyte of F95P rep1

description:
Column in matrix: F95PC1
gene_count.txt
gene_fpkm.txt


title: Control hepatocyte of M95 rep3

description:
Column in matrix: M95C3
gene_count.txt
gene_fpkm.txt


title: Control hepatocyte of M95 rep1

description:
Column in matrix: M95C1
gene_count.txt
gene_fpkm.txt


title: Control hepatocyte of F95P rep2

description:
Column in matrix: F95PC2
gene_count.txt
gene_fpkm.txt


title: Control hepatocyte of H20 rep1

description:
Column in matrix: H20C1
gene_count.txt
gene_fpkm.txt


title: Control hepatocyte of F95 rep3

description:
Column in matrix: F95C3
gene_count.txt
gene_fpkm.txt


title: Control hepatocyte of F95 rep1

description:
Column in matrix: F95C1
gene_count.txt
gene_fpkm.txt


title: Vec-3

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

data_processing:
Raw FASTQ files were trimmed by fastp 0.23.2
Trimmed FASTQ files were aligned to hg38 genome by STAR 2.7.10a
BAM files were assemblyed by stringtie
Deseq2 was used to perform differential analysis
Assembly: hg38
Supplementary files format and content: exprSet.csv, csv format, containing the raw counts.

source_name: leukemia

growth_protocol: Jurkat KO-1 cell lines were maintained in RPMI1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidfied atmosphere with 5%CO2 at 37℃.

extract_protocol:
Total RNA isolated using RNAiso Plus (Takara).
RNA libraries for RNA-seq were prepared using Tru-seq Library Prep Kit following manufacturer's protocols

value: leukemia

value: Jurkat

value: vector


title: Vec-1


title: OE-3

value: PDCD1^28 OE


title: OE-2


title: Vec-2


title: RNA_IDH_KDM3B_sh1_rep3

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

description: IDH2 R140Q TF-1 cells infected with KDM3B shRNA, biol rep 3

data_processing:
FASTQ files were demultiplexed using a java script from Takara.
FASTQ files were mapped, and transcript counts were enumerated using STAR.
Counts were input into R and RNA-sequencing analysis was completed using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited-text file includes raw counts for each sample

source_name: IDH2 R140Q TF-1 cells

growth_protocol: Cells were grown in RPMI with 10% FBS at 37 C 5% CO2.

extract_protocol:
RNA was harvested using zymo direct-zol RNA microprep kit. 500 ng was used for construction of sequencing libraries.
cDNA was generated with the SMART-Seq HT Kit (Takara) and RNA-sequencing libraries were prepared with the Nextera XT (Illumina) Kit following manufacturers’ protocols.

treatment_protocol: TF-1 cells were infected with shRNA targeting scrambled control or KDM3B.

value: IDH2 R140Q TF-1 cells

value: IDH2 R140Q

value: KDM3B shRNA


title: OE-1


title: ATAC_TF1_IDH2mut_shKDM3B1_rep3

data_processing:
Raw sequencing reads were trimmed and filtered for quality (Q>15) and adapter content using version 0.4.5 of TrimGalore and running version 1.15 of cutadapt and version 0.11.5 of FastQC.
Version 2.3.4.1 of bowtie2 was employed to align reads to mouse assembly mm10 and alignments were deduplicated using MarkDuplicates in Picard Tools v2.16.0.
Enriched regions were discovered using MACS2 with a p-value setting of 0.001, filtered for blacklisted regions, and a peak atlas was created using +/- 250 bp around peak summits.
The BEDTools suite was used to create normalized bigwig files.
Supplementary files format and content: hg38
Supplementary files format and content: normalized bigwigs

extract_protocol:
Cells were lysed in ATAC-Resuspension Buffer (RSB) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. Tn1 transposition was performed using 50 ul of transposition mixture by pipetting up and down 6 times. Transposition mix = (25 ul 2x TD buffer, 2.5 ul transposase (100nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O).
Libraries were constructed using the Takara ThruPLEX DNA-Seq Kit.


title: RNA_WT_SCR_sh1_rep3

description: WT TF-1 cells infected with SCR shRNA, biol rep 3

source_name: TF-1 cells

value: TF-1 cells

value: wild-type

value: SCR shRNA


title: Control hepatocyte of F95P rep3

description:
Column in matrix: F95PC3
gene_count.txt
gene_fpkm.txt

value: Liver

value: Primary hepatocyte

value: Control


title: ATAC_TF1_IDH2mut_shSCR_rep2

description: IDH2 R140Q TF-1 cells infected with SCR shRNA, biol rep 2


title: RNA_IDH_KDM3B_sh1_rep2

description: IDH2 R140Q TF-1 cells infected with KDM3B shRNA, biol rep 2


title: RNA_IDH_KDM3B_sh1_rep1

description: IDH2 R140Q TF-1 cells infected with KDM3B shRNA, biol rep 1


title: Moffat_54_BT972_PTP4A2_sgB_R3

city: Toronto

first: Jason

last: Moffat

state: Ontario

address: 686 Bay Street

department: Genetics and Genome Biology

institute: Hospital for Sick Children

data_processing:
FASTQ files were first filtered using a bespoke Perl script to remove reads shorter than 36bp.
Filtered FASTQ files were aligned to Gencode v25 gene annotations and hg38 genome build using the STAR short-read aligner (v2.4.2a)
Read count files generated by STAR were merged with gene annotations in R
Assembly: hg38
Supplementary files format and content: tab-delimited text read counts

source_name: glioblastoma

growth_protocol: Cells were cultured in Neurocult Complete media supplemented with 1X antibiotic/antimycotic. Cells were pelletted for RNA extraction and quantification by next-generation sequencing.

extract_protocol:
Total RNA was isolated from cultured GBM cells using Norgen total RNA purification kit following the manufacturer's instructions.
Directional RNA libraries were prepared using the NEBNext Ultra II library prep kits using either standard protocols.

treatment_protocol: CRISPR-edited cells were transduced with AAVS1- or PTP4A2-targeting sgRNAs, selected with puromycin, and cultured as indicated prior to RNA extraction.

value: glioblastoma

value: tumor-derived cell line

value: recurrent GBM

value: Transduced with PTP4A2-targeting sgRNA (B) (CTCATAGGAGATCTCCACAG) in lentiCRISPRv2.


title: RNA_IDH_SCR_sh1_rep2


title: RNA_IDH_SCR_sh1_rep1

description: IDH2 R140Q TF-1 cells infected with SCR shRNA, biol rep 1


title: Moffat_52_BT972_PTP4A2_sgB_R1


title: Moffat_49_BT972_PTP4A2_sgA_R1

value: Transduced with PTP4A2-targeting sgRNA (A) (TACTCTCAACAAGTTCACAG) in lentiCRISPRv2.


title: RNA_WT_SCR_sh1_rep2

description: WT TF-1 cells infected with SCR shRNA, biol rep 2


title: RNA_WT_SCR_sh1_rep1

description: WT TF-1 cells infected with SCR shRNA, biol rep 1


title: Moffat_47_BT972_AAVS1_R2

value: Transduced with AAVS1-targeting sgRNA (GGGGCCACTAGGGACAGGAT) in lentiCRISPRv2.


title: ATAC_TF1_IDH2mut_shKDM3B1_rep1


title: ATAC_TF1_IDH2mut_shSCR_rep3

description: IDH2 R140Q TF-1 cells infected with SCR shRNA, biol rep 3


title: Moffat_38_BT594_AAVS1_R2

value: primary GBM


title: ATAC_TF1_IDH2mut_shSCR_rep1


title: Control hepatocyte of F95 rep2

description:
Column in matrix: F95C2
gene_count.txt
gene_fpkm.txt


title: ATAC_TF1_WT_shSCR_rep3


title: BT972 cell line


title: ATAC_TF1_WT_shSCR_rep2


title: RNA_IDH_SCR_sh1_rep3


title: Moffat_43_BT594_PTP4A2_sgB_R1


title: ATAC_TF1_IDH2mut_shKDM3B1_rep2


title: Perturb-Seq replicate 2 [P_Seq2]

city: Stockholm

first: Peter

middle: Daniel

last: Saliba Gustafsson

state: Stockholm

address: C2:94, Karolinska Universitetssjukhuset Huddinge

department: Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

description: 10X Genomics

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation was carried out using Cell Ranger v. 6
Assembly: hg38
Supplementary files format and content: crispr_analysis generated from standard Cell Ranger v. 6 pipelines
Supplementary files format and content: filtered feature bc matrices generated from standard Cell Ranger v.6 pipelines

source_name: HepaRG

extract_protocol:
Freshly harvested differentiated HepaRG cells, sorted on Sytox Green negativity.
Library was prepared by the Stanford functional genomics core facility according to the manufacturers instruction (single cell 3' v2 protocol with feature barcodes for CRISPRi, 10X Genomics).

value: HepaRG

value: Hepatocyte

value: Differentiated


title: Moffat_51_BT972_PTP4A2_sgA_R3


title: Moffat_50_BT972_PTP4A2_sgA_R2


title: Moffat_53_BT972_PTP4A2_sgB_R2


title: ATAC_TF1_WT_shSCR_rep1


title: Moffat_48_BT972_AAVS1_R3


title: MCF10a_GSK_rep1

city: Singapore

first: Phuong

last: Hoang

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

description: Sheet 2_6DAYS_normalized count; column: MCF10a_GSK_rep1

data_processing:
Raw RNA sequencing files were subjected to quality control by FastQC
Adapter removal and read trimming by Trimmomatic
RNA-Seq read alignment was done by STAR module
Reference genome annotation by R Bioconductor org.Hs.eg.db package
Differential gene expression analysis by R Bioconductor DESeq2 package
Assembly: hg19
Supplementary files format and content: the processed data file in xlsx format whith 2 sheets for 24h and 6 days timepoints. The data file provided normalised count values for genes in each sample for comparison

growth_protocol: MCF10A cells were cultured in DMEM/F12 media (Invitrogen #11330-032) supplemented with 5% horse serum (Invitrogen #16050-122), 20ng/ml EGF (Peprotech), 0.5 mg/ml hydrocortisone (Sigma #H-0888), 100ng/ml Cholera toxin (Sigma #C-8052), 10µg/ml Insulin (Sigma, #I-1882), and 1% penicillin-streptomycin (Invitrogen #15070-063).

extract_protocol:
RNeasy Mini Kit, Qiagen
First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR are added to initiate the secondstrand enrichment

value: Normal breast epithelial

value: GSK591 1uM 6 days


title: MCF10a_GSK_Rep2

description: Sheet 2_6DAYS_normalized count; column: MCF10a_GSK_rep2


title: Moffat_45_BT594_PTP4A2_sgB_R3


title: MCF10a_DMSO_Rep1

description: Sheet 2_6DAYS_normalized count; column: MCF10a_DMSO_Rep1

value: DMSO 6 days


title: MCF10a_DMSO_Rep2

description: Sheet 2_6DAYS_normalized count; column: MCF10a_DMSO_Rep2


title: Moffat_44_BT594_PTP4A2_sgB_R2


title: Moffat_41_BT594_PTP4A2_sgA_R2


title: Moffat_42_BT594_PTP4A2_sgA_R3


title: MCF10a_combo_Rep1

description: Sheet 2_6DAYS_normalized count; column: MCF10a_combo_Rep1

value: HU 1mM + GSK591 1uM 6 days


title: BT594 cell line


title: Moffat_40_BT594_PTP4A2_sgA_R1


title: Merge_WT_2

description: Sheet 1_24H_normalized count; column: Merge_WT_2

value: DMSO 24h


title: Perturb-Seq replicate 5 [PSG_3]

description: 10X Genomics


title: Merge_HU_1

description: Sheet 1_24H_normalized count; column: Merge_HU_1

value: HU 1mM 24h


title: Moffat_37_BT594_AAVS1_R1


title: Merge_WT_1

description: Sheet 1_24H_normalized count; column: Merge_WT_1


title: Merge_GSKHU_1

description: Sheet 1_24H_normalized count; column: Merge_GSKHU_1

value: HU 1mM + GSK591 1uM 24h


title: Perturb-Seq replicate 4 [PSG_2]

description: 10X Genomics


title: Moffat_46_BT972_AAVS1_R1

value: glioblastoma


title: AML1026.3 - Total-seq D

description:
surface marker expression
raw data available in dbGap phs003015.v2

data_processing:
Demultiplexing of llumina sequencer's base call files (BCLs).
Alignment of raw reads to hg19, extraction of cell barcodes, DNA amplicons and oligotags using Tapestri pipeline.
Extraction of called variants and surface marker expression using Tapestri Insights v3.0.2.
Assembly: GRCh19
Supplementary files format and content: Allele frequencies and surface marker expression in tsv file format.
Library strategy: Single cell DNA sequencing and CITE-seq using Total-seq D oligotags.

extract_protocol:
Single cell suspensions were stained with Total-seq D surface marker oligotags followed loading onto Tapestri cartridge.
Single cell DNA and oligotag sequencing according to manufacturer's instructions (Mission Bio) using custom panels for mitochondrial and somatic nuclear DNA mutations.

value: bone marrow

value: ADT


title: Perturb-Seq replicate 1 [DIFF_HRG_PS]

description: 10X Genomics


title: MCF10a_HU_Rep2

description: Sheet 2_6DAYS_normalized count; column: MCF10a_HU_Rep2

value: HU 1mM 6 days


title: MCF10a_HU_Rep1

description: Sheet 2_6DAYS_normalized count; column: MCF10a_HU_Rep1


title: Perturb-Seq replicate 3 [PSG_1]

description: 10X Genomics


title: MCF10a_combo_Rep2

description: Sheet 2_6DAYS_normalized count; column: MCF10a_combo_Rep2


title: Merge_HU_2

description: Sheet 1_24H_normalized count; column: Merge_HU_2


title: Merge_GSK_2

description: Sheet 1_24H_normalized count; column: Merge_GSK_2

value: GSK591 1uM 24h


title: Merge_GSK_1

description: Sheet 1_24H_normalized count; column: Merge_GSK_1


title: Moffat_39_BT594_AAVS1_R3

value: tumor-derived cell line

value: Transduced with AAVS1-targeting sgRNA (GGGGCCACTAGGGACAGGAT) in lentiCRISPRv2.


title: AML1026.1 - Total-seq D

value: screening


title: AML1026.1 - scDNA-seq

description:
single cell DNA sequencing amplicons
raw data available in dbGap phs003015.v2

value: amplicon


title: CLL6 pre-FCR + CLL4 pre-FCR - scDNA-seq

description: single cell DNA sequencing amplicons

source_name: peripheral blood

value: peripheral blood

value: pooled samples


title: CLL4 post-HSCT + CLL5 pre-FCR - Total-seq D

description: surface marker expression


title: AML1026.12 TSA/TSB

description:
hashtags and surface marker expression
raw data available in dbGap phs003015.v2

data_processing:
Demultiplexing of llumina sequencer's base call files (BCLs) using cellranger-atac mkfastq.
Alignment of raw reads to hg38, extraction of cell barcodes and DNA fragments using cellranger-atac count.
Conversion of fastq files for TSA/TSB using ASAP to kite (https://github.com/caleblareau/asap_to_kite)
Pseudoalignment and quantification of TSA/TSB counts using kallisto | bustools (PMID 33795888).
Assembly: GRCh38
Supplementary files format and content: Feature count matrix and cell barcode list in tsv file format.
Supplementary files format and content: DNA fragments in tsv file format.
Library strategy: ASAP-seq (scATAC-seq and CITE-seq using Total-seq A/B oligotags)

source_name: bone marrow

extract_protocol:
Single cell suspensions were stained with Total-seq A hashtags and Total-seq B surface marker oligotags followed by fixation with 1% formaldehyde and lysis with NP-40 substitute to retain mitochondrial DNA as described by Lareau & Ludwig et al., Nature Biotechnology 2021 (PMID 32788668) and Mimitou et al., Nature Biotechnology 2021 (PMID 34083792).
Single Cell ATAC (Assay for Transposase Accessible Chromatin) using Chromium platform (10x Genomics) according to manufacturer's instructions.

value: ADT + HTO

tag: pooling

value: AML1026.1 A0251 (GTCAACTCTTTAGCG) and A0252 (TGATGGCCTATTGGG); AML1026.2 A0253 (TTCCGCCTCTCTTTG) and A0254 (AGTAAGTTCAGCGTA)

value: screening and decitabine


title: AML1012.34 TSA/TSB

value: AML1012.3 A0251 (GTCAACTCTTTAGCG) and A0252 (TGATGGCCTATTGGG); AML1012.4 A0253 (TTCCGCCTCTCTTTG) and A0254 (AGTAAGTTCAGCGTA)

value: C2 and end-of-treatment


title: CLL6 pre-FCR + CLL4 pre-FCR- Total-seq D

description: surface marker expression


title: CLL4 post-HSCT + CLL5 pre-FCR - scDNA-seq

description: single cell DNA sequencing amplicons


title: AML1026.34 TSA/TSB

value: AML1026.3 A0251 (GTCAACTCTTTAGCG) and A0252 (TGATGGCCTATTGGG); AML1026.4 A0253 (TTCCGCCTCTCTTTG) and A0254 (AGTAAGTTCAGCGTA)

value: C1 and end-of-treatment


title: AML1010.45 TSA/TSB

value: bone marrow

value: AML1010.4 A0251 (GTCAACTCTTTAGCG) and A0252 (TGATGGCCTATTGGG); AML1010.5 A0253 (TTCCGCCTCTCTTTG) and A0254 (AGTAAGTTCAGCGTA)

value: C4 and C10


title: AML1026.34 scATAC-seq

description:
single cell chromatin accessibility
raw data available in dbGap phs003015.v2

value: ATAC


title: AML1026.12 scATAC-seq


title: AML1012.34 scATAC-seq


title: AML1010.23 TSA/TSB

value: AML1010.2 A0251 (GTCAACTCTTTAGCG) and A0252 (TGATGGCCTATTGGG); AML1010.3 A0253 (TTCCGCCTCTCTTTG) and A0254 (AGTAAGTTCAGCGTA)

value: decitabine and C1


title: AML1010.1 scATAC-seq

value: screening


title: AML1010.45 scATAC-seq


title: AML1012.12 scATAC-seq

value: AML1012.1 A0251 (GTCAACTCTTTAGCG) and A0252 (TGATGGCCTATTGGG); AML1012.2 A0253 (TTCCGCCTCTCTTTG) and A0254 (AGTAAGTTCAGCGTA)


title: AML1010.23 scATAC-seq


title: IST4.2 TSB

description: surface marker expression

data_processing:
Demultiplexing of llumina sequencer's base call files (BCLs) using cellranger-atac mkfastq.
Alignment of raw reads to hg38, extraction of cell barcodes and DNA fragments using cellranger-atac count.
Conversion and demultiplexing of fastq files for TSA/TSB using ASAP to kite (https://github.com/caleblareau/asap_to_kite)
Pseudoalignment and quantification of TSA/TSB counts using kallisto | bustools (PMID 33795888).
Assembly: GRCh38
Supplementary files format and content: Feature count matrix and cell barcode list in tsv file format.
Supplementary files format and content: DNA fragments in tsv file format.
Library strategy: ASAP-seq (scATAC-seq and CITE-seq using Total-seq A/B oligotags)

extract_protocol:
Single cell suspensions were stained with Total-seq A streptavidin oligotag-tetramer conjugates and Total-seq B surface marker oligotags followed by fixation with 1% formaldehyde and lysis with NP-40 substitute to retain mitochondrial DNA as described by Lareau & Ludwig et al., Nature Biotechnology 2021 (PMID 32788668) and Mimitou et al., Nature Biotechnology 2021 (PMID 34083792).
Single Cell ATAC (Assay for Transposase Accessible Chromatin) using Chromium platform (10x Genomics) according to manufacturer's instructions.

value: peripheral blood

value: ADT

value: post-IST


title: AML1026.3 - scDNA-seq

value: amplicon


title: IST4.1 TSA

description: tetramer staining

value: pre-IST


title: IST4.2 TSA

description: tetramer staining


title: IST3.2 TSB

description: surface marker expression


title: IST3.2 TSA

description: tetramer staining


title: IST4.1 scATAC-seq

description: single cell chromatin accessibility


title: IST3.2 scATAC-seq

description: single cell chromatin accessibility


title: IST4.2 scATAC-seq

description: single cell chromatin accessibility


title: AML1012.12 TSA/TSB

value: ADT + HTO

value: screening and decitabine


title: IST2.2 TSA

description: tetramer staining


title: IST2.2 TSB

description: surface marker expression


title: IST2.2 scATAC-seq

description: single cell chromatin accessibility


title: IST2.1 TSA

description: tetramer staining


title: IST3.1 TSA

description: tetramer staining


title: IST2.1 scATAC-seq

description: single cell chromatin accessibility


title: IST2.1 TSB

description: surface marker expression


title: AML1010.1 TSB


title: IST1.2 BM TSB

description: surface marker expression


title: IST1.2 BM TSA

description: tetramer staining


title: IST1.1 BM scATAC-seq

description: single cell chromatin accessibility


title: IST1.2 BM scATAC-seq

description: single cell chromatin accessibility


title: IST1.1 BM TSB

description: surface marker expression


title: IST1.2 PB TSA

description: tetramer staining


title: IST1.1 BM TSA

description: tetramer staining


title: IST4.1 TSB

description: surface marker expression


title: MART1.3 TSB ratio 1:300

description:
surface marker expression
MART1.3 TSB

source_name: mix of T cell culture and PBMC 1:300

growth_protocol: MART1-specific T cells were transduced with a lentiviral expression vector as described in Oliveira et al., Nature 2021 (PMID 34290406) and Oliveira et al., Nature 2022 (PMID 35508657)

treatment_protocol: CD28/CD3 bead activation, IL7/IL15 T cell expansion, lentiviral expression with supernatant of HEK293T cells.

value: mix of T cell culture and PBMC 1:300

value: CD28/CD3 bead activation and IL7/IL15 T cell expansion; lentiviral transduction


title: IST3.1 TSB

description: surface marker expression


title: IST3.1 scATAC-seq

description: single cell chromatin accessibility


title: MART1.3 TSA ratio 1:300

description:
tetramer staining
MART1.3 TSA


title: IST1.1 PB TSA

description: tetramer staining


title: IST1.1 PB TSB

description: surface marker expression


title: MART1.2 scATAC-seq ratio 1:30

description:
single cell chromatin accessibility
MART1.2 scATAC-seq

source_name: mix of T cell culture and PBMC 1:30

value: mix of T cell culture and PBMC 1:30


title: MART1.1 TSA ratio 1:3

description:
tetramer staining
MART1.1 TSA

source_name: mix of T cell culture and PBMC 1:3

value: mix of T cell culture and PBMC 1:3


title: MART1.3 scATAC-seq ratio 1:300

description:
single cell chromatin accessibility
MART1.3 scATAC-seq


title: Fusion positive leukemic cells secondary transplant (mouse identifier CEI_TY_CG_M1.(2-1))  [SJAML063765_G1]

city: Palo Alto

first: Tanja

middle: A

last: Gruber

address: 1000 Welch Road Suite 300

department: Pediatrics

description:
Fusion positive leukemic cells secondary transplant (mouse identifier CEI_TY_CG_M1.(2-1))
RNASeq_rawcounts_heatmap.txt

data_processing:
Raw CUT&RUN-seq FASTQ files were aligned using Basepair (aligner Bowtie and reference genome hg19). MACS2 (v2.2.71) was used to call peaks (using parameters --shift 0 -m 5 50 -g 2700000000 --pvalue 1e-3 --call-summits -B --SPMR) against IgG control for each Sample. (Samples lines 29 - 48)
RNA-seq reads in BAM format (aligned to hg19 using STAR v2.3.0e) were converted to raw counts uing HTSeq (htseq-count, v0.11.2). Raw counts were processed for differential expression testing using DESeq2 (v1.32.0) R package installed in R v4.1, using default settings. (Sample lines 55-83)
For RNA-seq reads from the NHR2del experiment, raw RNA-seq reads in FASTQ format were pre-processed (trimmed using Trimmomatic v0.39) before aligned to hg38 using STAR (v2.7.1a). Raw counts were processed for differential expression testing using DESeq2 (v1.32.0) R package installed in R v4.1, using default settings. (Sample lines 49 - 54)
Assembly: hg19, hg38
Supplementary files format and content: tab-delimited MACS2 output for each Sample
Supplementary files format and content: tab-delimited raw gene counts for each Sample

source_name: Blood

extract_protocol:
EpiCypher CUTANA ChIC/CUT&RUN Kit
Trizol extraction
CUT&RUN sequencing was performed according to the manufacturer's instructions using the DNA library prep (NEBNext/ChIPSeq) kit
RNA sequencing was performed according to the manufacturer's instructions using the low input RNA (Ovation/NEB) library prep kit

value: Blood

value: Megakaryoblasts


title: IST1.1 PB scATAC-seq

description: single cell chromatin accessibility

value: ATAC


title: Fusion negative megakaryoblasts in vitro culture technical rep 3 [SJAML059893_G3]

description:
Fusion negative megakaryoblasts in vitro culture technical replicate 3
RNASeq_rawcounts_heatmap.txt


title: Fusion negative megakaryoblasts in vitro culture technical rep 2 [SJAML059892_G3]

description:
Fusion negative megakaryoblasts in vitro culture technical replicate 2
RNASeq_rawcounts_heatmap.txt


title: MART1.2 TSA ratio 1:30

description:
tetramer staining
MART1.2 TSA


title: MART1.1 TSB ratio 1:3

description:
surface marker expression
MART1.1 TSB


title: Fusion positive megakaryoblasts in vitro culture biological rep 3 technical rep 2 [SJAML059895_G3-CD34_pCDH_CG_8]

description:
Fusion positive megakaryoblasts in vitro culture biological replicate 3 technical replicate 2
RNASeq_rawcounts_tSNE.txt


title: Fusion positive leukemic cells secondary transplant (mouse identifier CEI_TY_CG_M1.(2-2))  [SJAML063766_G1]

description:
Fusion positive leukemic cells secondary transplant (mouse identifier CEI_TY_CG_M1.(2-2))
RNASeq_rawcounts_heatmap.txt


title: Fusion positive megakaryoblasts in vitro culture biological rep 2 technical rep 1 [SJAML059894_G2-CD34_pCDH_CG_4]

description:
Fusion positive megakaryoblasts in vitro culture biological replicate 2 technical replicate 1
RNASeq_rawcounts_tSNE.txt


title: IST1.2 PB TSB

description: surface marker expression


title: IST1.2 PB scATAC-seq

description: single cell chromatin accessibility


title: Fusion negative megakaryoblasts in vitro culture technical rep 1 [SJAML059891_G3]

description:
Fusion negative megakaryoblasts in vitro culture technical replicate 1
RNASeq_rawcounts_heatmap.txt


title: Fusion positive megakaryoblasts in vitro culture biological rep 1 technical rep 2 [SJAML059895_G1-CD34_pCDH_CG_2]

description:
Fusion positive megakaryoblasts in vitro culture biological replicate 1 technical replicate 2
RNASeq_rawcounts_tSNE.txt


title: MART1.1 scATAC-seq ratio 1:3

description:
single cell chromatin accessibility
MART1.1 scATAC-seq


title: Fusion positive megakaryoblasts in vitro culture biological rep 2 technical rep 2 [SJAML059895_G2-CD34_pCDH_CG_5]

description:
Fusion positive megakaryoblasts in vitro culture biological replicate 2 technical replicate 2
RNASeq_rawcounts_tSNE.txt


title: Fusion positive megakaryoblasts in vitro culture biological rep 1 technical rep 1 [SJAML059894_G1-CD34_pCDH_CG_1]

description:
Fusion positive megakaryoblasts in vitro culture biological replicate 1 technical replicate 1
RNASeq_rawcounts_tSNE.txt


title: Fusion positive megakaryoblasts in vitro culture biological rep 2 technical rep 3 [SJAML059896_G2-CD34_pCDH_CG_6]

description:
Fusion positive megakaryoblasts in vitro culture biological replicate 2 technical replicate 3
RNASeq_rawcounts_tSNE.txt


title: MART1.2 TSB ratio 1:30

description:
surface marker expression
MART1.2 TSB


title: Fusion positive leukemic cells tertiary transplant (mouse identifier pCDH_CG_M1.(2-1).(3-4))  [SJAML067175_C2-011020]

description:
Fusion positive leukemic cells tertiary transplant (mouse identifier pCDH_CG_M1.(2-1).(3-4))
RNASeq_rawcounts_tSNE.txt


title: Fusion positive megakaryoblasts in vitro culture biological rep 3 technical rep 3 [SJAML059896_G3-CD34_pCDH_CG_9]

description:
Fusion positive megakaryoblasts in vitro culture biological replicate 3 technical replicate 3
RNASeq_rawcounts_tSNE.txt


title: Fusion positive megakaryoblasts in vitro culture biological rep 1 technical rep 3 [SJAML059896_G1-CD34_pCDH_CG_3]

description:
Fusion positive megakaryoblasts in vitro culture biological replicate 1 technical replicate 3
RNASeq_rawcounts_tSNE.txt


title: Fusion positive leukemic cells tertiary transplant (mouse identifier pCDH_CG_M2.(2-1).(3-4))  [SJAML066706_C2-0919]

description:
Fusion positive leukemic cells tertiary transplant (mouse identifier pCDH_CG_M2.(2-1).(3-4))
RNASeq_rawcounts_tSNE.txt


title: Fusion positive leukemic cells tertiary transplant (mouse identifier pCDH_CG_M1.(2-1).(3-2))  [SJAML067175_C1-011020]

description:
Fusion positive leukemic cells tertiary transplant (mouse identifier pCDH_CG_M1.(2-1).(3-2))
RNASeq_rawcounts_tSNE.txt


title: Fusion positive leukemic cells tertiary transplant (mouse identifier pCDH_CG_M2.(2-1).(3-2))  [SJAML066706_C1-0919]

description:
Fusion positive leukemic cells tertiary transplant (mouse identifier pCDH_CG_M2.(2-1).(3-2))
RNASeq_rawcounts_tSNE.txt


title: Fusion positive leukemic cells primary transplant (mouse identifier pCDH_CG_M6)  [SJAML063772_G1-030419]

description:
Fusion positive leukemic cells primary transplant (mouse identifier pCDH_CG_M6)
RNASeq_rawcounts_tSNE.txt


title: Fusion positive leukemic cells primary transplant (mouse identifier pCDH_CG_M4)  [SJAML063770_G1-030419]

description:
Fusion positive leukemic cells primary transplant (mouse identifier pCDH_CG_M4)
RNASeq_rawcounts_tSNE.txt


title: Fusion positive leukemic cells primary transplant (mouse identifier pCDH_CG_M3)  [SJAML063769_G1-102318]

description:
Fusion positive leukemic cells primary transplant (mouse identifier pCDH_CG_M3)
RNASeq_rawcounts_tSNE.txt


title: Fusion positive leukemic cells secondary transplant (mouse identifier pCDH_CG_M5.(2-2))  [SJAML066706_C4-103119]

description:
Fusion positive leukemic cells secondary transplant (mouse identifier pCDH_CG_M5.(2-2))
RNASeq_rawcounts_tSNE.txt


title: Fusion positive megakaryoblasts  in vitro culture biological rep 3 technical rep 1 [SJAML059894_G3-CD34_pCDH_CG_7]

description:
Fusion positive megakaryoblasts  in vitro culture biological replicate 3 technical replicate 1
RNASeq_rawcounts_tSNE.txt


title: Fusion positive leukemic cells secondary transplant (mouse identifier pCDH_CG_M1.(2-2))  [SJAML063774_G1-030419]

description:
Fusion positive leukemic cells secondary transplant (mouse identifier pCDH_CG_M1.(2-2))
RNASeq_rawcounts_tSNE.txt


title: Fusion positive leukemic cells secondary transplant (mouse identifier pCDH_CG_M2.(2-2)) [SJAML066706_C3-103119]

description:
Fusion positive leukemic cells secondary transplant (mouse identifier pCDH_CG_M2.(2-2))
RNASeq_rawcounts_tSNE.txt


title: Fusion positive leukemic cells secondary transplant (mouse identifier pCDH_CG_M1.(2-1)) [SJAML063773_G1-030419]

description:
Fusion positive leukemic cells secondary transplant (mouse identifier pCDH_CG_M1.(2-1))
RNASeq_rawcounts_tSNE.txt


title: Fusion positive leukemic cells primary transplant (mouse identifier pCDH_CG_M5)  [SJAML063771_G1-030419]

description:
Fusion positive leukemic cells primary transplant (mouse identifier pCDH_CG_M5)
RNASeq_rawcounts_tSNE.txt


title: NHR2del fusion positive megakaryoblasts in vitro culture  [7756_EG_6]

description:
NHR2del fusion positive megakaryoblasts in vitro culture heatmap technical replicate 3
RNASeq_rawcounts_7756_EG_1_through_6.txt

value: CBFA2T3-GLIS2 NHR2del


title: NHR2del fusion positive megakaryoblasts in vitro culture  [7756_EG_5]

description:
NHR2del fusion positive megakaryoblasts in vitro culture heatmap technical replicate 2
RNASeq_rawcounts_7756_EG_1_through_6.txt


title: Fusion positive leukemic cells primary transplant (mouse identifier pCDH_CG_M2)  [SJAML063768_G1-102318]

description:
Fusion positive leukemic cells primary transplant (mouse identifier pCDH_CG_M2)
RNASeq_rawcounts_tSNE.txt


title: Fusion positive leukemic cells primary transplant (mouse identifier pCDH_CG_M1)  [SJAML063767_G1-102318]

description:
Fusion positive leukemic cells primary transplant (mouse identifier pCDH_CG_M1)
RNASeq_rawcounts_tSNE.txt


title: Wild type fusion positive megakaryoblasts in vitro culture  [7756_EG_3]

description:
Wild type fusion positive megakaryoblasts in vitro culture heatmap technical replicate 3
RNASeq_rawcounts_7756_EG_1_through_6.txt


title: NHR2del fusion positive megakaryoblasts in vitro culture  [7756_EG_4]

description:
NHR2del fusion positive megakaryoblasts in vitro culture heatmap technical replicate 1
RNASeq_rawcounts_7756_EG_1_through_6.txt


title: Wild type fusion positive megakaryoblasts in vitro culture  [7756_EG_2]

description:
Wild type fusion positive megakaryoblasts in vitro culture heatmap technical replicate 2
RNASeq_rawcounts_7756_EG_1_through_6.txt


title: Fusion negative megakaryoblasts in vitro culture CtBP1 IP  [7368_EG_34]

description:
Fusion negative megakaryoblasts in vitro culture CtBP1 IP biological replicate 1
macs2_output.xlsx

data_processing:
library strategy: CUT&RUN
Raw CUT&RUN-seq FASTQ files were aligned using Basepair (aligner Bowtie and reference genome hg19). MACS2 (v2.2.71) was used to call peaks (using parameters --shift 0 -m 5 50 -g 2700000000 --pvalue 1e-3 --call-summits -B --SPMR) against IgG control for each Sample. (Samples lines 29 - 48)
RNA-seq reads in BAM format (aligned to hg19 using STAR v2.3.0e) were converted to raw counts uing HTSeq (htseq-count, v0.11.2). Raw counts were processed for differential expression testing using DESeq2 (v1.32.0) R package installed in R v4.1, using default settings. (Sample lines 55-83)
For RNA-seq reads from the NHR2del experiment, raw RNA-seq reads in FASTQ format were pre-processed (trimmed using Trimmomatic v0.39) before aligned to hg38 using STAR (v2.7.1a). Raw counts were processed for differential expression testing using DESeq2 (v1.32.0) R package installed in R v4.1, using default settings. (Sample lines 49 - 54)
Assembly: hg19, hg38
Supplementary files format and content: tab-delimited MACS2 output for each Sample
Supplementary files format and content: tab-delimited raw gene counts for each Sample

tag: antibody

value: ThermoFisher 10972-1-AP


title: Wild type fusion positive megakaryoblasts in vitro culture  [7756_EG_1]

description:
Wild type fusion positive megakaroblasts in vitro culture heatmap technical replicate 1
RNASeq_rawcounts_7756_EG_1_through_6.txt


title: Fusion negative megakaryoblasts in vitro culture rabbit IgG IP [EG_019]

description:
Fusion negative megakaryoblasts in vitro culture rabbit IgG IP
macs2_output.xlsx

value: Epicypher 13-0042


title: Fusion negative megakaryoblasts in vitro culture CtBP1 IP  [7495_EG_19]

description:
Fusion negative megakaryoblasts in vitro culture CtBP1 IP biological replicate 2
macs2_output.xlsx


title: Fusion negative megakaryoblasts in vitro culture H3K27ac IP  [7368_EG_31]

description:
Fusion negative megakaryoblasts in vitro culture H3K27ac IP biological replicate 1
macs2_output.xlsx

value: Active Motif 39034


title: Fusion negative megakaryoblasts in vitro culture p300 IP  [8099_EG_13]

description:
Fusion negative megakaryoblasts in vitro culture p300 IP biological replicate 1
macs2_output.xlsx

value: ThermoFisher PA1848


title: Fusion positive leukemic cells rabbit (mouse identifier CEI_TY_CG_M1.(2-1)) IgG IP [EG_016]

description:
Fusion positive leukemic cells rabbit (mouse identifier CEI_TY_CG_M1.(2-1)) IgG IP
macs2_output.xlsx


title: Fusion negative megakaryoblasts in vitro culture ETO IP  [7368_EG_33]

description:
Fusion negative megakaryoblasts in vitro culture ETO IP biological replicate 1
macs2_output.xlsx

value: Bethyl A303-509A


title: Fusion positive leukemic cells secondary transplant (mouse identifier pCDH_CG_M2.(2-1))  [SJAML063775_G1-030419]

description:
Fusion positive leukemic cells secondary transplant (mouse identifier pCDH_CG_M2.(2-1))
RNASeq_rawcounts_tSNE.txt


title: Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-2)) TY IP [7495_EG_16]

description:
Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-2)) TY IP biological replicate 2
macs2_output.xlsx

value: GenScript A01004-40


title: Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-1)) H3K27ac IP [7368_EG_24]

description:
Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-1)) H3K27ac IP biological replicate 1
macs2_output.xlsx


title: Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-2)) CtBP1 IP [7621_EG_12]

description:
Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-2)) CtBP1 IP biological replicate 2
macs2_output.xlsx


title: Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-2)) H3K27ac IP [EG_014]

description:
Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-2)) H3K27ac IP biological replicate 2
macs2_output.xlsx


title: Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-1)) TY IP [7368_EG_23]

description:
Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-1)) TY IPbiological replicate 1
macs2_output.xlsx


title: Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-1)) CtBP1 IP [7368_EG_27]

description:
Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-1)) CtBP1 IP biological replicate 1
macs2_output.xlsx


title: Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-2)) ETO IP [8099_EG_11]

description:
Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-2)) ETO IP biological replicate 2
macs2_output.xlsx


title: Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-1)) ETO IP [7621_EG_8]

description:
Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-1)) ETO IP biological replicate 1
macs2_output.xlsx


title: Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-2)) p300 IP [7368_EG_28]

description:
Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-2)) p300 IP biological replicate 2
macs2_output.xlsx


title: Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-1))  p300 IP [8099_EG_12]

description:
Fusion positive leukemic cells (mouse identifier CEI_TY_CG_M1.(2-1))  p300 IPbiological replicate 1
macs2_output.xlsx


title: BX0279_067

city: Jena

first: Alberto

last: Garcia Lopez

state: Thuringia

address: Adolf-Reichwein-Straße 23

department: Microbiome Dynamics

institute: Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute

data_processing:
Quality of raw read data was checked using FastQC (v0.11.8).
Reads were quality- and adapter-trimmed using Trimmomatic (v0.39)
Reads were rRNA-filtered using SortMeRNA version (v2.1b) with a single rRNA database concatenated from all rRNA databases shipped with SortMeRNA.
Reads were mapped against the human reference genome and corresponding annotation GRCh38.99 (obtained from www.ensembl.org) using HiSAT2 (v2.1.0).
Differentially expressed genes (DEGs) were determined if significance was reported by either DESeq2 (v1.22.1), or edgeR (v3.24.3) and a |log2(fold change)|≥ 0.25.
Assembly: GRCh38.99
Supplementary files format and content: raw_counts.tsv = Raw counts of sequencing reads (matrix table)
Supplementary files format and content: mrn_counts.tsv = MRN (Median Ratio Normalization) counts of sequencing reads (matrix table)

source_name: Whole blood

growth_protocol: Blood was sampled from 61 patients with community-acquired pneumonia by SARS-CoV-2 (51 of those patients were classified as sepsis patients) of either sex within the first 24 h of hospital admission from three different study sites in Greece. Sampling was done before treatment with any biological disease-modifying drug or with corticosteroids

extract_protocol:
Total RNA was extracted from whole blood samples and preserved with RNAlater (ThermoFisher). 1.8 mL of RNAlater-preserved blood was used for manual RNA extraction using the RiboPure-Blood Kit (Thermofisher) and following the manufacturer’s instructions.
mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs(dUTP, dATP, dGTP and dCTP), RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Purification followed by AMPure XP beads, terminal repair, polyadenylation, sequencing adapter ligation, size selection and degradation of second-strand U-contained cDNA by the USER enzyme. The strand-specific cDNA library was generated after the final PCR enrichment. QC of the constructed library included testing library concentration preliminary with Qubit 2.0 Fluorometer (ThermoFisher), insert size with BioAnalyzer 2100 (Agilent) and qPCR to quantify effective library concentration. Qualified QC checked libraries were loaded on a NovaSeq 6000 S4 (Illumina) for sequencing using paired end mode with 150 bp read length (2x150 cycles)

value: Whole blood

tag: classification

value: Mild COVID-19


title: Fusion negative megakaryoblasts in vitro culture p300 IP  [7495_EG_21]

description:
Fusion negative megakaryoblasts in vitro culture p300 IP biological replicate 2
macs2_output.xlsx


title: BX0279_069

treatment_protocol: Blood was sampled from 61 patients with community-acquired pneumonia by SARS-CoV-2 (51 of those patients were classified as sepsis patients) of either sex within the first 24 h of hospital admission from three different study sites in Greece. Sampling was done before treatment with any biological disease-modifying drug or with corticosteroids


title: BX0279_068


title: Fusion negative megakaryoblasts in vitro culture H3K27ac IP  [7621_EG_6]

description:
Fusion negative megakaryoblasts in vitro culture H3K27ac IP biological replicate 2
macs2_output.xlsx


title: BX0279_066


title: Fusion negative megakaryoblasts in vitro culture ETO IP  [7495_EG_17]

description:
Fusion negative megakaryoblasts in vitro culture ETO IP biological replicate 2
macs2_output.xlsx


title: BX0279_063


title: BX0279_064


title: BX0279_065


title: BX0279_057

value: Severe COVID-19 (Sepsis)


title: BX0279_062


title: BX0279_059


title: BX0279_056


title: BX0279_060


title: BX0279_061


title: BX0279_054


title: BX0279_055


title: BX0279_053


title: Merge_GSKHU_2

description: Sheet 1_24H_normalized count; column: Merge_GSKHU_2

value: Normal breast epithelial

value: HU 1mM + GSK591 1uM 24h


title: BX0279_052


title: BX0279_051


title: BX0279_050


title: BX0279_047


title: BX0279_048


title: BX0279_045


title: BX0279_043


title: BX0279_046


title: BX0279_044


title: BX0279_041


title: BX0279_042


title: BX0279_040


title: BX0279_058


title: BX0279_039


title: BX0279_038


title: BX0279_035


title: BX0279_034


title: BX0279_037


title: BX0279_033


title: BX0279_032


title: BX0279_031


title: BX0279_028


title: BX0279_029


title: BX0279_036


title: BX0279_027


title: BX0279_030


title: BX0279_010


title: BX0279_011


title: BX0279_012


title: BX0279_049


title: BX0279_025


title: BX0279_016


title: BX0279_006


title: BX0279_015


title: BX0279_013


title: BX0279_003


title: BX0279_014


title: BX0279_005


title: BX0279_004


title: BX0279_009


title: BX0279_002


title: BX0279_007


title: BX0279_008


title: SIRS S225

extract_protocol:
Total RNA was extracted from whole blood pre-operative samples and preserved with RNAlater (ThermoFisher). 1.8 mL of RNAlater-preserved blood was used for manual RNA extraction using the RiboPure-Blood Kit (Thermofisher) and following the manufacturer’s instructions.
mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs(dUTP, dATP, dGTP and dCTP), RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Purification followed by AMPure XP beads, terminal repair, polyadenylation, sequencing adapter ligation, size selection and degradation of second-strand U-contained cDNA by the USER enzyme. The strand-specific cDNA library was generated after the final PCR enrichment. QC of the constructed library included testing library concentration preliminary with Qubit 2.0 Fluorometer (ThermoFisher), insert size with BioAnalyzer 2100 (Agilent) and qPCR to quantify effective library concentration. Qualified QC checked libraries were loaded on a NovaSeq 6000 S4 (Illumina) for sequencing using paired end mode with 150 bp read length (2x150 cycles)

tag: condition

value: SIRS+

tag: organ dysfunction

value: yes

tag: Sex

value: Male


title: S171

value: UInf+

value: no

value: Female


title: S061


title: S067

value: Sepsis+


title: C035

value: SIRS-


title: C032


title: BX0279_026


title: C290


title: BX0279_001


title: S155


title: S060


title: S194


title: S038


title: C010


title: S269


title: C169


title: S241


title: S292


title: SIRS S169


title: C257


title: SIRS S319


title: C137


title: S319


title: C084


title: C319


title: S210


title: C239


title: C210


title: C292


title: C323


title: C224


title: C278


title: C223


title: C212


title: SIRS S258


title: C284


title: C261


title: SIRS S278


title: C260


title: C250


title: C204


title: S257


title: S108


title: S198


title: S178


title: S137


title: SIRS S245


title: S278


title: C238


title: SIRS S239


title: C198


title: S280


title: SIRS S142


title: S113


title: C245


title: S284


title: S281


title: S238


title: S142


title: S263


title: S261


title: S197


title: S266


title: S239


title: S245


title: C159


title: C171


title: SIRS S191


title: C131


title: C142


title: C190


title: C113


title: C217


title: C214


title: C207


title: S264


title: C108


title: S250


title: S262


title: S246


title: S139


title: S249


title: C264


title: C215


title: SIRS S193


title: S204


title: SIRS S224


title: Y4Y-3

city: Lanzhou

first: shaoke

last: guo

state: Gansu

address: West Lake Street

department: Lanzhou institute of husbandry and pharmaceutical sciences

description: ribosome footprints

data_processing:
Fastp filters low-quality readings.
The short reading comparison tool Bowtie2 is used to map readings to ribosomal RNA (rRNA) databases, GenBank, and Rfam databases. Remove readings of rRNA, transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), and miRNA.
Compare the processed RNA seq readings with the genome.
A trinucleotide cycle diagram was drawn using the riboWaltz R software package.
Assembly: LU_Bosgru_v3.0
Supplementary files format and content: Calculate the number of reads in the open reading frame of coding genes using software RSEM, and normalize gene expression levels using FPKM method
Library strategy: Ribo-seq

organism: Bos grunniens

source_name: yak

growth_protocol: In this study, all animal-related procedures conformed to the China Council on Animal Care and the Ministry of Agriculture of the People’s Republic of China guidelines. All yak-handling procedures were approved by The Animal Care and Use Committee of the Lanzhou Institute of Husbandry and Pharmaceutical Sciences Chinese Academy of Agricultural Sciences (Permit No: LIHPS-2022-0144).

extract_protocol:
Grind the frozen tissue into powder using a mortar and pestle in liquid nitrogen, and then dissolve it in 400 μ L lysis buffer. The ribosomal profiling technique was carried out according to the report. Add short (50-80 base) antisense DNA probes complementary to rRNA sequences to a solution containing RFs, and then add RNase H and DNase I to digest rRNA and residual DNA probes. Finally, further purification of RFs was carried out using magnetic beads.
Add adapters to both ends of RFs and perform reverse transcription and PCR amplification. Enrich PCR products with sizes of 140-160bp to generate cDNA libraries, and sequence using Illumina HiSeqTM X10.

treatment_protocol: Three 6-month-old (6M), 18-month-old (18M), 4-year-old (4Y) male yaks and 4-year-old (4Y)  cattle-yaks were selected from the same cooperative in Xiahe County, Gannan Tibetan Autonomous Prefecture, Gansu Province (N34 ° 51'50 ', E102 ° 26'9') for castration to collect testicular tissue

value: testis

tag: developmental stage

value: sexual maturity


title: S223


title: C229


title: C202


title: SIRS S168


title: Y4Y-1

institute: Chinese Academy of Agricultural Sciences

description: ribosome footprints


title: Y4Y-2

description: ribosome footprints


title: C219


title: S225


title: C211


title: S118


title: Y18M-2

description: ribosome footprints

value: puberty


title: S230


title: Y18M-1

description: ribosome footprints


title: Y6M-1

description: ribosome footprints

value: Juvenile stage


title: S229

value: Whole blood


title: Y6M-2

description: ribosome footprints


title: S219


title: Si3

city: guiyang

first: Dijie

last: Zheng

address: No.8 beijing road

institute: guizhou medical universuty

data_processing:
RNA-seq raw FASTQ files were aligned to mm10 using STAR (v2.7.3a) with the default parameters.
The bam files were feed to featureCounts to generate expression levels of transcripts.
Assembly: mm10
Supplementary files format and content: txt
Supplementary files format and content: count

source_name: Vascular Smooth Muscle

growth_protocol: Mouse primary VSMCs were obtained from Procell Life Science & Technology Co., Ltd. (WuHan, China. CP-M076) and grown in medium at 37 °C and 5% CO2. To establish the in vitro AAA model, VSMCs were treated with 10–7 mol/L Ang II for 36 h, and the cells in the control group were treated with the same medium without Ang II.

extract_protocol:
About 1 million cells were used for each RNA-seq experiment. Cells were washed twice using PBS and lysed by 1 mL Trizol (Invitrogen 15596026) for 10 min at room temperature. 0.2 mL chloroform was added and incubated for 3 minutes at room temperature. The upper phase was transferred into a new tube after centrifuged at 12,000rpm for 10 min at 4°C, and mixed with 0.5 mL isopropanol. After incubation at room temperature for 10 minutes, the total RNA was precipitated by centrifuging at 12,000 rpm for 10 minutes at 4°C. The precipitated RNA was washed by 75% ethanol to remove salt. Air-dried RNA was dissolved by 100 nuclease-free H2O.
1ug RNA was used for extract mRNA by VAHTS mRNA Capture Beads (Vazyme N403-01), and RNA-seq library was constructed using VAHTS Universal V6 RNA-seq Library Prep Kit for MGI . The library was sequenced on the MGI platform.

treatment_protocol: VSMC cells are uniformly seeded to achieve a density of about 30% at the time of transfection. Diluted siRNA (supplied by Guangzhou Ruibo) is combined with riboFECTTM CP Buffer and Reagent, allowed to incubate at room temperature for 15 minutes, and then applied to the cell-plated wells. Following this, the cells are incubated at 37°C for 24 hours, with transfection efficiency subsequently evaluated through qRT-PCR and Western Blot analysis.

value: Vascular Smooth Muscle

value: VSMC

tag: cell type

value: Mouse Vascular Smooth Muscle Cells


title: S217


title: S216


title: Y18M-3

description: ribosome footprints


title: S199


title: S193


title: SIRS S157


title: S215


title: S212


title: Y6M-3

description: ribosome footprints


title: SIRS S156


title: S207


title: S211


title: SIRS S154


title: S202


title: S200


title: TG Non-Tumor Burden Mouse 2

city: Sioux Falls

first: Paola

middle: Drapkin

last: Vermeer

state: SD

address: 2301 East 60th street north

department: Cancer Biology and Immunotherapies Group

institute: Sanford Research

description: Control

data_processing: The normalization and data analysis was conducted according to manufacturers instructions. For the normalization, five housekeeping genes are included (actinb, B2M, Gusb, Gadph, and Hrpt). For normalization, actinb was not included in normalization due to significant expression differences between test and control samples. Normalization used the averages of B2M, Gusb, Gadph, and HRPT. Target gene signals were normalized to housekeeping genes: 2^-delta(Ct), where delta(Ct) = (CT_target - CT_HKG).

label: SYBR Green

source_name: Trigeminal ganglia from age-matched non-tumor burdened mouse

label_protocol: cDNA was generated by RT reaction using High Capacity cDNA Reverse Transcription kit from Applied Biosciences. cDNA was used to run on ScienCell qPCR arrays per manufacturer  and analyzed on CFX-96 BioRad.

growth_protocol: All animal experiments were performed in the Sanford Research Animal Resource Center which is a specific pathogen free facility. All mice were maintained in IVC Tecniplast Green line Seal Safe Plus cages. Animal rooms were maintained at 75°F, 30-70% humidity, with a minimum of 15 air changes per hour, and a 14:10 light/dark cycle. MOC2-7 cells were maintained in DMEM + 10%FBS + 1% pencillin/streptomycin.

extract_protocol: At day 28 post injection, mice were euthanized with CO gas and desaguinated with PBS so to maintain CNS integrity. Trigeminal ganglia were dissected from the skull base and RNA was isolated via Qiazol extraction reagent and further isolated through phenol-chloroform purification.

treatment_protocol: Mice were injected with 5 x 104 in 50 uL of cell culture media. Mice were anesthetized with a ketamine (87.5 mg/kg)/xylazine (10 mg/kg) mixture for initial injection. Mice were injected orthotopically in oral cavity with a 25 gauge needle. Tumors were measured every 7 days with caliper measurements while mice were sedated with isofluorane.

tag: strain

tag: gender

tag: tumor


title: Si1

tag: treatment


title: Si2

tag: tissue


title: SW-480 cells Vector#3

first: Zhihao

last: Chen

address: Jiangsu Province

institute: NANJING MEDICAL UNIVERSITY

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

growth_protocol: SW-480 cells were mainteined in RPMI 1640 supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

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

tag: cell line

value: Human colon adenocarcinoma cells

value: WT


title: NC2

value: Negative Control


title: SW-480 cells OE-PJA2#3

tag: genotype

value: PJA2 OE


title: S195

value: UInf+

value: Male


title: TG Non-Tumor Burden Mouse 3

description: Control


title: Hct116PCDH_2

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

data_processing:
Integrative Genomcs Viewer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a standard protocol from MajorBio company. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library of MajorBio.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

source_name: colorectal cancer

extract_protocol:
Culture medium were removed, washed by PBS, and RNA was harvested using Trizol reagent. Illumina NovaSeq X Plus was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colorectal cancer

value: Hct116 colorectal cancer cells

value: PCDH control


title: SIRS S179

value: SIRS+

value: yes


title: Hct116NCBP2_2

value: overexpressed NCBP2


title: NC1


title: NC3


title: Ipsilateral TG Tumor Burden Mouse 3

description: Test

source_name: Ipsilateral trigeminal ganglia from Head and neck cancer injected mouse

tag: tumor location

value: Oral Cavity

tag: tumor growth time

value: 28 days