title: 191N_normal

description:
Normal tissue
CP191N


title: control

status: Public on Jun 07 2024

type: SRA

city: Ube-shi

first: Kensuke

last: Shibata

state: Yamaguchi

address: 1-1 Minami-Kogushi 1-chome

country: Japan

institute: Yamaguchi univeristy

description: Sample 1

library_source: transcriptomic

data_processing:
Illumina RTA3 software used for basecalling.
Quality trimming, mapping onto the genome, and tag counting were performed using CLC Genomics Workbench v12.0.2.
Genome_build: GRCm38 release-95
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample.

molecule: total RNA

organism: Mus musculus

source_name: tumor

growth_protocol: Tumor cells were cultured in RPMI medium.

extract_protocol:
After the culture , total RNA was prepared using RNeasy Micro Kit (QIAGEN).
RNA libraries were NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and NEBNext Ultra Ⅱ RNA Library Prep Kit for Illumina (NEB).

tag: tissue

value: colon

tag: genotype/variation

value: control


title: M32

description: Sample 3

value: ENU mutant


title: M8

description: Sample 2


title: l3mbtPBac_Df_29C_3WL_rep3

city: Chapel Hill

first: Robert

middle: J.

last: Duronio

state: NC

address: 250 Bell Tower Dr., Gen. Sci. Bldg. 3356, CB7100

country: USA

institute: UNC Chapel Hill

description:
Tecan_Universal_Plus_RNA-Seq
L3mbtPBac_Df_29.vs.L3mbtPBac_Df_25

data_processing:
Paired-end FASTQ files were passed to the quant function within Salmon in mapping-based mode with the parameters validateMappings, seqBias, eVBOpt, numBootstraps 30 with protein-coding transcript indexes and decoys generated from the dm6 Drosophila genome build
Quant files were imported into R using Txiimport
Differential expression analysis was performed using DESeq2
Log2FC values were shrunk using the ashr method
Assembly: dm6
Supplementary files format and content: Set8null.vs.Oregon-R.txt Genes with significantly changed expression (log(2)FC > 1, padj < 0.01) in Set8null vs. Oregon-R. Columns in table are standard results columns from DESeq2: gene_symbol, baseMean, log2FoldChange, lfcSE, pvalue, padj
Supplementary files format and content: Set8RG.vs.Set8WT.txt Genes with significantly changed expression (log(2)FC > 1, padj < 0.01) in Set8RG vs. Set8WT. Columns in table are standard results columns from DESeq2: gene_symbol, baseMean, log2FoldChange, lfcSE, pvalue, padj
Supplementary files format and content: H4K20A.vs.HWT.txt Genes with significantly changed expression (log(2)FC > 1, padj < 0.01) in H4K20A vs. HWT. Columns in table are standard results columns from DESeq2: gene_symbol, baseMean, log2FoldChange, lfcSE, pvalue, padj
Supplementary files format and content: H4K20R.vs.HWT.txt Genes with significantly changed expression (log(2)FC > 1, padj < 0.01) in H4K20R vs. HWT. Columns in table are standard results columns from DESeq2: gene_symbol, baseMean, log2FoldChange, lfcSE, pvalue, padj
Supplementary files format and content: L3mbtWT_Df_25.vs.Oregon-R Genes with significantly changed expression (log(2)FC > 1, padj < 0.01) in L3mbtWT_Df_25 vs. Oregon-R. Columns in table are standard results columns from DESeq2: gene_symbol, baseMean, log2FoldChange, lfcSE, pvalue, padj
Supplementary files format and content: L3mbtWT_Df_29.vs.L3mbtWT_Df_25 Genes with significantly changed expression (log(2)FC > 1, padj < 0.01) in L3mbtWT_Df_29 vs. L3mbtWT_Df_25. Columns in table are standard results columns from DESeq2: gene_symbol, baseMean, log2FoldChange, lfcSE, pvalue, padj
Supplementary files format and content: L3mbtGM76_Df_25.vs.Oregon-R Genes with significantly changed expression (log(2)FC > 1, padj < 0.01) in L3mbtGM76_Df_25 vs. Oregon-R. Columns in table are standard results columns from DESeq2: gene_symbol, baseMean, log2FoldChange, lfcSE, pvalue, padj
Supplementary files format and content: L3mbtGM76_Df_29.vs.L3mbtGM76_Df_25 Genes with significantly changed expression (log(2)FC > 1, padj < 0.01) in L3mbtGM76_Df_29 vs. L3mbtGM76_Df_25. Columns in table are standard results columns from DESeq2: gene_symbol, baseMean, log2FoldChange, lfcSE, pvalue, padj
Supplementary files format and content: L3mbtPBac_Df_25.vs.Oregon-R Genes with significantly changed expression (log(2)FC > 1, padj < 0.01) in L3mbtPBac_Df_25 vs. Oregon-R. Columns in table are standard results columns from DESeq2: gene_symbol, baseMean, log2FoldChange, lfcSE, pvalue, padj
Supplementary files format and content: L3mbtPBac_Df_29.vs.L3mbtPBac_Df_25 Genes with significantly changed expression (log(2)FC > 1, padj < 0.01) in L3mbtPBac_Df_29 vs. L3mbtPBac_Df_25. Columns in table are standard results columns from DESeq2: gene_symbol, baseMean, log2FoldChange, lfcSE, pvalue, padj

organism: Drosophila melanogaster

source_name: whole larvae

growth_protocol: Animals were raised at standard 25C or 29C (as indicated)

extract_protocol:
8 larvae per replicate were homogenized in TRIzol (Invitrogen) and RNA was isolated using the Direct-zol RNA miniprep kit (Zymo)
RNA-seq libraries were prepared using the Universal Plus Total RNA-seq kit (Tecan) using the standard protocol

value: whole larvae

tag: Sex

value: female

tag: developmental stage

value: 3rd instar wandering

tag: genotype

tag: treatment

value: raised at 29C


title: 26T_tumor

type: genomic

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

description:
Tumor tissue
CO26T

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using the Illumina HiScan system.

data_processing:
DNA methylation data, described as beta values of continuous variables between 0 and 1, were recorded for each locus in each sample. The quality control parameters were followed, probes were filtered, normalized, and adjusted using the ChAMP package (v.2.24.0). Cross-reactive probes (≥49 bases), SNPs (Minor Allele Frequency >5%), gender-associated probes, low quality probes (p>0.05), and low bead count (<3) in at least 5% of samples were removed. Data were normalized using the BMIQ method and the annotation was performed according to the Illumina manifest (hg19) and HUGO Gene Nomenclature Committee. The sample groups were compared, and DMPs were identified using the limma package (v.3.50.3) considering a Bonferroni-adjusted p-value < 0.05 and a mean delta-beta (Δβ) ≥0.2 or ≤-0.2.
BMIQ-Normalized Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Oral cavity squamous cell carcinoma

label_protocol: Standard Illumina Protocol

growth_protocol: Not applicable

extract_protocol: Genomic DNA from tumor and normal tissues was extracted using phenol-chloroform method and quantified by Qubit® dsDNA BR Assay (Qubit® 2.0 Fluorometer, Life Technologies - Carlsbad, CA, USA).

treatment_protocol: Not applicable

tag: gender

value: Male

tag: age

tag: hpv status

value: Negative


title: l3mbtPBac_Df_29C_3WL_rep2


title: 14T_tumor

description:
Tumor tissue
CO14T


title: G401_shPHF6_H3K4me3_3

city: Memphis

first: Jacquelyn

middle: A

last: Myers

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children’s Research Hospital

description:
H3K4me3-AB5-SJMRT050486_C97-PM108_G401_shphf6_3
shPHF6 H3K4me3

library_source: genomic

data_processing:
trim_galore v0.6.3 remove adapter sequences.
Align quality reads using bwa mem v0.7.17 to a hybrid reference genome.
bamsormadup v2.0.87
samtools used to split bam file for hg19 and dm6 reads base on chromosome names.
samtools -F 1024 -q 1 to define quality reads.
Estimate fragment size using spp R package.
slopBed -r fragment size estimation determined by spp.
Normalize to 15M reads.
Genome_build: hg19+dm6 (Gencode GRCh37 and Ensembl r97)
Supplementary_files_format_and_content: Normalized coverage in the bigwig file format, macs2 narrow peaks.

source_name: G401 cell line

growth_protocol: G401 cells were grown in McCoy's 5A media supplemented with 10% fetal bovine serum and 1% Glutamax (Gibco) at 37°C and 5% CO2.

extract_protocol:
In brief, cells were cross-linked directly on the plate using 1% paraformaldehyde for 10 min at room temperature and quenched with glycine. Nuclei were isolated using the Covaris TruCHIP kit and Chromatin extracts were sonicated for 8 min using a Covaris E220 focused ultrasonicator at a peak power of 140, a duty factor of 5 and 200 cycles per burst. Chromatin immunoprecipitation was carried overnight with antibodies bound to dynabeads. Chromatin was de-crosslinked, digested with RNase and Proteinase K and DNA was purified using a Qiagen DNA kit. For MNase ChIP, CST kit guidelines were followed.
KAPA HyperPrep Kit (Kapa Biosystems, Cat# 7962363001).

treatment_protocol: G401 cells were infected with either control (shCTRL) or PHF6 (shPHF6) targeting shRNAs. 48hrs post infection, cells were selected with 1ug/mL puromycin for 72h and subsequently harvested.

tag: cell line

tag: shRNA

tag: chip antibody


title: l3mbtPBac_Df_29C_3WL_rep1


title: 291T_tumor

description:
Tumor tissue
CP291T

value: Positive


title: l3mbtPBac_Df_25C_3WL_rep3

description:
Tecan_Universal_Plus_RNA-Seq
L3mbtPBac_Df_25.vs.Oregon-R

value: raised at 25C


title: l3mbtPBac_Df_25C_3WL_rep2


title: 224N_normal

description:
Normal tissue
CP224N

source_name: Normal adjacent tissue


title: 52T_tumor

description:
Tumor tissue
CO52T


title: 78T_tumor

description:
Tumor tissue
CP78T


title: l3mbtGM76_Df_29C_3WL_rep4

description:
Tecan_Universal_Plus_RNA-Seq
L3mbtGM76_Df_29.vs.L3mbtGM76_Df_25


title: l3mbtPBac_Df_25C_3WL_rep1


title: 215T_tumor

description:
Tumor tissue
CP215T.A


title: 291N_normal

description:
Normal tissue
CP291N


title: l3mbtGM76_Df_29C_3WL_rep2


title: l3mbtGM76_Df_29C_3WL_rep3


title: 215N_normal

description:
Normal tissue
CP215N


title: l3mbtGM76_Df_29C_3WL_rep1


title: 224T_tumor

description:
Tumor tissue
CP224T


title: l3mbtGM76_Df_25C_3WL_rep4

description:
Tecan_Universal_Plus_RNA-Seq
L3mbtGM76_Df_25.vs.Oregon-R


title: E15.5 FL SE-hi coculture

city: Seattle

first: Brandon

last: Hadland

state: WA

address: 1100 Fairview Avenue N., D2-115, P.O. Box 19024

institute: Fred Hutchinson Cancer Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The Cell Ranger 2.1.1 pipeline (10X Genomics) was used to align reads to the mm10 reference genome and generate feature barcode matrix, filtering low-quality cells using default parameters.
The Monocle (v.3.1.2.9) platform was used for downstream analysis, combining read-depth normalized data across samples where applicable.
Assembly: mm10
Supplementary files format and content: 10X Cell Ranger output files in filtered feature-barcode matrix: "genes.tsv" contains gene information, "barcodes.tsv" contains cellular barcodes, and "matrix.mtx" contains a sparse matrix of UMIs.
Supplementary files format and content: Monocle cell data set files: "SampleX.RDS" contains monocle cell data sets for sample(s) X imported from 10Xoutput files; "SampleX_P.RDS" contains cell data set for sample(s) X following pre-processing, dimensionality reduction, and clustering steps.

molecule: polyA RNA

source_name: Fetal Liver

extract_protocol:
FACS-isolated primary cells or cultured cells harvested by trypsinization (for FL-EC) or pipetting (for co-cultured hematopoietic cells) were washed with PBS/0.04% ultrapure BSA, and resuspended in PBS/BSA for loading into the 10X Genomics Chromium Single Cell B Chip, and processed in the Chromium single cell controller.
The 10X Genomics Version 3.1 single cell 3’ kit was used to prepare single cell mRNA libraries for freshly isolated primary cells or FL-EC, while the 10X Genomics Version 3.1 with Feature Barcoding technology for Cell Surface Protein Sequencing was used for co-cultured cells. Both kits were used according to manufacturer protocols with the Index Kit T Set A. Sequencing was performed for pooled libraries from each sample on an Illumina NextSeq 500 using the 75 cycle, high output kit.

tag: cell type

value: Hematopoietic cells, primary

value: Fetal Liver

tag: strain

tag: cell fraction


title: G401_shCTRL_H3K36me2_3

description:
H3K36me2-AB3-SJMRT050486_C85-PM96_G401_shctrl_3
shCTRL H3K36me2

value: shCTRL


title: G401_shCTRL_H3K36me2_1

description:
H3K36me2-AB3-SJMRT050486_C83-PM94_G401_shctrl_1
shCTRL H3K36me2


title: G401_shPHF6_H3K27ac_1

description:
H3K27Ac-AB2-SJMRT050486_C98-PM109_G401_shphf6_1
shPHF6 H3K27ac


title: G401_shCTRL_H3K4me3_3

description:
H3K4me3-AB5-SJMRT050486_C76-PM87_G401_shctrl_3
shCTRL H3K4me3


title: G401_shCTRL_H3K4me1_1

description:
H3K4me1-AB2-SJMRT050486_C71-PM82_G401_shctrl_1
shCTRL H3K4me1


title: G401_shCTRL_H3K27me3_2

description:
H3K27me3-AB3-SJMRT050486_C70-PM81_G401_shctrl_2
shCTRL H3K27me3


title: G401_shPHF6_H3K4me1_2

description:
H3K4me1-AB2-SJMRT050486_C93-PM104_G401_shphf6_2
shPHF6 H3K4me1


title: G401_shPHF6_H3K4me1_3

description:
H3K4me1-AB2-SJMRT050486_C94-PM105_G401_shphf6_3
shPHF6 H3K4me1


title: G401_shPHF6_H3K4me1_1

description:
H3K4me1-AB2-SJMRT050486_C92-PM103_G401_shphf6_1
shPHF6 H3K4me1


title: G401_shCTRL_H3K27me3_1

description:
H3K27me3-AB3-SJMRT050486_C69-PM80_G401_shctrl_1
shCTRL H3K27me3


title: G401_shPHF6_H3K27ac_2

description:
H3K27Ac-AB2-SJMRT050486_C99-PM110_G401_shphf6_2
shPHF6 H3K27ac


title: G401_shCTRL_H3K4me1_3

description:
H3K4me1-AB2-SJMRT050486_C73-PM84_G401_shctrl_3
shCTRL H3K4me1


title: G401_shPHF6_H3K4me3_2

description:
H3K4me3-AB5-SJMRT050486_C96-PM107_G401_shphf6_2
shPHF6 H3K4me3


title: G401_shCTRL_H3K4me3_2

description:
H3K4me3-AB5-SJMRT050486_C75-PM86_G401_shctrl_2
shCTRL H3K4me3


title: G401_shCTRL_H3K36me2_2

description:
H3K36me2-AB3-SJMRT050486_C84-PM95_G401_shctrl_2
shCTRL H3K36me2


title: G401_shPHF6_H3K4me3_1

description:
H3K4me3-AB5-SJMRT050486_C95-PM106_G401_shphf6_1
shPHF6 H3K4me3


title: G401_shCTRL_H3K4me1_2

description:
H3K4me1-AB2-SJMRT050486_C72-PM83_G401_shctrl_2
shCTRL H3K4me1


title: l3mbtGM76_Df_25C_3WL_rep3

description:
Tecan_Universal_Plus_RNA-Seq
L3mbtGM76_Df_25.vs.Oregon-R


title: 287T_tumor

description:
Tumor tissue
CP287T

value: Female


title: G401_shCTRL_H3K27ac_2

description:
H3K27Ac-AB2-SJMRT050486_C78-PM89_G401_shctrl_2
shCTRL H3K27ac


title: G401_shCTRL_H3K27ac_3

description:
H3K27Ac-AB2-SJMRT050486_C79-PM90_G401_shctrl_3
shCTRL H3K27ac


title: 248N_normal

description:
Normal tissue
CP248N.2


title: l3mbtGM76_Df_25C_3WL_rep2


title: G401_shCTRL_H3K27ac_1

description:
H3K27Ac-AB2-SJMRT050486_C77-PM88_G401_shctrl_1
shCTRL H3K27ac


title: 290N_normal

description:
Normal tissue
CP290N


title: l3mbtWT_Df_29C_3WL_rep3

description:
Tecan_Universal_Plus_RNA-Seq
L3mbtWT_Df_29.vs.L3mbtWT_Df_25


title: 287N_normal

description:
Normal tissue
CP287N


title: G401_shPHF6_H3K27ac_3

description:
H3K27Ac-AB2-SJMRT050486_C100-PM111_G401_shphf6_3
shPHF6 H3K27ac


title: 78N_normal

description:
Normal tissue
CP78N


title: 288T_tumor

description:
Tumor tissue
CP288T


title: 222N_normal

description:
Normal tissue
CP222N


title: l3mbtWT_Df_29C_3WL_rep1


title: 290T_tumor

description:
Tumor tissue
CP290T


title: Pb-Input

city: Hefei

first: Danyang

last: Li

address: No. 193 Tunxi Road

country: China

institute: Hefei university of technology

data_processing:
Illumina Novaseq 6000 sequencer
Paired-end reads were harvested from Illumina Novaseq 6000 sequencer. 3’ adaptor-trimming and low-quality reads removing by cutadapt software (v1.9.3).
Clean reads of input libraries were aligned to reference genome (UCSC RN5) by STAR software.
Reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4).
Assembly: UCSC RN5
Supplementary files format and content: Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
Library strategy: me-RIP-Seq

organism: Rattus norvegicus

source_name: Brain(Hippocampus )

growth_protocol: Hippocampi were dissociated by enzymatic digestion in 0.03% trypsin for 19min at 37 °C and then triturated with a fire-polished Pasteur pipette. Neurons were plated on poly-L-lysine (0.5mg/ml; Sigma P-2636)-treated 25mm glass coverslips at a density of 100,000 cells per coverslip. Change 70% of media to neurobasal on DIV (day in vitro) 2 and change half the media with neurobasal on DIV7 with Ara-C (1 μL/ml from 4mM stock, sigma C6645-25MG).

extract_protocol:
Total RNA was extracted using RNA isolater Total RNA Extraction Reagent (R401-01, Vazyme, China) according to the manufacturer’s instructions.
m6A RNA immunoprecipitation was performed with the GenSeqTM m6A-MeRIP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. The library was used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA).

treatment_protocol: Neurons were exposed to Pb for 48hrs on DIV 12-14

value: Brain(Hippocampus )

value: Primary hippocampal neurons

value: Exposed to PbAc with 5mM for 48h on DIV 12-13


title: G401_shCTRL_H3K14ac_2

description:
H3K14Ac-AB1-SJMRT050486_C81-PM92_G401_shctrl_2
shCTRL H3K14ac


title: G401_shPHF6_H3K14ac_2

description:
H3K14Ac-AB1-SJMRT050486_C102-PM113_G401_shphf6_2
shPHF6 H3K14ac


title: D3D_BM_Tcm_ATAC_2

city: Shanghai

first: duan

middle: cai

last: wen

address: 1678 dongfang road

institute: Shanghai Children's Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2 with parameters -l 15 -q 0.2 -n 0.05
Sequenced reads were mapped to GRCm38 whole genome using STAR 2.7.6a  with parameters  --runMode alignReads --runThreadN 5  --genomeLoad NoSharedMemory  --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts
The gene expression level (TPM) was calculated according to the Sequencing depth and gene length, and remove batch effect by R package ComBat
Align ATAC-seq reads: STAR v2.5.0c [disable splicing alignment]
Remove ATAC-seq duplicated reads: Picard v1.141
Call ATAC-seq peaks: MACS2 v2.1.1
scRNA-seq and scTCR-seq data processing: cellranger v6.1.2
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: bone marrow

extract_protocol:
For ATAC-seq, genomic DNA was isolated and processed according to Buenrostro et al. Curr Protoc Mol Biol. 2015; 109
Transposed DNA fragments were isolated, amplified and size-selected.

treatment_protocol: CD8 cells were stained with antibodies CD44 and CD62L and sorted by flow cytometry.

value: bone marrow

value: 3 days post DNR chemotherapy of AF9 AML mice


title: l3mbtWT_Df_25C_3WL_rep3

description:
Tecan_Universal_Plus_RNA-Seq
L3mbtWT_Df_25.vs.Oregon-R

value: whole larvae


title: G401_shCTRL_H3K14ac_1

description:
H3K14Ac-AB1-SJMRT050486_C80-PM91_G401_shctrl_1
shCTRL H3K14ac


title: 288N_normal

description:
Normal tissue
CP288N


title: Pb-IP


title: l3mbtWT_Df_25C_3WL_rep2

value: female


title: l3mbtWT_Df_25C_3WL_rep1

value: 3rd instar wandering


title: 222T_tumor

description:
Tumor tissue
CP222T


title: 248T_tumor

description:
Tumor tissue
CP248T


title: D3D_BM_Tcm_ATAC_1


title: H4K20R_3WL_rep4

description:
Tecan_Universal_Plus_RNA-Seq
H4K20R.vs.HWT.txt

value: deltaHisC; {12xK20R}


title: l3mbtGM76_Df_25C_3WL_rep1


title: 185N_normal

description:
Normal tissue
CP185N

value: Male


title: H4K20R_3WL_rep3


title: G401_shCTRL_S5P_2

description:
2140164_PM272_G401ShCTRL_POLIIS5P
shCTRL S5P


title: 5055T_tumor

description:
Tumor tissue
X5055


title: G401_shPHF6_S5P_1

description:
2140173_PM281_G401ShPHF6_POLIIS5P
shPHF6 S5P


title: l3mbtWT_Df_29C_3WL_rep2

value: raised at 29C


title: G401_shPHF6_S5P_2

description:
2140174_PM282_G401ShPHF6_POLIIS5P
shPHF6 S5P


title: G401_shPHF6_H3K14ac_1

description:
H3K14Ac-AB1-SJMRT050486_C101-PM112_G401_shphf6_1
shPHF6 H3K14ac


title: 5N_normal

description:
Normal tissue
CO5N

value: Negative


title: G401_shCTRL_S5P_1

description:
2140163_PM271_G401ShCTRL_POLIIS5P
shCTRL S5P


title: D3D_BM_Teff_ATAC_1


title: H4K20R_3WL_rep1

value: raised at 25C


title: G401_shCTRL_input_Phos_1

description:
2088002_PM263_G401ShCTRL_Input
input control for S2P and S5P


title: H4K20A_3WL_rep3

description:
Tecan_Universal_Plus_RNA-Seq
H4K20A.vs.HWT.txt

value: deltaHisC; {12xK20A}


title: AF9_SI_Tim_ATAC_2

source_name: small intestine

value: small intestine

value: AF9 AML mice


title: AF9_SI_Tim_ATAC_1


title: G401_shPHF6_input_Phos_1

description:
2088003_PM264_G401ShPHF6_Input
input control for S2P and S5P


title: 17678T_tumor

description:
Tumor tissue
X17678


title: 178N_normal

description:
Normal tissue
CP178N


title: G401_shPHF6_S2P_2

description:
2088001_PM262_G401_ShPHF6_RNAPOLIIS2P
shPHF6 S2P


title: H4K20A_3WL_rep2


title: D3D_SI_Tim_ATAC_1


title: D3D_BM_Teff_ATAC_2


title: 5008T_tumor

description:
Tumor tissue
X5008


title: H4K20A_3WL_rep1


title: G401_shCTRL_S2P_2

description:
2087996_PM257_G401_ShCTRL_RNAPOLIIS2P
shCTRL S2P

value: shCTRL


title: AF9_BM_Tim_ATAC_2


title: G401_shCTRL_S2P_1

description:
2087995_PM256_G401ShCTRL_RNAPOLIIS2P
shCTRL S2P


title: HWT_3WL_rep4

description:
Tecan_Universal_Plus_RNA-Seq
NA

value: deltaHisC; {12xHWT}


title: G401_shPHF6_S2P_1

description:
2088000_PM261_G401_ShPHF6_RNAPOLIIS2P
shPHF6 S2P


title: AF9_BM_Tim_ATAC_1


title: H4K20R_3WL_rep2


title: HWT_3WL_rep3

description:
Tecan_Universal_Plus_RNA-Seq
NA


title: AF9_BM_Tcm_ATAC_2


title: HWT_3WL_rep2

description:
Tecan_Universal_Plus_RNA-Seq
NA


title: AF9_BM_Tcm_ATAC_1


title: G401_shPHF6_input_1

description:
2041087_PM252_G401ShPHF6_Input
input control for total POLII


title: 17597T_tumor

description:
Tumor tissue
X17597


title: 5T_tumor

description:
Tumor tissue
CO5T


title: G401_shCTRL_input_1

description:
2041086_PM251_G401ShCTRL_Input
input control for total POLII


title: AF9-D5D-Tn_3

description:
batch2
counts_BM.txt

extract_protocol:
Total RNA was isolated using the TRIzol reagent; mRNA is reversely transcribed into cDNA using the Smart-seq2, and then amplified using KAPA HiFi DNA polymerase. The protocol from Jun Chen  et al., nature protocols, 2017.
DNA libraries were prepared for sequencing using TruePrep DNA Library Prep Kit V2 for Illumina(VazymeTD502)

value: 5 days post DNR chemotherapy of AF9 AML mice


title: Set8rg_3WL_rep3

description:
Tecan_Universal_Plus_RNA-Seq
Set8RG.vs.Set8WT.txt

value: yw;;{Set8rg}, Set820


title: AF9-D5D-Tn_2

description:
batch2
counts_BM.txt

value: bone marrow


title: G401_shPHF6_POLII_2

description:
2041085_PM250_G401_ShPHF6_RNAPOLII
shPHF6 POLII

value: POLII


title: 176N_normal

description:
Normal tissue
CP176N


title: AF9-D5D-Tn_1

description:
batch1
counts_BM.txt


title: AF9-D5D-Teff_3

description:
batch1
counts_BM.txt


title: 233N_normal

description:
Normal tissue
CP233N


title: G401_shPHF6_POLII_1

description:
2041083_PM248_G401ShPHF6_RNAPOLII
shPHF6 POLII


title: 233T_tumor

description:
Tumor tissue
CP233T


title: G401_shCTRL_POLII_1

description:
2041081_PM246_G401ShCTRL_RNAPOLII
shCTRL POLII


title: 171N_normal

description:
Normal tissue
CP171N


title: shPHF6_11

description:
PM215
loss PHF6 G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt

data_processing:
trim_galore v0.6.3 remove adapter sequences.
Alignment with STAR2.7.3a --twopassMode Basic
Read counts quantified by RSEMv1.3.1.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: shCTRL_shPHF6_RNASEQ_COUNTS.txt: Quantified read counts are provided in the txt format for every sample for gencode v19.

growth_protocol: All cells were cultured at 37°C with 5% humidity and 5% CO2.

extract_protocol:
Trizol and the DirectZol Mini Prep Plus kit (Zymo Research, R2070).
TruSeq Stranded mRNA Library Prep kit.

treatment_protocol: G401 cells were cultured in McCoy’s media with 10% FBS (Sigma Aldrich) and 1% Glutamax (GIBCO). G401 cells infected with pLV-mCherry-TRE3G>{hPHF6*.mut} were sorted for mCherry expressing cells by the Flow Sorting facility at St. Jude Children’s Research Hospital. G401 Tet3G mCherry TRE3GhPHF6 cells were subsequently subjected to infection with either ShPHF6 or non-targeting control and subsequent selection in puromycin (1µg/µl) for 72 hours.


title: Set8wt_3WL_rep3

description:
Tecan_Universal_Plus_RNA-Seq
NA

value: whole larvae

value: yw;;{Set8wt}, Set820


title: AF9-D5D-Teff_2

description:
batch1
counts_BM.txt


title: 186N_normal

description:
Normal tissue
CP186N


title: AF9-D5D-Teff_1

description:
batch2
counts_BM.txt


title: 17671T_tumor

description:
Tumor tissue
X17671


title: 94T_tumor

description:
Tumor tissue
CP94T

value: Female

value: Positive


title: shPHF6_10

description:
PM214
loss PHF6 G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt


title: Set8rg_3WL_rep2

value: female

value: 3rd instar wandering


title: G401_shCTRL_POLII_2

description:
2041082_PM247_G401_ShCTRL_RNAPOLII
shCTRL POLII


title: AF9-D5D-Tcm_3

description:
batch1
counts_BM.txt


title: Set8wt_3WL_rep2

description:
Tecan_Universal_Plus_RNA-Seq
NA


title: 152T_tumor

description:
Tumor tissue
CP152T

value: Male


title: Set8wt_3WL_rep1

description:
Tecan_Universal_Plus_RNA-Seq
NA

value: raised at 25C


title: Set8rg_3WL_rep1


title: AF9-D5D-Tcm_2

description:
batch2
counts_BM.txt


title: shPHF6_9

description:
PM213
loss PHF6 G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt


title: Set8null_3WL_rep4

description:
Tecan_Universal_Plus_RNA-Seq
Set8null.vs.Oregon-R.txt


title: shCTRL_9

description:
PM212
control G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt


title: 196N_normal

description:
Normal tissue
CP196N.A

value: Negative


title: HWT_3WL_rep1

description:
Tecan_Universal_Plus_RNA-Seq
NA


title: 154N_normal

description:
Normal tissue
CP154N


title: Set8wt_3WL_rep4

description:
Tecan_Universal_Plus_RNA-Seq
NA


title: AF9-D5D-Tcm_1

description:
batch1
counts_BM.txt


title: Set8null_3WL_rep2


title: 196T_tumor

description:
Tumor tissue
CP196T


title: Set8null_3WL_rep3


title: WT-Tn_3

description:
batch2
counts_BM.txt

value: C57 mice


title: shPHF6_8

description:
PM178
loss PHF6 G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt


title: WT-Tn_2

description:
batch2
counts_BM.txt


title: shPHF6_7

description:
PM177
loss PHF6 G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt


title: Set8null_3WL_rep1


title: 94N_normal

description:
Normal tissue
CP94N


title: WT-Tn_1

description:
batch2
counts_BM.txt


title: WT-Teff_3

description:
batch1
counts_BM.txt


title: 152N_normal

description:
Normal tissue
CP152N


title: shCTRL_7

description:
PM175
control G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt


title: Oregon-R_3WL_rep4

description:
Tecan_Universal_Plus_RNA-Seq
NA

value: Oregon-R


title: Oregon-R_3WL_rep3

description:
Tecan_Universal_Plus_RNA-Seq
NA


title: shPHF6_6

description:
PM176
loss PHF6 G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt


title: shCTRL_6

description:
PM174
control G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt

value: shCTRL


title: shCTRL_8

description:
PM211
control G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt


title: WT-Teff_1

description:
batch2
counts_BM.txt


title: WT-Tcm_3

description:
batch1
counts_BM.txt


title: 154T_tumor

description:
Tumor tissue
CP154T


title: Oregon-R_3WL_rep1

description:
Tecan_Universal_Plus_RNA-Seq
NA


title: 112T_tumor

description:
Tumor tissue
CP112T


title: shPHF6_5

description:
PM126
loss PHF6 G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt


title: 22T_tumor

description:
Tumor tissue
CO22T


title: Tassel, FM-S3, scRNA-seq, Replicate2

city: Wuhan

first: liang

last: dong

address: No.1,Shizishan Street

institute: Huazhong Agricultural University

description:
scTFM-S3 rep2
singlecell_raw_counts.matrix

data_processing:
For bulk RNA-seq, the quality of raw sequencing data was controlled using Trimmomatic with parameters “LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:20”. For scRNA-seq, the adaptor sequence and the low-quality reads were filtered by fastp with the default parameters.
For bulk RNA-seq, clean data from all samples were mapped to the B73 AGPv4 reference genome using HISAT2 with default parameters. For scRNA-seq, the UMI-based clean data were mapped to the maize genome (B73 RefGen_v4) utilizing STAR mapping with customized parameters to obtain the UMI counts of each sample.
For bulk RNA-seq, we used featureCounts (v.1.6.3) to measure the abundance of RNA with the parameter (-p). “bamCoverage” in deeptools (v3.3.0) were used for bw files.
Assembly: B73 RefGen_v4
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample
Supplementary files format and content: matrix files

organism: Zea mays

source_name: Tassel FM-S3

growth_protocol: All samples were harvested from maize plants growing in the field

extract_protocol:
For bulk RNA-seq, RNA was extracted  using direct-zol RNA Miniprep (Zymo Research).For scRNA-seq, protoplasts were prepared as previously described (Satterlee et al., 2020). For each replicate, the freshly dissected FM-S2 or FM-S3 tissues from 15-20 ear or tassel were digested in protoplast lysis buffer for 2 hours at room temperature in the dark with gentle shaking. The mixture was then filtered twice through a 30 μm cell strainer (sysmex, 04-0042-2316) and the protoplasts were collected by horizontal centrifugation at 300 g for 3 min at room temperature. The supernatant was gently removed without disturbing the protoplast pellet. Next, the pellet was resuspended and washed two times using protoplast washing buffer (lysis buffer without enzyme) by the same centrifugation condition as before. After washing, the pellet was resuspended into 600 μl washing buffer and then filtered through the 30 μm cell strainer to remove adherent multicellular mass.
Bulk RNA-seq librarys were constructed using NEBNext Ultra Directional RNA Library Prep Kit or MGIEasy RNA Library Prep Kit according to the instructions. scRNA-seq librarys were constructed using BD Rhapsody™ Whole Transcriptome Analysis Amplification Kit.

value: Tassel FM-S3


title: Tassel, FM-S3, scRNA-seq, Replicate1

description:
scTFM-S3 rep1
singlecell_raw_counts.matrix


title: 171T_tumor

description:
Tumor tissue
CP171T


title: shPHF6_4

description:
PM125
loss PHF6 G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt


title: WT-Tcm_1

description:
batch1
counts_BM.txt


title: 107T_tumor

description:
Tumor tissue
CP107T


title: Tassel, FM-S2, scRNA-seq, Replicate2

description:
scTFM-S2 rep2
singlecell_raw_counts.matrix

source_name: Tassel FM-S2

value: Tassel FM-S2


title: WT-Tcm_2

description:
batch1
counts_BM.txt


title: WT-Teff_2

description:
batch2
counts_BM.txt


title: Oregon-R_3WL_rep2

description:
Tecan_Universal_Plus_RNA-Seq
NA


title: 9T_tumor

description:
Tumor tissue
CO9T


title: shCTRL_5

description:
PM173
control G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt


title: 3N_normal

description:
Normal tissue
CO3N


title: HFDCCL4 Liver cre, c

city: Ann Arbor

first: Jun

last: Wu

address: 210 Washtenaw Ave.

institute: University of Michigan

data_processing:
The reads were trimmed using Cutadapt v2.3 (Martin, 2011).
FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010).
Fastq Screen v was used to screen for various types of contamination (Wingett and Andrews, 2018).
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.
Multiqc v1.7 compiled the results from several of these tools and provided a detailed and comprehensive quality control report (Ewels et al., 2016)
Assembly: GRCm38 (ENSEMBL)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
Total RNA was extracted using GenElute™ Mammalian Total RNA Miniprep Kit, according to the provided instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: HFD CCL4


title: shPHF6_3

description:
PM124
loss PHF6 G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt


title: shCTRL_4

description:
PM122
control G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt


title: 112N_normal

description:
Normal tissue
CP112N


title: HFDCCL4 Liver cre, b


title: shCTRL_3

description:
PM121
control G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt


title: 107N_normal

description:
Normal tissue
CP107N


title: Tassel, FM-S2, scRNA-seq, Replicate1

description:
scTFM-S2 rep1
singlecell_raw_counts.matrix


title: HFDCCL4 Liver cre, a


title: 147T_tumor

description:
Tumor tissue
CP147T


title: Ear, FM-S3, scRNA-seq, Replicate1

description:
scFM-S3 rep1
singlecell_raw_counts.matrix

source_name: Ear FM-S3

value: Ear FM-S3


title: 9N_normal

description:
Normal tissue
CO9N


title: shPHF6_2

description:
PM55
loss PHF6 G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt


title: HFDCCL4 Liver flox, c


title: shPHF6_1

description:
PM54
loss PHF6 G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt


title: 254N_normal

description:
Normal tissue
CP254N.2


title: Ear, FM-S2, scRNA-seq, Replicate2

description:
scFM-S2 rep2
singlecell_raw_counts.matrix

source_name: Ear FM-S2

value: Ear FM-S2


title: Ear, FM-S2, scRNA-seq, Replicate1

description:
scFM-S2 rep1
singlecell_raw_counts.matrix


title: shCTRL_2

description:
PM53
control G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt


title: HFDCCL4 Liver flox, a


title: 147N_normal

description:
Normal tissue
CP147N


title: shCTRL_1

description:
PM52
control G401
shCTRL_shPHF6_RNASEQ_COUNTS.txt


title: SC207

city: Pittsburgh

first: Yuechen

last: Zhou

state: PA

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

data_processing:
FASTQ generation, demultiplexing, barcode assignment, gene counting and antibody counting were performed using 10X Genomics' Cell Ranger software v6 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: raw_feature_bc_matrix.h5

source_name: Lung

extract_protocol:
Explanted lungs were finely diced and digested for 1 hour in a mix of either Collagenase A/DNase I or Liberase DL/DNase I.  A single cell suspension was generated by filtering lungs through 70 micron filters and resuspending cells in PBS containing 0.04% BSA.  For some lungs, certain cell populations were partially depleted with Miltenyi magnetic bead separation. Two samples (SC401female81 and SC401male95) were labelled with HTO1 and HTO2 respectively. Cells were loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed per the manufacturer’s instructions (Single Cell 3' v1, 3' v2, 3' v3, 5' v1, 5' v2). In short, lung cells were added to the master mix and loaded into the chip; subsequently, gel beads and partitioning oil were added into the chip which was then loaded into the Chromium instrument, generating the gel bead-in-emulsion (GEM). Once emulsified, cells were lysed and poly-A RNA transcribed to cDNA, adding an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and 10x Barcode. Silane DynaBeads were then used to clean up the pooled and barcoded cDNA which was then amplified by PCR.  SPRIselect reagent was used to select the appropriately sized fragments for library construction. Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added during the library construction protocol.

value: Lung

tag: disease state

value: idiopathic pulmonary arterial hypertension

tag: core code

tag: protocol

value: 10X Genomics 3PrimeV2


title: P291_18_18-PSA5

status: Public on Jun 06 2024

type: RNA

city: Gießen

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

country: Germany

institute: JLU Gießen

hyb_protocol: 3.8 µg of fragmented and labeled ss cDNA were hybridized to Applied Biosystems GeneChip Clariom S rat arrays for 16 h at 45°C and 60 rpm in an Applied Biosystems GeneChip hybridization oven 640.

scan_protocol: Hybridized arrays were washed and stained in an Applied Biosystems GeneChip Fluidics Station FS450, and the fluorescent signals were measured with an Applied Biosystems GeneChip Scanner 3000 7G System. Fluidics and scan functions were controlled by the Applied Biosystems GeneChip Command Console v4.3.3 software.

data_processing: Summarized probe set signals in log2 scale were calculated by using the GCCN-SST-RMA algorithm with the Applied Biosystems GeneChip Expression Console v1.4 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes (FC) and significance P-values were calculated.

label: Biotin

organism: Gallus gallus

label_protocol: 200 ng of total RNA was used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA were purified and reverse transcribed into single-stranded (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

growth_protocol: The five-week feeding trial with 72 male, 1-day-old broiler chickens (Cobb 500, Cobb-Vantress, Weidemar, Germany) was approved by the Animal Welfare Officer of the Justus Liebig University Giessen (approval no.: JLU 843_M). All experimental procedures described followed established guidelines for laboratory animals care and handling.

extract_protocol: Aliquots from the liver (20-30 mg) were used for total RNA extraction using TRIzol reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer´s protocol. Total RNA was analyzed for quantity and quality using an Infinite 200M microplate reader with a NanoQuant plate (both from Tecan, Mainz, Germany). The mean RNA concentration and A260/A280 ratio of all total RNA samples was 385 ± 64 µg/mL and 1.91 ± 0.02 (N = 36 or n = 12/group) for liver.

treatment_protocol: The broilers were randomly assigned to three different groups (4 broilers/cage, 6 cages/group), with a similar mean initial body weight (38.1 ± 2.9 g; mean ± SD; N = 72) across the groups. The broilers were housed in 2.1 m2 cages with nipple drinkers and feed automates and had free access to feed and water. The floor was covered with hemp-based litter (Hemparada, HempFlax Group B.V., Oude Pekela, Netherlands) which allowed scratching, pecking and dustbathing and was exchanged two times per week during the first two weeks and every two days during the last three weeks of the trial. In addition, broilers were provided with perches in elevated position for resting and sleeping. Light regime followed a schedule of 24 h:0 h, 23 h:1 h, 22 h:2 h, 21 h:3 h, 20 h:4 h, 19 h:5 h (light:dark) at days 1, 2, 3, 4, 5, 6, and 18 h:6 h from day 7 onward and the light intensity was constantly 40 Lux, as recommended by the breeder. The room temperature decreased from 28-29°C on day one, measured at pen height, to 23-24°C on day 35. Infrared lamps (Albert Kerbl GmbH, Buchbach, Germany) were used as additional heat sources during the first 6 days to adjust the temperature at the cage floor to 34°C. Mean relative humidity was 60.0 ± 1.9%. The groups were fed three different nutrient adequate diets containing either 0% (group PSA-0), 2.5% (group PSA-2.5) or 5% (group PSA-5.0) P. sapidus mycelium in a three-phase feeding system (starter diet form day 1-10, grower diet from day 11-21, finisher diet from day 22-35). The composition of the three diets is shown in Table 1. The composition of the diets met the broiler’s requirements of nutrients and energy according to the breeder’s recommendations (Cobb-Vantress, 2022). Diets were provided in crumbled form during the first three days, and in pellet form (2 mm diameter) from day 3 until the end of the trial. On days 1, 10, 21 and 35 body weight (individually) and feed intake (per cage) were determined. The feed:gain ratio was calculated from feed intake and body weight gains on cage basis.

tag: tissue

value: 5% Pleurotus sapidus (PSA)


title: Ear, FM-S3, scRNA-seq, Replicate2

description:
scFM-S3 rep2
singlecell_raw_counts.matrix


title: P291_15_15-PSA5


title: P291_06_6-PSA5


title: P291_12E_30-PSA5


title: P291_17_17-PSA2-5

value: 2.5% Pleurotus sapidus (PSA)


title: P291_03_3-PSA5


title: P291_09_9-PSA5


title: P291_05_5-PSA2-5


title: P291_02_2-PSA2-5


title: P291_11_11-PSA2-5


title: P291_14_14-PSA2-5


title: P291_07_7-PSA0

value: 0% Pleurotus sapidus (PSA)


title: HFDCCL4 Liver flox, b


title: P291_13_13-PSA0


title: P291_04_4-PSA0


title: P291_10_10-PSA0


title: P291_16_16-PSA0


title: P291_01_1-PSA0


title: hPDAC_Sen4

city: Jerusalem

first: Ittai

last: Ben-Porath

address: Ein-Kerem

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University Faculty of Medicine

data_processing:
FASTQ files were trimmed and filtered with trim_galore (v0.6.1) for adapter sequences, polyA tails and low quality bases.
Trimmed and filtered reads were mapped with salmon quant function (v1.6.0) to the transcriptome.
Normalization and exploration of differentially expressed genes was perfofrmed with Deseq2 (v1.40.1)
Assembly: hg38
Supplementary files format and content: Tab-delimited text file consisting of raw gene counts for each sample.

source_name: Pancreatic carcinoma

extract_protocol:
Total RNA was extracted and isolated using TRI reagent (Sigma) and RNA isolation kit (Zymo Research).
Libraries for expression profile were prepared using standard CEL-Seq protocol.
CEL-Seq

treatment_protocol: Human surgical PDAC samples were acquired, dissociated, and underwent FACS sorting. CAFs were isolated by FACS with selection for CD90+, Epcam–, Cd45– cells.

value: Pancreatic carcinoma

value: Fibroblast

tag: cell state

value: Sen

value: PDAC


title: hPDAC_Non-sen3

value: Non-Sen


title: hPDAC_Sen2


title: hPDAC_Non-sen4


title: hPDAC_Sen3


title: hPDAC_Non-sen1


title: hPDAC_Non-sen2


title: Cultured human CAFs_Sen4

data_processing:
FASTQ files were trimmed and filtered with trim_galore (v0.6.1) for adapter sequences, polyA tails and low quality bases.
Trimmed and filtered reads were mapped with salmon quant function (v1.6.0) to the transcriptome.
Normalization and exploration of differentially expressed genes was perfofrmed with Deseq2 (v1.40.1)
Assembly: hg38 and mm39
Supplementary files format and content: Tab-delimited text file consisting of raw gene counts for each sample.

source_name: Pancreas

treatment_protocol: Human and mouse primary CAFs were grown in culture. Senescence was induced by activating a Cre-ER vector that excised hTERT and SV40-LT-Antigen.

value: Pancreas

value: Fibroblasts


title: Cultured human CAFs_Sen3


title: hPDAC_Sen1


title: P291_08_8-PSA2-5

value: Liver


title: Cultured human CAFs_Sen1


title: Cultured human CAFs_Sen2


title: Cultured human CAFs_Non-sen3


title: Cultured human CAFs_Non-sen2


title: W/W Vehicle-3

city: CHARLOTTESVILLE

first: Ira

middle: Glenn

last: Schulman

state: Virginia

address: 1340 Jefferson Park Ave, Jordan Hall, room 5218

department: Pharmacology

institute: University of Virginia

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Assembly: GRCm38 mm10
Supplementary files format and content: Microsoft Excel Comma Separated Value File (.csv)

growth_protocol: Liver RNA was isolated from 11-12 week old male mice fed a MASH promoting diet (Teklad TD.96121) for 4 weeks. After 2 weeks mice  remained on diet and were treated daily with vehicle (V) or 10 mg/kg T0901317 (T) by oral gavage. Liver RNA was isolated from an independent cohort of 11-12 week old male mice that were maintained on a normal chow diet.

extract_protocol:
Liver samples were solubilized in Trizole, extracted with choloform and the RAN was purified from the aqueous layer using Quick-RNA miniprep kits.
Libraries were conctructed by Azenta Life Sciences

treatment_protocol: Mice were fed a MASH promoting diet (Teklad TD.96121) for 4 weeks. After 2 weeks mice  remained on diet and were treated daily with vehicle (V) or 10 mg/kg T0901317 (T) by oral gavage.

value: W/W

value: MASH + Vehicle


title: Cultured human CAFs_Non-sen1


title: W/W Vehicle-2


title: W/W T0901317-4


title: W/W T0901317-3


title: W/W Vehicle-4


title: W/W Vehicle-1


title: W/W T0901317-1


title: W/W N4

value: Normal Chow


title: WW T0901317-2


title: W/W N3


title: W/F Vehicle-4

value: W/F


title: W/W N2


title: W/WN1


title: W/F Vehicle-2


title: W/F T0901317-1


title: W/F Vehicle-3


title: W/F T0901317-3


title: W/F T0901317-4


title: W/F N2


title: W/F Vehicle-1


title: W/F N4


title: W/F N3


title: F/F Vehicle-4

value: F/F


title: F/F Vehicle-3


title: F/F Vehicle-1


title: F/F T0901317-4


title: F/F T0901317-3


title: F/F N4


title: F/F Vehicle-2


title: F/F T0901317-1


title: F/F N3


title: RNAseqAged1

city: Tianjin

first: Jianwei

last: Wang

address: 10 Yuexin Street, Binhai New Area

institute: HAIHE LABORATORY OF CELL ECOSYSTEM

data_processing:
Hi-C: Hi-C data analysis was performed with HiC-Pro(https://github.com/nservant/HiC-Pro).
CUT&RUN and CUT&Tag: CTCF CUT&RUN data was performed with CUT&RUNTools piplines(https://bitbucket.org/qzhudfci/cutruntools/src/master/).
RNA-seq:Reads were mapped to reference genome mm10 by Hisat2(version 2.2.1), and then counted for each gene by htseq-count(version 0.11.1). Next, DEseq2(version 1.26.0) was used to get differentially expressed genes
Assembly: mm10
Supplementary files format and content: hic(Hi-C data valid pairs)
Supplementary files format and content: bigWig(CTCF signal), bed(seacr peaks)
Supplementary files format and content: tab-delimited text (RNA-seq counts), matrix table (gene TPM counts for every gene and every sample)

source_name: Bone marrow

extract_protocol:
Fus low and Fus high HSCs(lineage-, c-kit+ Sca-1+ CD34-) from bone marrow of mice using fus gtp; Young(2 months) and Aged(30 months) HSCs(lineage-, c-kit+ Sca-1+ CD34-) from bone marrow of mice
Hi-C: We performed in tagHi-C on FUSlow HSCs and FUShigh HSCs(Cell reports 32, 108206 (2020)). In briefly, 20,000 HSCs were sorted and crosslinked in 100 uL 1% formaldehyde for 10 minutes at room temperature. Cell pellet was collected by centrifuged for 5 minutes at 3,000 g at 4℃ and lysed in 25uL of Hi-C lysis buffer. Next MboI restriction enzyme in 2.5uL of 10x NEB buffer 2 were added to digest chromatin. Then DNA fragments were ligated by incubated in Ligation master mix (66.3 uL of ddH2O, 12 uL of 10 x T4 DNA ligase buffer, 10 uL of 10% (v/v) Triton X-100, 1.2 uL of 100 x BSA and 1 uL of 400 U/uL T4 DNA ligase).Next, DNA was extracted by150 uL Phenol-Chloroform-Isoamyl alcohol (25:24:1). Next, 20 uL of DNA fragmentation mix (4 uL of 5 x TTBL, 5 uL of TTE Mix V1, 5 ng DNA and ddH2O) was used for PCR amplification. After amplification, the samples were purified with AMPure beads once and resolved with ddH2O to prepare for sequencing library after the DNA concentration was quantified with Qubit. The libraries were sequenced using an Illumina Hiseq platform with 150-bp paired-end.
CUT&RUN: Young HSCs and Aged HSCs were sorted from 2-month mice and 30-month mice. 100,000 HSCs were centrifuged at 1,000g for 5min at 4℃, and washed with 200uL PBS.le. Then the conA beads were separated by magnet and resuspended with 200 μl Antibody Buffer (2mM EDTA, 0.02% digitonin and CTCF antibody (1:250, EMD Millipore, 07-729) in washing buffer)》 Next, DNA was digested using 200 μL pA-MNase Buffer. Next, Endprep reaction system(25uL DNA and H2O, 1.5 μLNEB Next Ultra II Endprep Enzyme Mix, 3.5uLNEB Next Ultra II Endprep Reaction Buffer) was subjected to PCR amplification. After amplification, the samples were purified with 0.3× -0.6× VATHS Beads and resolved with ddH2O to prepare for sequencing library after the DNA concentration was quantified with Qubit. The libraries were sequenced using an Illumina Hiseq platform with 150-bp paired-end.
CUT&Tag: FUSlow HSCs and FUShigh LSK cells were sorted from 2-4 month fus-gfp mice. 50,000 LSK cells were collected at 500g for 5min at RT, and performed according to the protocol of CUT&Tag Assay Kit(TD903, Vazyme)
RNA-seq: First, 100 HSCs (Lineage- Sca-1+ c-kit+ CD34- GFPlow/high) from Fus-gfp mice were sorted into lysis buffer directly. The transcriptome libraries were prepared using Smart-seq2 method. Then, Agilent Bioanalyzer 2100 system (Agilent Technologies) was used to assess the insertion size, and HiSeq PE Cluster Kit v4-cBot-HS (Illumina) was used to perform the clustering of the index-coded samples according the manufacturer’s instructions. Finally, the libraries were sequenced using an Illumina Hiseq platform with 150-bp paired-end.

value: Bone marrow

value: hematopoietic stem cells


title: RNAseqAged3


title: F/F N2


title: WF T0901317-2


title: RNAseqAged2


title: RNAseqYoung2


title: RNAseqNewYoung2


title: RNAseqNewYoung3


title: W/F N1


title: RNAseqYoung3


title: RNAseqNewYoung1


title: RNAseqYoung1


title: RNAseqNewAgedKDFus2


title: RNAseqNewAgedKDFus3


title: RNAseqNewAgedKDFus1


title: RNAseq_new_Aged2


title: F/F T0901317-2


title: RNAseq_new_Aged1


title: FusLow,HSCs, CTCF, CUT&Tag,rep1

data_processing:
Library strategy: CUT&RUN
Hi-C: Hi-C data analysis was performed with HiC-Pro(https://github.com/nservant/HiC-Pro).
CUT&RUN and CUT&Tag: CTCF CUT&RUN data was performed with CUT&RUNTools piplines(https://bitbucket.org/qzhudfci/cutruntools/src/master/).
RNA-seq:Reads were mapped to reference genome mm10 by Hisat2(version 2.2.1), and then counted for each gene by htseq-count(version 0.11.1). Next, DEseq2(version 1.26.0) was used to get differentially expressed genes
Assembly: mm10
Supplementary files format and content: hic(Hi-C data valid pairs)
Supplementary files format and content: bigWig(CTCF signal), bed(seacr peaks)
Supplementary files format and content: tab-delimited text (RNA-seq counts), matrix table (gene TPM counts for every gene and every sample)


title: FusLow,HSCs, CTCF, CUT&Tag,rep2


title: Aged, HSCs, tagHi-C, rep1


title: FusHigh,HSCs, CTCF, CUT&Tag,rep2


title: FusHigh,HSCs, CTCF, CUT&Tag,rep1


title: F/F N1


title: RNAseq30high-3

data_processing:
Hi-C: Hi-C data analysis was performed with HiC-Pro(https://github.com/nservant/HiC-Pro).
CUT&RUN: CTCF CUT&RUN data was performed with CUT&RUNTools piplines(https://bitbucket.org/qzhudfci/cutruntools/src/master/).
RNA-seq:Reads were mapped to reference genome mm10 by Hisat2(version 2.2.1), and then counted for each gene by htseq-count(version 0.11.1). Next, DEseq2(version 1.26.0) was used to get differentially expressed genes
Assembly: mm10
Supplementary files format and content: hic(Hi-C data valid pairs)
Supplementary files format and content: bigWig(CTCF signal), bed(seacr peaks)
Supplementary files format and content: tab-delimited text (RNA-seq counts), matrix table (gene TPM counts for every gene and every sample)

extract_protocol:
Fus low and Fus high HSCs(lineage-, c-kit+ Sca-1+ CD34-) from bone marrow of mice using fus gtp; Young(2 months) and Aged(30 months) HSCs(lineage-, c-kit+ Sca-1+ CD34-) from bone marrow of mice
RNA-seq: First, 100 HSCs (Lineage- Sca-1+ c-kit+ CD34- GFPlow/high) from Fus-gfp mice were sorted into lysis buffer directly. The transcriptome libraries were prepared using Smart-seq2 method. Then, Agilent Bioanalyzer 2100 system (Agilent Technologies) was used to assess the insertion size, and HiSeq PE Cluster Kit v4-cBot-HS (Illumina) was used to perform the clustering of the index-coded samples according the manufacturer’s instructions. Finally, the libraries were sequenced using an Illumina Hiseq platform with 150-bp paired-end.

tag: fus level

value: high


title: RNAseq36high-6


title: RNAseq36high-3


title: RNAseq36high-5


title: RNAseq32high-1


title: RNAseq30high-6


title: RNAseq30high-4


title: RNAseq36low.6

value: low


title: RNAseq36low.1


title: RNAseq32low-5


title: RNAseq_new_Aged3


title: RNAseq32low-3


title: RNAseq32low-6


title: RNAseq30low-1


title: Fus, high, HSCs, tagHi-C, rep2

extract_protocol:
Fus low and Fus high HSCs(lineage-, c-kit+ Sca-1+ CD34-) from bone marrow of mice using fus gtp; Young(2 months) and Aged(30 months) HSCs(lineage-, c-kit+ Sca-1+ CD34-) from bone marrow of mice
Hi-C: We performed in tagHi-C on FUSlow HSCs and FUShigh HSCs(Cell reports 32, 108206 (2020)). In briefly, 20,000 HSCs were sorted and crosslinked in 100 uL 1% formaldehyde for 10 minutes at room temperature. Cell pellet was collected by centrifuged for 5 minutes at 3,000 g at 4℃ and lysed in 25uL of Hi-C lysis buffer. Next MboI restriction enzyme in 2.5uL of 10x NEB buffer 2 were added to digest chromatin. Then DNA fragments were ligated by incubated in Ligation master mix (66.3 uL of ddH2O, 12 uL of 10 x T4 DNA ligase buffer, 10 uL of 10% (v/v) Triton X-100, 1.2 uL of 100 x BSA and 1 uL of 400 U/uL T4 DNA ligase).Next, DNA was extracted by150 uL Phenol-Chloroform-Isoamyl alcohol (25:24:1). Next, 20 uL of DNA fragmentation mix (4 uL of 5 x TTBL, 5 uL of TTE Mix V1, 5 ng DNA and ddH2O) was used for PCR amplification. After amplification, the samples were purified with AMPure beads once and resolved with ddH2O to prepare for sequencing library after the DNA concentration was quantified with Qubit. The libraries were sequenced using an Illumina Hiseq platform with 150-bp paired-end.


title: Young, HSCs, CTCF, CUT&RUN

data_processing:
Hi-C: Hi-C data analysis was performed with HiC-Pro(https://github.com/nservant/HiC-Pro).
CUT&RUN: CTCF CUT&RUN data was performed with CUT&RUNTools piplines(https://bitbucket.org/qzhudfci/cutruntools/src/master/).
RNA-seq:Reads were mapped to reference genome mm10 by Hisat2(version 2.2.1), and then counted for each gene by htseq-count(version 0.11.1). Next, DEseq2(version 1.26.0) was used to get differentially expressed genes
Assembly: mm10
Supplementary files format and content: hic(Hi-C data valid pairs)
Supplementary files format and content: bigWig(CTCF signal), bed(seacr peaks)
Supplementary files format and content: tab-delimited text (RNA-seq counts), matrix table (gene TPM counts for every gene and every sample)
Library strategy: CUT&RUN

extract_protocol:
Fus low and Fus high HSCs(lineage-, c-kit+ Sca-1+ CD34-) from bone marrow of mice using fus gtp; Young(2 months) and Aged(30 months) HSCs(lineage-, c-kit+ Sca-1+ CD34-) from bone marrow of mice
CUT&RUN: Young HSCs and Aged HSCs were sorted from 2-month mice and 30-month mice. 100,000 HSCs were centrifuged at 1,000g for 5min at 4℃, and washed with 200uL PBS.le. Then the conA beads were separated by magnet and resuspended with 200 μl Antibody Buffer (2mM EDTA, 0.02% digitonin and CTCF antibody (1:250, EMD Millipore, 07-729) in washing buffer)》 Next, DNA was digested using 200 μL pA-MNase Buffer. Next, Endprep reaction system(25uL DNA and H2O, 1.5 μLNEB Next Ultra II Endprep Enzyme Mix, 3.5uLNEB Next Ultra II Endprep Reaction Buffer) was subjected to PCR amplification. After amplification, the samples were purified with 0.3× -0.6× VATHS Beads and resolved with ddH2O to prepare for sequencing library after the DNA concentration was quantified with Qubit. The libraries were sequenced using an Illumina Hiseq platform with 150-bp paired-end.

value: not determined


title: Aged, HSCs, CTCF, CUT&RUN


title: Fus, high, HSCs, tagHi-C, rep1


title: RNAseq30low-5


title: Fus, low, HSCs, tagHi-C, rep2


title: preterm,replicate 3,scRNAseq

first: Meng

last: Yao

address: 22 Qixiangtai Road

institute: Tianjin Medical University

description: 10x Genomics

data_processing:
The raw data were preprocessed using Cell Ranger (version 7.0). The R toolkit Seurat (version 4.0.1) were used for downstream analysis
Assembly: mm10
Supplementary files format and content: Tab-separeted values files and matrix files

source_name: Peripheral blood

extract_protocol:
Peripheral blood samples were collected from 3 full-term, 3 preterm and 3 adult controls. Single-cell suspensions of peripheral blood mononuclear cells (PBMCs) were obtained by centrifuging human blood samples on a Ficoll gradient. Briefly, blood was mixed with an equal volume of 2% FBS in PBS and gently layered on the Ficoll gradient. Cells were centrifuged at 1000 x g for 25 min, without braking. The cells in the middle layer were then washed once with PBS and red cells were removed using ACK lysing buffer, resuspended in 2% FBS in PBS for use. The PBMC suspensions were stained with surface markers at 30 min at 4°C in dark. The strategy for MDSCs was CD11b+HLA-DR-/lo. Live immature myeloid cell in RPMI1640 supplemented with 20% FBS were sorted in a BD FACSAria III cell sorter (BD Biosciences).
Droplet-based scRNA-seq library praperarion: single cells were captured via the GemCode Single Cell Platform using the GemCode Gel Bead, Chip and 30-end Library Kits (103 Genomics), according to the manufacturer’s protocol. Flow sorted CD11b+HLA-DR- cell which were pre-labeled with hashtag antibodies (Biolegend), were pooled and loaded at 60,000 cells per channel. The cells were then partitioned into the GemCode instrument, where individual cells were lysed and mixed with beads carrying unique barcodes in individual oil droplets. The products were subjected to reverse transcription, emulsion breaking, cDNA amplification, and sample index attachment

value: Peripheral blood

value: immature myeloid cells


title: RNAseq30low-4


title: f_term,replicate 2,scRNAseq

description: 10x Genomics


title: preterm,replicate 1,scRNAseq

description: 10x Genomics


title: RNAseq32high-6


title: preterm,replicate 2,scRNAseq

description: 10x Genomics


title: f_term,replicate 3,scRNAseq

description: 10x Genomics


title: RNAseq32high-2


title: adult,replicate 3,scRNAseq

description: 10x Genomics


title: adult,replicate 2,scRNAseq

description: 10x Genomics


title: RNAseq36low.2


title: f_term,replicate 1,scRNAseq

description: 10x Genomics


title: Rbpms2-mApple uncrosslinked (SR2)

city: New York

first: Florence

middle: L

last: Marlow

address: Madison Ave

department: CDRB

institute: Icahn  School of Medicine Mount Sinai

data_processing:
Basespace illumina platform was used and reads were mapped using tophate2 aligner.
Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome (GRCz10).
Reads were aligned with the TopHat Alignment App.
GRCz10
CSV file that compiled includes tracking ids, gene loci, and FPKMs for each samples
CSV files include tracking and gene id, gene short name, tss id, locus, and FPKM for each sample

organism: Danio rerio

source_name: Gonad

extract_protocol:
RNA was extracted with an Rneasy Mini Kit (Qiagen, 74104)
Libraries were generated with an Illumina Truseq RNA Library Prep kit (Illumina, 20020589)

value: Gonad

value: Germline and somatic

tag: genotype

value: Wildtype


title: adult,replicate 1,scRNAseq

description: 10x Genomics


title: Fus, low, HSCs, tagHi-C, rep1


title: mApple control uncrosslinked (SR6)


title: rbpms2 mutant 1, 21 dpf

data_processing:
Expression count (STAR) basepair pipeline was used
GRCz10
XLSX file includes all gene ids, symbols, counts, FPKMs, and TPMs for each sample
CSV files include gene id, symbol, count, FPKM, and TPM for each sample

extract_protocol:
RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit (400753)
Libraries were generated with a low input SMART-Seq HT with Nxt HT kit (Clontech Laboratories, 634947)

value: rbpms2a ae30; rbpms2b sa MM


title: rbpms2 mutant 4, 21 dpf


title: mApple control crosslinked (SR8)


title: Rbpms2-mApple crosslinked (SR3)


title: rbpms2 mutant 3, 21 dpf


title: rbpms2 wildtype 2, 21 dpf


title: rbpms2 wildtype 3, 21 dpf


title: rbpms2 wildtype 1, 21 dpf


title: ASC,HFS, H3K4me3, 2

city: Mexico City

first: Armando

middle: Roberto

last: Tovar Palacio

state: México City

address: Belisario Dominguez 15

country: Mexico

institute: Instituto Nacional de Ciencias Médicas y Nutrición

data_processing:
Data quality was assessed with FastQC.
Adapters were trimmed using TrimGalore, and alignment files were referenced to the rat mRatBN7.2/rn7 reference genome with Bowtie2 with default parameters.
Mitochondrial and PCR duplicate reads were removed using Samtools and PicardTools, respectively.
Peaks were called using MACS2 with the flag  “--keep-dup all”. We generated a consensus peak set per treatment with the overlapping peaks from the two biological replicates of each treatment.
Differential H3K4me3 enrichment analysis was made using the getDifferentialPeaks tool from HOMER, where a peak region with a fold change >1.5 and a Poisson p-value <0.0001 was considered to be differentially enriched.
Assembly: mRatBN7.2/rn7
Supplementary files format and content: BigWing

source_name: Inguinal Adipose Tissue

growth_protocol: ASCs were isolated from inguinal adipose tissue using the collagenase digestion method  and maintained in DMEM F12 supplemented with 10.0% FBS and 1.0% antibiotic/antimycotic B (penicillin/streptomycin/amphotericin) in an incubator at 37°C with 5.0% CO2

extract_protocol:
ASCs and Ads were fixed in 0.8% formaldehyde for 10 minutes at room temperature, followed by 5 minutes with glycine (0.125 mM) as a quenching reagent. Nuclei were isolated from mature adipocytes. ASCs and Ads nuclei were lysated and chromatin was sheared to 300-500 bp using the EpiSonic 1100 equipment
Libraries were generated using the NEBnext® Ultratm ii DNA Kit for Illumina with 13 cycles of amplification. For each study time, two libraries were generated, with 3-4 rats each.

treatment_protocol: After reaching confluence, ASCs were exposed to induction medium (DMEM F12 supplemented with 5.0 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxanthine, and 10.0 μg/mL insulin) for 3 days, followed by maintenance medium (DMEM F12 supplemented with 10.0 μg/mL insulin) for 7 days

value: Inguinal Adipose Tissue

value: Adipose-Derived Stem Cells

value: WT

tag: treatment

value: High Fat and Sucrose Diet


title: AD,C, H3K4me3, 2

value: Control Diet


title: ASC,HFS, H3K4me3, 1


title: ASC,C, H3K4me3, 2


title: AD,C, H3K4me3, 1


title: ASC,C, H3K4me3,1


title: AD,HFS, 2

data_processing:
Data quality was assessed using FastQC.
Alignments of paired-end samples were generated using STAR with default parameters using the mRatBN7.2/rn7 reference genome and annotations.
Raw gene count matrices were generated using FeatureCounts.
Differential gene expression was analysed with DESeq2; genes with an adjusted p-value <0.05 and a log2 fold change >2 were considered differentially expressed.
Assembly: mRatBN7.2/rn7
Supplementary files format and content: txt

extract_protocol:
RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer's instructions
mRNA was isolated using the NEBNext rRNA depletion kit. Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #E7770), and 50 bp paired-end reads were obtained from two libraries per condition

value: Mesenchymal stem cells


title: AD,HFS, 1


title: AD,C, 1


title: AD,C, 2


title: ASC,HFS, 2


title: ASC,HFS, 1


title: ASC,C, 2


title: Fluoxetine Rep4

city: Singapore

first: Nirmala

last: Arul Rayan

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Using all spots from the 14 tissue sections, we removed spots that had nFeature (number of unique genes) <300, pMito (percentage of reads mapped to the mitochondrial genome) >30% and pHb (percentage of reads mapped to hemoglobin genes) >20%. Integration of the resulting ~33K spots, followed by clustering, revealed no major batch effects, as expected since all sections were processed as a single batch.
We used BANKSY for identifying tissue domains
Assembly: rn6
Supplementary files format and content: rds files
Library strategy: Spatial RNA-seq

source_name: Pre- and infra- limbic cortex (PLC, ILC)

extract_protocol:
10 μM fresh frozen brain sections (coronal) of PLC and ILC regions were placed on capture areas of Visium slides. As per manufacturer's protocol (10x Genomics Visium Spatial Gene Expression kit), sections were then methanol-fixed and permeabilized. The released mRNA molecules were reverse transcribed to produce spatially barcoded cDNA which were then amplified. Libraries were prepared and sequenced on the Illumina NovaSeq, PE150. Reads were trimmed to 28 cycles for read 1 and 90 cycles for read 2.
10x Genomics Visium Spatial Gene Expression kit

treatment_protocol: 2 month old Charles River rats were treated with water (Sham group), fluoxetine, maltodextrin or probiotics  (n=4 for Sham, FT, Pro; n=2 for Mal) ad libitum for 3 weeks.

tag: replicate

value: Fluoxetine


title: Probiotics Rep3

value: Pre- and infra- limbic cortex (PLC, ILC)

value: Probiotics


title: Sham Rep3

value: Sham


title: Sham Rep4


title: AD,HFS, H3K4me3, 1


title: Fluoxetine Rep2


title: Fluoxetine Rep3


title: Probiotics Rep2


title: Maltodextrin Rep1

value: Maltodextrin


title: ASC,C, 1


title: RMB4418

data_processing:
RNA-seq data were aligned to the Rattus norvegicus rn6 genome (Rn6 UCSC) with the STAR aligner. Read counts were concurrently calculated using Htseq
Any dataset that failed the default Fastqc sequencing parameters and < 75% mapping rate was discarded.
Assembly: rn6
Supplementary files format and content: fastq and read count files

source_name: brain

growth_protocol: Tissue RNA-seq. Brains were removed and frozen immediately on dry ice. Frozen brains were cryosectioned at 250um thickness onto poly-lysine coated slides. The anatomical regions subject to punching were verified using the rat brain atlas of Paxinos and Watson

extract_protocol:
Frozen, pooled brain tissue punches for each region were thawed on ice in 1 ml Trizol. Tissue was then homogenized using a manual glass douncer with 7-15 slow strokes on ice. RNA was extracted from each replicate sample using the Qiagen RNA Mini kit (Qiagen, Cat# 74104) as per the manufacturer’s instructions with on-column DNase I treatment. RNA quality was examined using a Bioanalyzer 2100 (Agilent technologies, Santa Clara, USA). RNA Integrity Number (RIN) values ranged from 7.1 to 10, with a median value of 9.5. cDNA libraries were prepared using 300 ng of total RNA, from 27 regions in every replicate, using the Illumina TruSeq Stranded Total RNA LT set (Illumina, Cat# RS-122-2301). Paired-end, 150 bp read length RNA-seq was carried out on the Illumina HiSeq 4000 at a depth of 20M reads per sample.
llumina TruSeq Stranded Total RNA LT set (Illumina, Cat# RS-122-2301)

treatment_protocol: Animals: 60-day old Long Evans uncharacterized male rats ordered from Charles River.  Treatment: Three weeks administration ad libitum in drinking water. There are 6 treatment groups.   Dosages for each treatment group are as follows:  Fluoxetine: 13mg/kg/day (Sigma Aldrich (PHR1394));  Desipramine: 7.5 mg/kg/day;  Bupropion: 15mg/kg/day;  Probiotic: 1.5 x 10 9 CFU/day (1 billion CFU/day);  Maltodextrin control: 10 g/L ;  Water control group

tag: brain region_name

value: venDG

value: Control

value: brain


title: Fluoxetine Rep1


title: Maltodextrin Rep2


title: RMB4415

value: NACShell


title: RMB4414

value: mPOA


title: RMB4416

value: PLC


title: Sham Rep2


title: Probiotics Rep1


title: RMB4413

value: LConly


title: RMB4411

value: dorDG


title: RMB4410

value: CGC


title: RMB4409

value: BLA


title: Probiotics Rep4


title: RMB4408


title: RMB4417

value: Raphe


title: RMB4406


title: RMB4407


title: RMB4405


title: Sham Rep1


title: RMB4403


title: RMB4401


title: RMB4396


title: RMB4402

value: ILC


title: RMB4395


title: RMB4397


title: RMB4404


title: RMB4399


title: RMB4400


title: RMB4398


title: RMB4392


title: RMB4394


title: RMB4412


title: RMB4391


title: RMB4388


title: RMB4393


title: RMB4386


title: RMB4384


title: RMB4385


title: RMB4380


title: RMB4383


title: RMB4382


title: RMB4379


title: RMB4381


title: RMB4378


title: RMB4377


title: RMB4376


title: RMB4387


title: RMB4372


title: RMB4367


title: RMB4390


title: RMB4373


title: RMB4368


title: RMB4375


title: RMB4374


title: RMB4365


title: RMB4366


title: RMB4369


title: RMB4364


title: RMB4362


title: RMB4371


title: RMB4360


title: RMB4389


title: RMB4359


title: RMB4356


title: RMB4358


title: RMB4357


title: RMB4363


title: RMB4361


title: RMB4355


title: RMB4354


title: RMB4353


title: RMB4351


title: RMB4352


title: RMB4350


title: RMB4370


title: RMB4349


title: RMB4348


title: RMB4345


title: RMB4347


title: RMB4342


title: RMB4343


title: RMB4344


title: RMB4346


title: RMB4340


title: RMB4339


title: RMB4337


title: RMB4334


title: RMB4333


title: RMB4335


title: RMB4331


title: RMB4328


title: RMB4329


title: RMB4327


title: RMB4325


title: RMB4330


title: RMB4324


title: RMB4322


title: RMB4326


title: RMB4320


title: RMB4321


title: RMB4319


title: RMB4341


title: RMB4318


title: RMB4317


title: RMB4336


title: RMB4314


title: RMB4312


title: RMB4316


title: RMB4310


title: RMB4315


title: RMB4311


title: RMB4332


title: RMB4308


title: RMB4307


title: RMB4305


title: RMB4304


title: RMB4303


title: RMB4306


title: RMB4301


title: RMB4323


title: RMB4302


title: RMB4300


title: RMB4338


title: RMB4298


title: RMB4297


title: RMB4296


title: RMB4293


title: RMB4292


title: RMB4313


title: RMB4291


title: RMB4290


title: RMB4295


title: RMB4309


title: RMB4294


title: RMB4287


title: RMB4285


title: RMB4283


title: RMB4284


title: RMB4288


title: RMB4299


title: RMB4282


title: RMB4281


title: RMB4278


title: RMB4276


title: RMB4274


title: RMB4279


title: RMB4280


title: RMB4273


title: RMB4275


title: RMB4271


title: RMB4289


title: RMB4286


title: Culex adults, insulin, WNV, 24 h, biol rep 8

city: Pullman

first: Alan

middle: G.

last: Goodman

state: WASHINGTON

address: 100 Dairy Rd., BLS 202

department: School of Molecular Biosciences

institute: Washington State University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were imported using Illumina paired importer (FASTQ).
Trimmed sequence reads were mapped to GCA_000209185.1 using CLC genomic benchwork (parameters: Discard read names=No, Discard quality scores=No, Paired orientation=Paired reads (forward-reverse), Minimum distance=200, Maximum distance=300, Quality score=NCBI/Sanger or Illumina Pipeline 1.8 and later, Remove failed reads=Yes, MiSeq de-multiplexing=No).
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: GCA_000209185.1
Supplementary files format and content: tab-delimited text file of raw gene expression data for all samples

organism: Culex quinquefasciatus

source_name: Whole animal

growth_protocol: Adult female mosquitoes were fed on defibrinated chicken blood in hog sausage casing. Adults were provided continuous access to sucrose.

extract_protocol:
Animals were homogenized in Trizol reagent. RNA was harvested using Trizol reagent and Direct-Zol RNA extraction kit (Zymo Research). 2.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following manufacturer's protocols.

treatment_protocol: 6-9 day old adult female mosquitoes were fed on defibrinated chicken blood experimental glass feeders with 1e7 PFU WNV-Kunjin +/- 170 pM bovine insulin. Mosquitoes were deprived of sucrose 48 hours prior to experimental feedings.

value: Whole animal

value: WT

value: 170 pM insulin, WNV infection


title: Culex adults, insulin, WNV, 24 h, biol rep 7


title: RMB4270

value: Probiotics


title: Culex adults, insulin, WNV, 24 h, biol rep 5


title: Culex adults, insulin, WNV, 24 h, biol rep 6


title: RMB4269


title: RMB4268

value: Desipramine


title: RMB4267


title: Culex adults, insulin, WNV, 24 h, biol rep 2


title: Culex adults, insulin, WNV, 24 h, biol rep 4


title: Culex adults, insulin, WNV, 24 h, biol rep 1


title: RMB4266


title: RMB4265


title: Culex adults, insulin, WNV, 24 h, biol rep 3


title: Culex adults, mock, WNV, 24 h, biol rep 8

value: 0 pM insulin, WNV infection


title: RMB4263


title: RMB4264


title: RMB4277


title: Culex adults, mock, WNV, 24 h, biol rep 6


title: Culex adults, mock, WNV, 24 h, biol rep 7


title: RMB4272


title: RMB4262


title: RMB4260


title: Culex adults, mock, WNV, 24 h, biol rep 4


title: RMB4261


title: Culex adults, mock, WNV, 24 h, biol rep 3


title: RMB4259


title: Culex adults, mock, WNV, 24 h, biol rep 2


title: RMB4258

value: venDG


title: Culex adults, mock, WNV, 24 h, biol rep 1


title: RMB4257

value: brain


title: RMB4255

value: NACShell


title: RMB4256


title: NIH3T3, CIC::DUX4, clone D8

city: San Francisco

first: Ross

last: Okimoto

address: 513 Parnassus Ave

institute: University of California, San Francisco

description: Column name in processed data: CDD8

data_processing:
FASTQ files were aligned to GRCm39 using STAR (version 2.7.10b).
Gene counts were extracted during alignment using STAR parameter --quantMode GeneCounts
Differental expression analysis was performed in R (version 4.2.2) with edgeR (version 3.40.2).
Log2(cpm) data were obtained from TMM-normalized data using edgeR with the cpm function (log = T) which with this version of edgeR adds an average prior count of 2.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file, STAR gene counts for all samples, data taken from column 4 of STAR output due to the strandedness of the library prep kit used. File name = counts_NIH3T3_dC1.txt.
Supplementary files format and content: Tab-delimited text file, log2(counts per million) measurements for all samples after edgeR processing. File name = log2_of_cpm.txt.

growth_protocol: Transduced and clonally selected NIH/3T3 cells were maintained in DMEM (high glucose, +L-Glutamine, +Sodium Pyruvate) with 10% fetal bovine serum (FBS) and 1% Pen-Strep (100 U/mL Penicillin, 100 ug/mL Streptomycin) at 37C in a 5% CO2 humidified incubator.

extract_protocol:
RNA was extracted using the RNeasy Mini kit (Qiagen) including an on-column Dnase digest (Qiagen) and an additional short Buffer RPE wash. Samples were also cleaned up with Monarch RNA Cleanup Kit (NEB) and checked for integrity on a TapeStation (Agilent).
Libraries were constructed by Novogene by polyA-enriching RNA and then using the NEBNext Ultra II Directional Library Prep Kit for Illumina (NEB).

treatment_protocol:
NIH/3T3 cells were transduced with ecotropic retrovirus encoding a gene-IRES-EGFP construct where the gene was one of the following: empty (empty vector), full-length CIC::DUX4, or C1-deleted CIC::DUX4.
Clonal populations were derived by sorting EGFP+ cells via FACS into single wells of 96 well plates, expanding, and validating transgene expression by Western blot.
Cell lines were seeded at 150,000 cells in a single well of a 6-well plate, allowed to grow for approximately 48 hours, and harvested for RNA.

value: fibroblast

tag: genetic modification

value: full length CIC::DUX4 transduced


title: RMB4254

value: mPOA


title: RMB4253

value: LConly


title: NIH3T3, EV, clone E8

description: Column name in processed data: EVE8

tag: cell line

value: EV transduced


title: NIH3T3, dC1, clone C10

description: Column name in processed data: delC10

value: C1-deleted CIC::DUX4 transduced


title: NIH3T3, dC1, clone B5

description: Column name in processed data: delB5


title: Culex adults, mock, WNV, 24 h, biol rep 5


title: RMB4252


title: NIH3T3, EV, clone B6

description: Column name in processed data: EVB6


title: RMB4251

value: dorDG


title: RMB4250

value: CGC


title: RMB4249

value: BLA


title: RMB4247

value: Raphe


title: 5852.G9aKOPDXCre.AcutePanc ST

city: Milwaukee

first: Gwen

last: Lomberk

state: Wisconsin

address: 8701 W Watertown Plank Rd, Milwaukee, WI 53226

institute: Medical College of Wisconsin

data_processing:
The 10X Libraries were sequenced on the Illumina NovaSeq6000 sequencer with pair-end reads (28 bp for read 1, 10 bp for i5, 10 bp for i7, and 50 bp for read 2).
Alignment, tissue detection, fiducial detection, and barcode/UMI counting were performed by Spaceranger Count
read alignment, reference transcriptome was mouse mm10-2020-A with mouse Visium Probe_Set_v1.0
Assembly: mm10-2020-A
Supplementary files format and content: CAVG.tif: CytAssit image
Supplementary files format and content: _merge_.tif: BrightField image
Supplementary files format and content: _Fiducial.json: Fiducial alignment in json format
Supplementary files format and content: _barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: _features.tsv.gz: list of gene IDs
Supplementary files format and content: _matrix.mtx.gz: gene expression count data
Library strategy: Spatial transcriptomics

source_name: pancreas

growth_protocol: Standard mouse housing with controlled temperature, humidity and light cycles and provided with ad libitum standard rodent chow and water.

extract_protocol:
10x CytAssist Protocol
10x Visium

treatment_protocol: For induction of acute pancreatitis, cohorts of mice were fasted for 12 h before the first caerulein injection. Caerulein or saline control was administered via IP injection at a dose of 50 μg/kg once an hour for a total of eight injections. Food was returned after the first dose. Animals were euthanized 18 h after the initial dose.

value: pancreas

value: EHMT2 knockout (KO) PDX-Cre

value: Caerulein IP injection at 50 μg/kg once per hour for a total of 8 injections


title: RMB4248

value: Desipramine


title: 5910.G9aKOP48Cre.AcutePanc RNA

description: DEAnalyses_acute panc PDX and P48

data_processing:
Sequencing reads were processed through the MAP-Rseq version 3.0.0 workflow
Differential Expression Analysis using GLM model in edgeR (version 3.28.1)
Pathway analysis of DEGs using RITAN , R package
Assembly: Genome_build: Gencode vM23 (GRCm38.p6)
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text files include RAW and RPKM values for each Sample

extract_protocol:
Pancreas was taken at time of euthanasia, minced in RNAlater and snap frozen with liquid nitrogen. RNA extraction was completed with ToTALLY RNA Kit (Ambion, Cat# AM1910) according to manufacturer’s protocols. Precipitated RNA was cleaned up according to Qiagen’s protocol on the miRNeasy column (Qiagen, Cat# 217004), with an on-column DNA digestion and RNaseOUT (Invitrogen, Cat# 10777019) added to final elution to reduce degradation during storage at -80°C.
Illumina TruSeq RNA v2 library preparation

value: EHMT2 knockout (KO) P48-Cre


title: 5854.G9aKOPDXCre.AcutePanc ST


title: 5805.PDXCre.AcutePanc ST

value: PDX1-Cre (WT)


title: RMB4246

value: PLC

value: brain


title: 5817.PDXCre.AcutePanc ST


title: 5904.G9aKOP48Cre.AcutePanc RNA

description: DEAnalyses_acute panc PDX and P48


title: RMB4245

value: NACShell


title: 5844.P48Cre.AcutePanc RNA

description: DEAnalyses_acute panc PDX and P48

value: P48-Cre (WT)


title: NIH3T3, CIC::DUX4, clone D4

description: Column name in processed data: CDD4

value: fibroblast

value: full length CIC::DUX4 transduced


title: 5901.G9aKOP48Cre.AcutePanc RNA

description: DEAnalyses_acute panc PDX and P48


title: 5839.P48Cre.AcutePanc RNA

description: DEAnalyses_acute panc PDX and P48


title: RMB4243

value: LConly


title: RMB4244

value: mPOA


title: RMB4242

value: ILC


title: 5854.G9aKOPDXCre.AcutePanc RNA

description: DEAnalyses_acute panc PDX and P48; DEAnalyses_W_WO Acute Panc PDX


title: 5817.PDXCre.AcutePanc RNA


title: 5852.G9aKOPDXCre.AcutePanc RNA


title: RMB4239

value: BLA


title: 5807.PDXCre.AcutePanc RNA


title: RMB4241

value: dorDG


title: RMB4238

value: venDG


title: RMB4240

value: CGC


title: RMB4236


title: RMB4237

value: Raphe


title: 5453-5_G9aKOPDXCre_10dPanc RNA

value: pancreas

value: EHMT2 knockout (KO) PDX-Cre


title: 5804.PDXCre.AcutePanc RNA

value: PDX1-Cre (WT)


title: RMB4235

value: Desipramine


title: 5036-8_PDXCre_10dPanc RNA


title: 5455-5_G9aKOPDXCre_10dPanc RNA


title: 5036-7_PDXCre_10dPanc RNA


title: RMB4231

value: brain


title: RMB4233


title: RMB4230


title: ID3978.G9aKOPDXCre.Adult RNA

description: DEAnalyses_W_WO Acute Panc PDX; DEAnalyses_PN_YA


title: RMB4228


title: ID3954.G9aKOPDXCre.Adult RNA


title: RMB4229


title: ID3951.G9aKOPDXCre.Adult RNA


title: 5038-8_PDXCre_10dPanc RNA


title: 5805.PDXCre.AcutePanc RNA


title: ID4015.PDXCre.Adult RNA


title: ID3999.PDXCre.Adult RNA


title: RMB4226

value: PLC


title: RMB4225

value: NACShell


title: RMB4223


title: RMB4227


title: RMB4234


title: 0.4 T RMF3

first: Ruowen

last: Guo

state: Anhui

address: 350 Shushanhu Road

institute: Hefei institutes of physical science

data_processing:
we aligned reads of all samples to the Gallus gallus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: Hippocampus

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)

value: Hippocampus

value: Neurons


title: 0.4 T RMF2


title: RMB4232


title: 5453-4_G9aKOPDXCre_10dPanc RNA


title: 0.4 T RMF4


title: RMB4224


title: 0.4 T RMF1


title: RMB4221


title: RMB4220


title: Sham3


title: Sham1


title: RMB4218

value: Bupropion


title: Sham4


title: control4


title: RMB4217


title: control2


title: control3


title: control1


title: RMB4215


title: RMB4214

value: mPOA


title: RMB4213

value: LConly


title: RMB4212

value: ILC


title: RAWOCCEV

city: Tokyo

first: Takaaki

last: Tamura

address: 6-7-1 Nishishinjuku, Shinjyuku-ku

institute: Tokyo Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped
Read count extraction and normalization were performed
Assembly: mm 10
Supplementary files format and content: TPM counts for each sample

extract_protocol:
Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA quantity and quality were evaluated with a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
RNA libraries were prepared using NEBNext Ultra II Directional RNA Library prep for Illumina, NEBNext rRNA Depletion Kit and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs), and yields were evaluated using Agilent 2100 BioAnalyzer.

value: osteoclastic cell

value: osteoclastic diffrentiation


title: RAWOCPEV


title: RMB4211

value: dorDG


title: RMB4222


title: RAWOCNEV


title: RAW5112


title: RMB4209

value: BLA


title: RAWNC


title: RMB4219


title: mOBOCCEV

extract_protocol:
Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA quantity and quality were evaluated with a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
RNA libraries were prepared using NEBNext Ultra II Directional RNA Library prep for Illumina, NEBNext rRNA Depletion Kit and NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB), and yields were evaluated using Qubit DNA Assay (Thermo Fisher Scientific) and TapeStation D1000 ScreenTape (Agilent Technologies).

value: osteoblastic cell

value: osteoblastic diffrentiation


title: RMB4206


title: mOBOCNEV


title: RMB4207

value: Raphe


title: RMB4208

value: venDG


title: RMB4210

value: CGC

value: brain


title: mOBNC


title: RMB4204


title: RMB4216

value: PLC


title: mOB1963


title: RMB4205

value: NACShell


title: CUT&TAG_H3K27ac_SALL4-WT Day6

city: zhejiang, china

first: jin

last: ming

address: 西湖大学

institute: Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.

data_processing:
CUT&Tag library construction was performed using Hyperactive InSitu ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme, TD901) and TruePrep Index Kit V2 for Illumina (Vazyme, TD202). In brief, around 10000 living cells per sample were obtained and mixed with activated Concanavalin A beads, followed by sequentially incubated with primary and secondary antibodies. The beads were then washed and resuspended in pA(G)-Tn5 buffer supplemented with 10 mM MgCl2 for DNA tagmentation. Next, DNA fragments were indexed using TruePrep Index Kit V2 for Illumina (Vazyme, TD202) and PCR amplified. After purified by VAHTS DNA Clean Beads (Vazyme, N411), libraries were subjected to Illumina Novaseq instruments for sequencing. Antibodies against Nanog (Abcam, ab214549, 1:50), H3K4me (Abcam, ab313500, 1:50), H3K27ac (Abcam, ab4729, 1:50), flag (Sigma, F1804, 1:50), and Smarca4 (Cell Signaling Technology, 52251, 1:50) were used in this study.
The CUT&Tag reads were trimmed by Trim Galore (v0.6.4) and then mapped to the mm10 reference genome using bowtie2 (v2.4.5). SAMtools (v1.16.1) was used to remove the repetitive, low sequencing quality (mapq<30) and the mitochondrial DNA mapped reads in the total mapped reads. The value were further compressed into a binary format for downstream analysis and data visualization. Replicates were merged using samtools merge and then peak calling was performed using MACS (v1.4.2) with parameters as follows: -g mm --keep-dup 1 --nomodel --shiftsize 25. The signals were normalized to one million reads for each sample. Promoters were defined as regions ± 2 kb around transcription start sites (TSSs) of genes.
Assembly: mm10
Supplementary files format and content: BigWig, Peaks bed
Library strategy: CUT&TAG

source_name: MEF

extract_protocol:
DNA was harvested using Hyperactive InSitu ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme, TD901), 100000 cells per sample was used for sequencing libraries construction
Libraries were constructed by Hyperactive InSitu ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme, TD901) and TruePrep Index Kit V2 for Illumina (Vazyme, TD202).

value: MEF

value: mouse embryonic fibroblast


title: RMB4203

value: Bupropion


title: RMB4202


title: CUT&TAG_SALL4_SALL4-delN12 Day6


title: CUT&TAG_SALL4_SALL4-WT Day6


title: RMB4201


title: CUT&TAG_H3K27ac_SALL4-delN12 Day6


title: RMB4199


title: RMB4198


title: RMB4200


title: ATAC-seq_Day11 SALL4-WT

data_processing:
ATAC-seq was performed according to the previous study (Buenrostro et al., 2013, Buenrostro et al., 2015a). Briefly, a total of 50,000 cells were collected and incubated with 50 μL lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630) for 10 min on ice. The suspension of nuclei was centrifuged for 5 min at 500g at 4 °C, then resuspended in 50 μl transposition reaction mix (10 μl 5× TTBL, 5 μl TTE Mix V50 and 35 μl nuclease-free H2O) from the TruePrep DNA Library Prep Kit V2 for Illumina (TD501-TD503, Vazyme), and incubated at 37 °C for 30 min. DNA fragments were then PCR amplified and purified with a Qiaquick PCR (QIAGEN) column. Library concentration was detected by a VAHTS Human Genomic DNA Quantification and QC Kit (NQ201, Vazyme) according to the manufacturer’s protocol. Finally, libraries were indexed using TruePrep Index Kit V2 for Illumina (Vazyme, TD202), and sequencing was performed on Illumina Novaseq PE150 platform.
The ATAC-seq reads were trimmed by Trim Galore (v0.6.4) and then mapped to the mm10 reference genome using bowtie2 (v2.4.5), and SAMtools (v1.16.1) was used to remove the repetitive, low sequencing quality (mapq<30) and the mitochondrial DNA mapped reads in the total mapped reads. In order to make the data comparable between different sequencing depths, the signals were normalized to one million reads for each sample, and the value were further compressed into a binary format (bigWig) for downstream analysis and data visualization. Peak calling was performed using MACS (v1.4.2) with parameters as follows: -g mm --keep-dup all --nomodel --shiftsize 25.
Assembly: mm10
Supplementary files format and content: BigWig, Peaks bed

extract_protocol:
DNA was harvested using TruePrep DNA Library Prep Kit V2 for Illumina kit (TD501-TD503, Vazyme),100000 cells per sample was used for sequencing libraries construction
Liarbries were constructed by TruePrep DNA Library Prep Kit V2 for Illumina (TD501-TD503, Vazyme)

value: Mouse embryonic fibroblast


title: mOBOCPEV


title: ATAC-seq_Day9 SALL4-delN12


title: RMB4197


title: ATAC-seq_Day9 SALL4-WT


title: ATAC-seq_Day11 SALL4-delN12


title: RMB4195


title: RMB4193

value: LConly


title: RMB4194

value: mPOA


title: ATAC-seq_Day1 SALL4-delN12


title: RMB4196


title: ATAC-seq_Day1 SALL4-WT


title: ATAC-seq_Day5 SALL4-delN12


title: RMB4192

value: ILC


title: ATAC-seq_Day5 SALL4-WT


title: Day7 of JGESO reprogramming without BMP4 treatment

data_processing:
The RNA-seq reads were trimmed using Trim Galore (v0.6.4)and then mapped to the mm10 reference genome with HISAT2 (v2.2.1), and StringTie (v2.2.1) was used to quantify the transcription level of each gene in each sample into FPKM (Fragments per kilobase of exon model per million mapped reads).
GFOLD (v1.1.4) was used to perform differential expression analysis between conditions. The differentially expressed genes were identified with gfold value > 0.5.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

source_name: reprogramming cells from E13.5 mouse embryonic fibroblast

growth_protocol: BMP4- group cells were cultured in iCD3 medium with TV,Vitamin C,mLIF, bFGF,CHIR99021, SGC0946, LSD1-HCL and Y27632 after transfected by JGES virus for 2 days, BMP4+ group cells were cultured by the same way plus BMP4; WT_SALL4 and delN12_SALL4 groups were also cultured in iCD3. Cells are collected after 0.25% trypsin-EDTA digestion.

extract_protocol:
Total RNAs were extracted by FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, RC112-01)
In brief, 1 μg total RNAs were used, library strategy are followed by mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, NR611), library DNA was purified by VAHTS DNA Clean Beads (VAHTS, #NR411). High- throughput sequencing was performed using Illumina HiSeq Xten (Illumina) platform with PE150.

treatment_protocol: BMP4+ group cells were treated with BMP4(10 ng/ml) for 7 days, BMP4- group were not treated by BMP4, so as WT_SALL4 and delN12_SALL4 groups


title: Day7 of JGESO reprogramming with BMP4 treatment

value: reprogramming cells from E13.5 mouse embryonic fibroblast


title: Patient 7 HCC 14

city: Toronto

first: Mamatha

last: Bhat

address: 101 college street

country: Canada

institute: University Health Network

data_processing: To account for background noise and sample variation across multiple runs on the nCounter platform, raw gene expression count data was normalized in NanoString nSolver 4.0 using six positive controls and eight negative controls. A manual calculation of the background threshold was carried out by taking the Mean of negative controls ± 2 standard deviations of negative control probes to exclude lowly expressed targets before conducting gene expression analysis. The nSolver 4.0 software integrated housekeeping gene probes and facilitated data normalization through the GeNorm Algorithm.

label: NanoString

source_name: Recurrent HCC

extract_protocol: Five μm thick scrolls were sectioned from formalin-fixed, paraffin-embedded (FFPE) tumor tissue blocks. Total RNA was extracted using the RNeasy FFPE Kit (QIAGEN) according to the manufacturer’s protocol, using xylene for deparaffinization. The Nanostring nCounter tumor signaling 360 panel was utilized for gene expression analysis, and data was acquired with Nanostring's Digital Analyser (FOV, 555).

value: liver


title: Day7 of JGEO reprogramming with BMP4 treatment


title: Day7 of JGE reprogramming with BMP4 treatment


title: RMB4190


title: Patient 6 HCC 12


title: Patient 6 HCC 11

source_name: Primary HCC


title: Day7 of JGE reprogramming without BMP4 treatment

source_name: reprogramming cells from E13.5 mouse embryonic fibroblas


title: RMB4189

value: BLA


title: RMB4188


title: MEFs treated with IL-17-2

city: cleveland

first: Lingzi

last: Hong

state: oh

address: 10900 Euclid Avenue

department: biochemistry

institute: Case western reserve university

data_processing:
RNA-seq reads were aligned against the mm10 using STAR(2.7.0e).
The number of reads mapped to mouse genome mm10 was counted using RSEM(1.3.3).
Differential gene expression was determined using the R-package DEseq2
Assembly: mm10
Supplementary files format and content: csv file containing normalized count reads and adjusted p-values

source_name: flag-Act1KO/WT MEF cells

growth_protocol: Act1-/- Mouse Embryonic Fibroblasts transfected with flag-tagged Act1 wild-type (flag-Act1KO/WT) MEFs were maintained and propogated in DMEM supplemented with 10%FBS  and antiboitics at 37 °C under a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol according to the manufacturer’s instructions followed by isopropanol precipitation. Total RNAs were further purified using Qiagen's miRNeasy micro kit (217084, Qiagen) plus Qiagen’s DNase set (79254, Qiagen) for on-column DNase digestion option.
Sequencing library preparation and RNA-seq were conducted by Novogene. mRNA was purified using PolyA+ selection.

treatment_protocol: flag-Act1KO/WT MEF cells were untreated or treated with IL-17A (50ng/mL) for 1h

value: flag-Act1KO/WT MEF cells

value: Mouse Embryonic Fibroblasts

value: WT

value: IL-17 stimulated


title: ATAC-seq_MEF


title: WT

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

data_processing:
The pre-processing steps such as generation and demultiplexing of FASTQ files from raw sequencing reads (bclfastq, v2.20), aligning to UCSC mm10 transcriptome, and generating raw count matrices were conducted using Cell Ranger (v6.0.1) with default parameters. Cumulus software v1.5.0 was used to combine expression matrices and to remove cell doublets by Scrublet v0.2.1. The pipelines were run in Terra Cloud Platform (https://app.terra.bio/).  Seurat v3.2.2 was used to perform downstream analysis following the standard pipeline using cells with >=500 genes, resulting in 4,135 WT mouse cells, 3,979 vehicle treated RPE65 cells, and 5,901 TMB treated RPE65 cells. Principal Component (PC) analysis was performed on a submatrix of the top 1,000 most variable genes computed using the function FindVariableGenes in Seurat. Batch effect between experimental conditions was minimzed using the Harmony package v0.1.0 to remove non-cell-type-specific factors that may impact clustering. The number of top PCs was assessed by the elbow method. Cells were clustered using a shared nearest neighbor modularity optimization-based algorithm (FindClusters in Seurat).
Assembly: mm10
Supplementary files format and content: ExpressionMatrix.mtx.gz: Expression Matrix is sparse format.
Supplementary files format and content: MetaData.csv.gz: Metadata related to columns (cells) of the Expression Matrix.
Supplementary files format and content: Genes.txt.gz: Gene symbols related to rows of the Expression Matrix.
Supplementary files format and content: CellIDs.txt.gz: Cellular barcodes in the Expression Matrix.

source_name: retina

growth_protocol: All mice were housed under a standard 12-hour light (≤150 lux)/12-hour dark cycle, fed ad libitum, and maintained using standard procedures.

extract_protocol:
Eyes were enucleated for retinal tissue isolation. After removing the anterior chamber and lens, the retina was dissected from the posterior eye cup. Then, the retinal cells were dissociated using the Papain Dissociation System (#LK003153, Worthington Biochemical) following the manufacturer's instructions.
Sublibraries were generated and sequenced independently on Illumina NovaSeq6000 at an average sequencing depth of 50,000 reads/cell, for a projected total of 5 billion reads for the entirety of the 100,000 cell barcoded library. Reads from identical cells from each of the sublibraries were consolidated during analysis and processing of raw reads.

treatment_protocol: Dietary vehicle (normal pellets) or TMB treatment was started at P21-P24.

value: retina

tag: time

value: 2 months

value: Standard pellet


title: Patient 5 HCC 9


title: Rpe65-KO vehicle


title: Patient 5 HCC 10


title: MEFs treated with IL-17-1


title: RMB4187

value: Raphe

value: brain