title: MDA-MB-231 siPCMT1_3

data_processing:
Raw reads with more than 2-N bases were initially discarded. Then adaptors and low-quality bases were trimmed off raw sequencing reads using a FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also discarded.
Following that, clean reads were aligned to the GRCh38 genome by HISAT2 (Kim, Langmead et al. 2015) allowing 4 mismatches. Uniquely mapped reads were used to calculate gene reads number and fragments per kilobase of transcript per million fragments mapped (FPKM) (Trapnell, Williams et al. 2010).
The R Bioconductor package DESeq2 (Love, Huber et al. 2014) was used to screen the DEGs. The corrected p-value < 0.05 and fold change (FC) >2 or < 0.5 were set as the cut-off criteria to identify DEGs.
The ABLas pipeline was used to define and quantify the ASEs and regulated alternative splicing events (RASEs) between the samples as previously described (Jin, Li et al. 2017, Xia, Chen et al. 2017). Briefly, based on the splice junction reads, ABLas detected 9 types of ASEs, comprising exon skipping (ES), alternative 5' splice site (A5SS), alternative 3'splice site (A3SS), mutually exclusive exons (MXE), mutually exclusive 5'UTRs (5pMXE), mutually exclusive 3'UTRs (3pMXE), cassette exon, A3SS&ES, and A5SS&ES.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: MDA-MB-231 cells

extract_protocol:
Total RNAs were treated with RQ1 DNase (Promega, Madison, WI. ) to remove DNAs. The quality and quantity of the purified RNAs were determined by measuring the absorbance at 260nm/280nm (A260/A280) using SmartSpec Plus (BioRad, Hercules, CA. ). RNA integrity was further confirmed using 1.5% agarose gel electrophoresis.
For each sample, 1 μg of total RNA was used for RNA-seq library preparation. mRNAs were captured by VAHTS mRNA capture Beads (Vazyme, N401). The purified RNAs was treated with RQ1 DNase (Promega, Madison, WI.) to remove DNAs before being used for directional RNA-seq library preparation by VAHTS Universal V8 RNA-seq Library Prep Kit on Illumina (NR605). Polyadenylated mRNAs were purified and fragmented. Fragmented mRNAs were converted into double-strand cDNAs. Following end repair and A tailing, the DNAs were ligated to Adaptor (N323). After purifying the ligation product and fractioning the size to 300-500bps, the ligated products were amplified, purified, quantified, and stored at -80℃ for subsequent sequencing. The strand marked with dUTP (the 2nd cDNA strand) is not amplified, allowing strand-specific sequencing.For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina NovaSeq 6000 system for 150 nt paired-end sequencing.

value: MDA-MB-231 cells

value: PCMT1 knockdown in MDA-MB-231 cell


title: STR3_Propranolol_Control_dHC_Rep_8

status: Public on Oct 05 2023

type: SRA

city: Zürich

first: Lukas

middle: Matthias

last: von Ziegler

address: Winterthurerstrasse 190

department: D-HESZ

country: Switzerland

institute: ETH Zürich

library_source: transcriptomic

data_processing:
Pseudoalignment using kallisto (version 0.44.0) on the GENCODE M17 transcriptome
Aggregation on the protein coding level
Assembly: GRCm38
Supplementary files format and content: .tar.gz zipped directories with kallisto output (pseudoaligned read counts and tpm measures of trancripts) containing .h5 and .tsv files

molecule: total RNA

organism: Mus musculus

source_name: brain

extract_protocol:
Trizol
illumina TrueSeq

tag: strain

tag: tissue

value: brain

tag: brainregion

value: hippocampus

tag: group

tag: subregion

value: dHC

tag: Sex

value: female

tag: injection

value: Propranolol

tag: treatment

value: Control

tag: animalid

tag: replicate


title: Periferal blood father [PL1400_Father]

type: genomic

city: Maastricht

first: Rick

last: Essers

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Centre (MUMC+)

hyb_protocol: According to the manual of Infinium II Assay (Illumina, USA).

scan_protocol: The scanning of the bead-chips was performed on an iScan, using the iScan Control software (Illumina, USA)

data_processing:
The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. We subsequently fed these data into haplarithmisis (Zamani Esteki et al. 2019, Nature medicine).
Image data was analyzed using Genomestudio with genotyping module (Illumina). Subsequently, genotype calls (AA,AB,BB,or NC (no call), SNP B-allele frequency values, LogR.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Periferal blood

label_protocol: The samples were not labelled before the hybridization. The staining is based on post-hybridization Cy5/Cy3 labelling by extension, according to the manual of Infinium II Assay (Illumina, USA).

growth_protocol: The tissues were chopped with scissors to small fragments, and long-term cultures were set up in 25 cm2 flasks with 5 mL of DMEM/F12 (1:1) medium (Gibco) supplemented with 20% fetal bovine serum (HyClone), 1% MEM NEAA solution (Gibco), 1% Pen-Strep (Gibco). Tissues were incubated at 37°C with once-weekly medium renewal.

extract_protocol: Genomic DNA was extracted using a standard phenol-chloroform extraction method that allows for the isolation of up to 900 ng DNA from the tissues. Likewise, genomic DNA was extracted from peripheral blood of parents using the standard phenol-chloroform method.

treatment_protocol: The two tissues were mechanically separated and the yield of chorionic cytotrophoblast cells was increased by maceration of chorionic villi under an Axiovert 200 inverted microscope (Carl Zeiss, Germany) and treatment with 70% acetic acid for 3-5 min followed by three washes of the obtained cell suspension with PBS according to a modified protocol (Simoni, G. et al. Efficient direct chromosome analyses and enzyme determinations from chorionic villi samples in the first trimester of pregnancy. Human Genetics 63, 349-357 (1983)).

tag: gender

value: Male

tag: family member

value: Father

value: Periferal blood


title: STR3_Saline_Control_dHC_Rep_8

value: Saline


title: MDA-MB-231 siPCMT1_2

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

description:
expressed_gene_FPKM.txt
expressed_gene_reads.txt

tag: cell line

tag: cell type


title: 2208_CP-4047

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

country: USA

institute: University of North Carolina at Chapel Hill

data_processing:
STAR aligner algorithm was used to aligned the fastq files to the mouse mm10 reference genome.
Resulting BAM files were sorted and indexed using Samtools. Quality control was completed using Picard.
Salmon was used to determine the transcript read counts
The resulting data was upper quantile normalized
Upper quantile normalized data was log2 transformed
Assembly: mm10
Supplementary files format and content: Tab-delimited text file of gene expression matrix (82 samples, genes as rows)
Supplementary files format and content: Tab-delimited text file of gene expression matrix (82 samples, upper quantile normalized, genes as rows)

source_name: Mammary Tumor

extract_protocol:
Cryopreserved tumors were homogenized using a tissue homogenizer. The RNeasy Mini Kit (#74104, Qiagen) was used to iolate the RNA according to the manufacturer's protocol
The Agilent Bioanalyzer was used to asses the mRNA quality and libraries for mRNA-seq were constructed using total RNA and the Illumina TruSeq mRNA sample preparation kit

value: Mammary Tumor

value: BALB/c


title: Extraembryonic mesoderm fetal biopsy [PL1400_EM3041]

source_name: Extraembryonic mesoderm

value: Product of conception

value: Extraembryonic mesoderm


title: STR3_Propranolol_Stress_dHC_Rep_8

value: Stress


title: MDA-MB-231 siPCMT1_1

value: MDA-MB-231 cells


title: STR3_Saline_Stress_dHC_Rep_8


title: Chorionic villi fetal biopsy [PL1400_CV3041]

source_name: Chorionic villi

value: Chorionic villi


title: MDA-MB-231 NC_3

value: MDA-MB-231 cell (control plasmid)


title: H9C2_Ctrl_2

data_processing:
Adaptors and low-quality bases were sheared using FASTX-Toolkit (Version 0.0.13) and reads less than 16 nt were filtered after discarding more than 2-N bases from raw sequencing reads.
Cleaned reads were mapped to the mRatBN7.2 genome with four mismatches using HISAT2. Reads with unique mapping were utilized to calculate fragments per kilobase of transcript per million fragments mapped (FPKM) value for each gene.
The R Bioconductor package DESeq2 (Love, Huber et al. 2014) was utilized to screen   out the differentially expressed genes (DEGs). The P value <0.05 and fold change>1.5 or   < 2/3 were set as the cut-off criteria for identifying DEGs.
Assembly: mRatBN7.2 genome
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus

extract_protocol:
Total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using Nanodrop One (Thermo). RNA integrity was further verified by 1.5% agarose gel electrophoresis.  For each sample, 1 μg of total RNA was used for RNA-seq library preparation by KAPA Stranded mRNA-Seq Kit for Illumina® Platforms (#KK8544). Polyadenylated mRNAs were purified by VAHTS mRNA capture Beads (N401-01) and Fragmented. Fragmented mRNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to Diluted Roche Adaptor (KK8726). After purification of ligation product and size fractioning to 300-500bps , the ligated products were amplified and purified, quantified and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) is not amplified, allowing strand-specific sequencing.
For high-throughput sequencing, the libraries were applied to Illumina Novaseq 6000 system for 150 nt paired-end sequencing.

tag: genotype

value: control plasmid


title: H9C2_Ctrl_1


title: 2NNK-EGFP in-vitro ligation library 1st

city: Tianjin

first: Shuai

last: Li

state: Tianjin

address: Huanhuxi Road

institute: Tianjin Tumor Hospital

description: Library: 2NNK EGFP-chromophore-randomized library (65-66); FACS Rounds: first (1st); Strategy: piggyBac-in-vitro ligation

library_source: other

data_processing:
PE reads were assigned to samples based on barcodes.
Reads were filtered by QIIME quality filters.
Clean reads were merged by FLASH software.
Assembly: NA
Supplementary files format and content: fasta files, containing nucleotide sequence of the library, were generated for each sample.

molecule: other

growth_protocol: HEK293T cells were maintained in DMEM (CORNING) supplemented with 10% FBS (CORNING) and 1% penicillin-streptomycin solution (CORNING) at 37℃ with 5% CO2.

extract_protocol:
The positive cell genome was extracted after flow sorting.Genomic DNAs were extracted with a TaKaRa MiniBEST Universal Genomic DNA Extraction Kit Ver. 5.0 (TaKaRa).  High-fidelity KOD-Plus-Neo DNA polymerase was used to amplify the sequences containing the degenerate codons.
PCR products were subjected to sequencing library construction by using TruSeq® DNA PCR-Free Sample Preparation Kit (Illumina).

treatment_protocol: For the transfection of piggyBac-in-vitro ligation library, HEK293T cells were plated in 6-well plates the day before transfection, and reached a 70~80% confluency on the day of transfection. piggyBac-in-vitro ligation library dsDNAs (1 μg/well) were co-transfected with hyperactive piggyBac transposase expression vector (1 μg/well) into HEK293T cells using Lipofectamine 2000. For the transfection of piggyBac-in-vitro ligation-PCR library, HEK293T cells were plated in 10-cm dishes the day before transfection, and reached a 70~80% confluency on the day of transfection. Library dsDNAs (6 μg/dish) and hyperactive piggyBac transposase expression vector (6 μg/dish) were co-transfected into HEK293T cells using Lipofectamine 2000. Forty-eight hours after transfection, a 10-day selection with puromycin was performed.For the identification of novel transcriptional activator peptide, HEK293T cells were plated in 10-cm dishes the day before transfection, and reached a 70-80% confluency on the day of transfection. Library dsDNAs with the promoter-GAL4-XTEN-<NNK>12-PAS expression cassette (6 μg/dish) and hyperactive piggyBac transposase expression vector (6 μg/dish) were co-transfected into HEK293T cells using Lipofectamine 2000. Forty-eight hours after transfection, a 5-day selection with puromycin was performed. The obtained cells with successful genomic integration were re-seeded into eight 10-cm dishes and transfected with pG5egfp vector (6 μg/dish). Forty-eight hours after transfection, cells were harvested for the following FACS sorting.

value: Human embryonic kidney


title: Periferal blood mother [PL140_Mother]

value: Female

value: Mother


title: STR3_Saline_Stress_dHC_Rep_7

value: brain

value: hippocampus

value: dHC

value: male


title: MDA-MB-231 NC_2


title: 2208_CP-2630


title: Periferal blood father [PL140_Father]

value: Male

value: Father

value: Periferal blood


title: STR3_Propranolol_Stress_dHC_Rep_7

value: Propranolol


title: MDA-MB-231 NC_1


title: 2208_CP-2629

value: Mammary Tumor

value: BALB/c


title: Extraembryonic mesoderm fetal biopsy [PL140_EM981]

value: Product of conception

value: Extraembryonic mesoderm


title: 2208_CP-2032


title: STR3_Propranolol_Control_dHC_Rep_7

value: Control


title: M16-sh-3 [M16_sh2-Input_L2]

city: Shanghai

first: Yuan

last: Zhang

address: 650 Xinsongjiang Road

department: Department of Gastrointestinal Surgery

institute: Shanghai General Hospital

data_processing:
library strategy: MeRIP-seq
Base calling software: BCL convert
Data filter: fastp(0.19.4)，remove adapters, repeat sequences and low quality sequences
reads alignment : HISAT2(2.0.4)
Peak calling diffpeak : R package: exomePeak (1.5.0)
Peak annotation : ANNOVAR
Transcript assembly and quantification : StringTie (2.1.2)
Differential Expression Analysis :R package: edgeR(4.1)
Motif: HOMER(4.10)
Assembly: Homo_sapiens.GRCh38.Ensembl107
Supplementary files format and content: 1.Diffpeak
Supplementary files format and content: BVSA_diffPeak_result.xlsx
Supplementary files format and content: The results show which genes have different methylation modifications between groups, and contain important information such as the position of each peak on the chromosome, annotation, and the degree of methylation modification of the gene.
Supplementary files format and content: 2.Gene_differential_expression
Supplementary files format and content: B_inputVSA_input_Gene_differential_expression.xlsx
Supplementary files format and content: From this result, it can be known which genes have changed their transcription levels in the assembly.
Supplementary files format and content: 3. Expression profile files
Supplementary files format and content: 4_genes_fpkm_expression.xlsx
Supplementary files format and content: The expression of each gene in each sample was displayed, and the quantitative method was FPKM
Supplementary files format and content: 4. Joint analysis of results
Supplementary files format and content: BVSA_diffPeak_Gene_differential_expression.xlsx
Supplementary files format and content: It shows which genes have differences in transcription level and methylation modification level.

source_name: AGS

growth_protocol: AGS cells were maintained in RAPI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
10ug shNC and shMETTL16 plasmids, 25ul Lipofectamine 2000 were co-transfected into AGS cells and were cultured for another 2 days. Then the total RNAs were extracted using Trizol.
Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: AGS cells were cultured and transfected with shNC and shMETTL16 plasmids using Lipofectamine 2000 at different time.

value: AGS

value: gastric cancer

value: METTL16 knockdown


title: Periferal blood mother [PL1397_Mother]

value: Female

value: Mother


title: M16-sh-3 [M16_sh2-Input_L1]


title: 2208_CP-4046


title: 2208_CP-2031


title: STR3_Saline_Control_dHC_Rep_7

value: brain

value: hippocampus

value: Saline


title: Periferal blood father [PL1397_Father]

value: Male


title: 2208_CP-2631


title: M16-NC-3 [M16_ctrl-IP]

value: negative control


title: STR3_Propranolol_Stress_dHC_Rep_6

value: dHC

value: male

value: Stress


title: Extraembryonic mesoderm fetal biopsy [PL1397_EM3227]


title: 2208_CP-2027

value: Mammary Tumor

value: BALB/c


title: Chorionic villi fetal biopsy [PL140_CV981]

value: Product of conception

value: Chorionic villi


title: M16-NC-3 [M16_ctrl-Input]

value: AGS


title: 2208_CP-2028


title: STR3_Saline_Control_dHC_Rep_6

value: female

value: Control


title: M16-sh-3 [M16_sh2-IP]

value: gastric cancer

value: METTL16 knockdown


title: 2208_CP-1976


title: STR3_Saline_Stress_dHC_Rep_6

value: brain


title: STR3_Propranolol_Control_dHC_Rep_6

value: hippocampus

value: Propranolol


title: M16-sh-2 [B_2_IP]


title: 2153_CP-4075


title: STR3_Saline_Stress_dHC_Rep_5

value: Saline


title: Periferal blood mother [PL1373_Mother]

value: Female

value: Mother

value: Periferal blood


title: M16-sh-2 [B_2_input]


title: 2153_CP-4074


title: Periferal blood father [PL1373_Father]

value: Male

value: Father


title: STR3_Propranolol_Control_dHC_Rep_5

value: dHC


title: M16-sh-1 [B_1_IP]


title: 2153_CP-4073

value: Mammary Tumor

value: BALB/c


title: STR3_Saline_Control_dHC_Rep_5

value: male


title: Extraembryonic mesoderm fetal biopsy [PL1373_EM3190]

value: Product of conception

value: Extraembryonic mesoderm


title: M16-sh-1 [B_1_input]

value: AGS

value: gastric cancer


title: 2153_CP-2613


title: STR3_Propranolol_Stress_dHC_Rep_5

value: brain

value: female

value: Stress


title: Chorionic villi fetal biopsy [PL1373_CV3190]

value: Chorionic villi


title: Chorionic villi fetal biopsy [PL1397_CV3227]


title: M16-NC-2 [A_2_IP]

value: negative control


title: STR3_Saline_Control_dHC_Rep_4

value: hippocampus

value: Saline

value: Control


title: Periferal blood mother [PL137_Mother]

value: Female

value: Mother

value: Periferal blood


title: Periferal blood father [PL137_Father]

value: Male

value: Father


title: 2153_CP-2612

value: Mammary Tumor

value: BALB/c


title: M16-NC-1 [A_1_IP]

value: AGS


title: STR3_Saline_Stress_dHC_Rep_4

value: dHC


title: M16-NC-2 [A_2_input]

value: gastric cancer


title: M16-NC-1 [A_1_input]


title: Chorionic villi fetal biopsy [PL137_CV944]

value: Product of conception


title: 2153_CP-2611


title: 2153_CP-1977


title: STR3_Saline_Control_dHC_Rep_3

value: brain

value: female


title: Extraembryonic mesoderm fetal biopsy [PL137_EM944]

value: Extraembryonic mesoderm


title: astrocyte, sorting, rep3

first: Dong-Dong

state: Shanghai

address: 130 Dong'an Road

institute: Fudan University

data_processing:
Ubuntu terminal environment in minutes with Windows Subsystem for Linux (WSL), v 20.04.4. Conda for managing and deploying applications, environments and packages in RNA-Seq, v 4.14.0.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim-galore, v 0.6.7  (parameter: --quality score 25, --cores 4, --phred 33, --length 35, --stringency 3).
Trimmed sequence reads were processed to Quality control using FastQC, v 0.11.9  and MultiQC, v 1.13.
Trimmed sequence reads were mapped to GrCM38 using Salmon index, and then were genetic quantified using Salmon quant, v 1.4.0.
Read count extraction and matrix were performed using tximport package in R, v 4.1.0.
Assembly: Grcm38
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: cerebral cortex

growth_protocol: The transgenic mice, including SMACreER:Ai14 and hGFAPCreER:Ai14, were bred, then for cell sorting.

extract_protocol:
RNA was harvested using RNeasy plus mini kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Ovation RNA-Seq system V2 and Ovation Ultralow system V2 (NuGEN) following manufacturer's protocols.

treatment_protocol: Using the Ai14 reporter mice, the tdtomato positive cells labeling aSMCs or astrocytes were acquired by fluorescence-activated cell sorting (FACS), then for RNA extraction.

value: cerebral cortex

value: astrocyte

value: sorting


title: STR3_Propranolol_Stress_dHC_Rep_4

value: hippocampus

value: Propranolol

value: Stress


title: astrocyte, sorting, rep2


title: Periferal blood mother [PL1362_Mother]

value: Female

value: Mother

value: Periferal blood


title: STR3_Propranolol_Control_dHC_Rep_4

value: male

value: Control


title: PER403 EPZ_96_1 [S18]

city: boston

first: Chris

middle: A

last: French

state: MA

address: 75 francis st.

department: Pathology

institute: BWH

data_processing:
Quality-controlled reads are aligned to the human genome (GRCh38/hg38) and to ERCC92 spike-in sequences using a splice-aware aligner (STAR89) with Ensembl. transcriptome annotations.
Differential expression (DE) analysis is performed using RUVSeq to identify unwanted variation followed by edgeR91 and/or DESeq2
Assembly: GRCh38/hg38
Supplementary files format and content: TDF files (IGV's compressed and indexed bedgraph format)
Supplementary files format and content: Excel files with raw and log2 normalized counts

growth_protocol: DMEM supplemented with either 10% FBS (10-15) or 20% BGS (PER-403).

extract_protocol:
RNA was harvested using RNAeasy (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries. ERCC92 spike-in RNA is added to normalize reads.
RNA libraries for RNA-seq were prepared using the Roche KAPA HyperPrep RNA RiboErase Kit following manufacturer's protocols.

value: NUT carcinoma cell line

tag: timepoint


title: PER403 EPZ_96_2 [S22]


title: Periferal blood father [PL1362_Father]

value: Male

value: Father


title: astrocyte, sorting, rep1


title: cortex, homogenate, rep6

value: cortical cell

value: WT

value: homogenate


title: PER403 DMSO_96_2 [S21]

source_name: PER403, 96h, DMSO

value: DMSO


title: Extraembryonic mesoderm fetal biopsy [PL1362_EM3160]

value: Product of conception

value: Extraembryonic mesoderm


title: STR3_Propranolol_Stress_dHC_Rep_3

value: brain

value: hippocampus

value: dHC


title: STR3_Propranolol_Control_dHC_Rep_3

value: female

value: Propranolol


title: Chorionic villi fetal biopsy [PL1362_CV3160]

value: Chorionic villi


title: PER403 DMSO_96_1 [S17]


title: PER403 ABBV075_EPZ_96_2 [S24]

value: 15.87nM ABBV075+1uM EPZ


title: Periferal blood mother [PL1359_Mother]

value: Female

value: Mother

value: Periferal blood


title: cortex, homogenate, rep5

value: cerebral cortex


title: cortex, homogenate, rep4

value: cortical cell


title: STR3_Propranolol_Stress_dHC_Rep_2

value: Stress


title: STR3_Propranolol_Control_dHC_Rep_2

value: Control


title: PER403 ABBV075_96_2 [S23]

value: NUT carcinoma cell line


title: cortex, homogenate, rep2

value: WT

value: homogenate


title: cortex, homogenate, rep3


title: Periferal blood father [PL1359_Father]

value: Male

value: Father


title: STR3_Propranolol_Stress_dHC_Rep_1

value: brain

value: hippocampus

value: dHC

value: male


title: Extraembryonic mesoderm fetal biopsy [PL1359_EM3031]

value: Product of conception

value: Extraembryonic mesoderm


title: PER403 ABBV075_96_1 [S19]


title: cortex, homogenate, rep1


title: Chorionic villi fetal biopsy [PL1359_CV3031]

value: Female

value: Chorionic villi


title: STR3_Saline_Control_dHC_Rep_2

value: female

value: Saline


title: Periferal blood mother [PL135_Mother]

value: Mother

value: Periferal blood


title: arteriolar smooth muscle cell, sorting, rep8

source_name: cerebral arteriole

value: cerebral arteriole

value: arteriolar smooth muscle cell

value: sorting


title: PER403 ABBV744_6_2 [S16]

value: NUT carcinoma cell line


title: STR3_Saline_Stress_dHC_Rep_3

value: Stress


title: STR3_Propranolol_Control_dHC_Rep_1

value: brain

value: Propranolol

value: Control


title: PER403 ABBV744_6_1 [S15]


title: Periferal blood father [PL135_Father]

value: Male

value: Father


title: STR3_Saline_Stress_dHC_Rep_2

value: hippocampus

value: dHC

value: male


title: PER403 ABBV075_EPZ_96_1 [S20]

value: 15.87nM ABBV075+1uM EPZ


title: Extraembryonic mesoderm fetal biopsy [PL135_EM977]

value: Female

value: Product of conception

value: Extraembryonic mesoderm


title: PER403 ABBV075_6_2 [S14]


title: STR3_Saline_Stress_dHC_Rep_1

value: female

value: Saline


title: Chorionic villi fetal biopsy [PL135_CV977]

value: Chorionic villi


title: PER403 ABBV075_6_1 [S13]

value: NUT carcinoma cell line


title: MO5 tumor GFP+ replicate 4

city: Paris

first: Lucie

last: Peduto

address: 25 rue du Docteur Roux

country: France

institute: Institut Pasteur

data_processing:
reads were trimmed from adapters using cutadapt 3.4
reads were mapped to the genome assembly GRCm38 from Ensembl using STAR 2.7.3a
Genes were counted using FeatureCounts 2.0.1
Differential expression testing was conducted using DESeq2 library 1.22.2.The normalization and dispersion estimation were performed with DESeq2 using the default parameters; statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between conditions. Raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Assembly: mm10 (GRCm38) from Ensembl
Supplementary files format and content: tab-delimited text files from DESeq2 include raw and norm values for each Sample

source_name: MO5 tumor

extract_protocol:
Cells were isolated by FACS from MO5 tumros and collected in lysis buffer + 1% ß-mercaptoethanol.
Librairies were prepared from total mRNA using the SMARTer® Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (Takara Bio) and sequenced using Illumina NextSeq 500/550 High Output kit v2.5.

value: MO5 tumor

value: PDGFR{alpha}+ Pdpn+ stromal cells

value: GFP+


title: Periferal blood mother [PL129_Mother]

value: Mother

value: Periferal blood


title: MO5 tumor GFP- replicate 4

value: GFP-


title: MO5 tumor GFP- replicate 3


title: 10-15 EPZ_96_1 [S6]


title: 10-15 DMSO_96_2 [S9]

value: DMSO


title: Periferal blood father [PL129_Father]

value: Male

value: Father


title: MO5 tumor GFP+ replicate 3


title: Chorionic villi fetal biopsy [PL129_CV940]


title: MO5 tumor GFP- replicate 2


title: 10-15 DMSO_96_1 [S5]


title: arteriolar smooth muscle cell, sorting, rep7

value: cerebral arteriole

value: arteriolar smooth muscle cell

value: sorting


title: MO5 tumor GFP+ replicate 1


title: Extraembryonic mesoderm fetal biopsy [PL129_EM940]

value: Product of conception

value: Extraembryonic mesoderm


title: Periferal blood mother [PL1246_Mother]

value: Female


title: 10-15 ABBV075_EPZ_96_2 [S12]

value: 0.702nM ABBV075+1uM EPZ


title: macrophages, ML792-2

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the mouse genome mm10 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: bone marrow

extract_protocol:
n/a
RNA was extracted using the miRNeasy Micro Kit (Qiagen, Valencia, CA).
RNA sequencing libraries were prepared with Kapa mRNA HyperPrep kit (Kapa Biosystems, Cat KR1352) according to the manufacturer's protocol. The final libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit.
RNA-seq was performed on Illumina NovaSeq6000 with S4 Reagent kit v1.5 (Illumina, Cat 20028313) at Tgen with the sequencing length of 2x101. Real-time analysis (RTA) 3.4.4 software was used to process the image analysis.

value: bone marrow

value: macrophage


title: 10-15 ABBV075_EPZ_96_1 [S8]

value: NUT carcinoma cell line


title: MO5 tumor GFP+ replicate 2

value: MO5 tumor

value: PDGFR{alpha}+ Pdpn+ stromal cells

value: GFP+


title: MO5 tumor GFP- replicate 1

value: GFP-


title: macrophages, ML792-1


title: Periferal blood father [PL1246_Father]

value: Periferal blood


title: STR3_Saline_Control_dHC_Rep_1

value: brain

value: hippocampus

value: dHC

value: male

value: Saline

value: Control


title: 10-15 EPZ_96_2 [S10]


title: Extraembryonic mesoderm fetal biopsy [PL1246_EM3088]

value: Product of conception

value: Extraembryonic mesoderm


title: macrophages, WT-2

value: Vehicle


title: 10-15 ABBV075_96_2 [S11]


title: MO5 tumors DTR+ replicate 3

data_processing:
reads were trimmed from adapters using cutadapt 3.4
reads were mapped to the genome assembly GRCm38 from Ensembl using STAR 2.7.3a
Genes were counted using FeatureCounts 2.0.1
Differential expression testing was conducted using DESeq2 library 1.22.2.The normalization and dispersion estimation were performed with DESeq2 using the default parameters; statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between conditions. Raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Assembly: mm10 (GRCm38) from Ensembl
Supplementary files format and content: tab-delimited text file from DESeq2 include raw and norm values for each Sample

source_name: MO5 tumors

extract_protocol:
Cells were isolated by FACS from MO5 tumors and collected in lysis buffer + 1% ß-mercaptoethanol.
Librairies were prepared from total mRNA using the SMARTer® Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (Takara Bio) and sequenced using Illumina NextSeq 500/550 High Output kit v2.5.

value: MO5 tumors

value: DTR+

value: + Diphteria toxin


title: macrophages, WT-1

value: bone marrow

value: macrophage


title: Chorionic villi fetal biopsy [PL1246_CV3088]

value: Female

value: Chorionic villi


title: 10-15 ABBV744_6_2 [S4]

value: NUT carcinoma cell line


title: 10-15 ABBV075_96_1 [S7]


title: Periferal blood mother [PL1063_Mother]

value: Mother

value: Periferal blood


title: JAK2V617F/V617F - Hmga1+/- Rep2

city: BALTIMORE

first: Linda

last: Resar

state: Maryland

address: 720 Rutland Avenue

department: Department of Medicine / Division of Hematology

institute: Johns Hopkins University

data_processing:
Reads were aligned, filtered, de-duplicated, and converted into a digital count matrix using Cell Ranger 1.2 (10X Genomics).
Additional quality control (QC) was performed by visual inspection of QC plots using Seurat.
Count matrix files from Cellranger alignments/counting of cells from male and female animals with JAK2V617F/V617F and  JAK2V617F/V617F-Hmga1+/-, were imported into Seurat.
Cells with <700 or >7000 detectable genes were removed as outliers, as were genes found in fewer than 50 cells. Individual samples were combined into a single object using the ‘merge’ function in Seurat with default parameters.
Counts for individual cells were scaled and logged using the ‘NormalizeData’ function with default parameters, followed by ‘FindVariableFeatures’ with loess correction to stabilize variables and identify the 3000 most variable features for input into clustering and dimension reduction algorithms. Finally, the ‘ScaleData’ function was used with default parameters to scale count levels of individual features.  Single cells were clustered over the top 20 components of a PCA, using ‘FindNeighbors’ function followed by ‘FindClusters’ with resolution set to 0.5.
Genome_build: mm10
Supplementary_files_format_and_content: a .h5 file containing cellranger filtered cell barcodes and gene expression counts

source_name: LSK cell from bone marrow

extract_protocol: Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (Dual Index) and Chromium instrument (10X Genomics) were used following the manufacturer’s protocol.

value: LSK cells


title: MO5 tumors DTR+ replicate 2

value: PDGFR{alpha}+ Pdpn+ stromal cells


title: MO5 tumors DTR- replicate 3

value: DTR-


title: Extraembryonic mesoderm fetal biopsy [PL1063_EM2009]

value: Male


title: MO5 tumors DTR- replicate 2


title: MO5 tumors DTR- replicate 1


title: 10-15 ABBV075_6_2 [S2]


title: MO5 tumors DTR+ replicate 1


title: 10-15 ABBV075_6_1 [S1]


title: JAK2V617F/V617F Rep1


title: Hair matrix cells, cultured, biol rep 3 [MA_3 RNA-seq]

status: Public on Oct 04 2023

city: lanzhou

first: zhang

last: xiaolan

address: Lanzhou Institute of Husbandry and Pharmaceutical Sciences

institute: Chinese Academy of Agricultural Sciences

data_processing:
Trimmomatic, 0.36
hisat2, 2.2.1.0, --rna-strandness rf --fr
DESeq, 1.20.0, qvalue<0.05, |log2FoldChange|>1
Assembly: Bosgru_v3.0
Supplementary files format and content: FPKM values  for each sample

organism: Bos grunniens

source_name: skin

growth_protocol: DPCs and HMCs were cultured in DMEM/F12 medium supplemented with 1% penicillin-streptomycin, 10 ng/mL IGF1, 20 ng/mL EGF , and 10% FBS in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA of DPCs and HMCs were extracted using Trizol reagent.
For mRNA sequencing, six libraries from DPCs (n=3) and HMCs (n=3) were constructed using TruSeq Stranded mRNA LT Sample Prep Kit. For miRNA sequencing, a total amount of 1 µg RNA per sample was used for the small RNA library construction using TruSeq Small RNA Sample Prep Kits.

value: skin

value: Hair matrix cells

value: epidermal cell

value: WT

value: isolated and cultured


title: Hair matrix cells, cultured, biol rep 2 [MA_2 RNA-seq]


title: Dermal papilla cells, cultured, biol rep 3 [DP3 RNA-seq]

value: Dermal papilla cells

value: dermal cell


title: Hair matrix cells, cultured, biol rep 1 [MA_1 RNA-seq]


title: Dermal papilla cells, cultured, biol rep 1 [DP1 RNA-seq]


title: Dermal papilla cells, cultured, biol rep 2 [DP2 RNA-seq]


title: 10-15 ABBV744_6_1 [S3]


title: Periferal blood father [PL1063_Father]

value: Father


title: JAK2V617F/V617F Rep2


title: JAK2V617F/V617F - Hmga1+/- Rep1


title: Chorionic villi fetal biopsy [PL1063_CV2009]

value: Product of conception


title: pup (D28) kidney, maternal protein restriction sample for biological rep5

type: RNA

city: Tokyo

first: Xuguang

address: 1-1-1 Yayoi, Bunkyo-ku

country: Japan

institute: Tokyo University

description: Gene expression data from the kidneys of pups exposed to a low-protein diet throughout their fetal life

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Rat Genom 230 2.0 Array. GeneChips were washed and stained in the Gene Chip Fluidics Station 400 (Affymetrix).

scan_protocol: After washing and staining, the arrays were scanned using an Affymetrix GeneChip Scanner 3000 (Affymetrix).

data_processing: The obtained intensity files were analyzed using the statistical analysis software R. For intergroup comparison, Rank products were utilized after normalizing the intensity files. The expression change was selected when the false discovery rate (FDR) value was < 0.2.

label: biotin

organism: Rattus norvegicus

source_name: pup (D28) kidney of fetal exposure to maternal low-protein diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: The present study was approved and carried out in strict accordance with the guidelines stipulated by the Animal Usage Committee of the Graduate School of Agricultural and Life Sciences at The University of Tokyo (Approval No. P09-376). Rats were kept at a temperature of 22 ± 1 ℃with 60 ± 5% humidity, in a 12-h light/dark cycle (8:00 to 20:00).

extract_protocol: The total RNA from kidney samples was extracted using a NucleoSpin® TriPrep Kit (Takara Bio Inc.) according to the manufacturer’s instructions.

treatment_protocol: Pregnant dams were randomly assigned to be supplied either a 20% (control diet, CN) or a 9% (low-protein diet, LP) casein diet during pregnancy . After delivery, all dams were fed a commercial diet. Next, male pups were separated from their dams at the fourth postnatal week and provided ad libitum drinking water and a commercial diet. Finally, 5-day-old (D5-CN or D5-LP), 10-day-old (D10-CN or D10-LP), and 4-week-old male (D28-CN or D28-LP) offspring were culled, and their kidneys were collected.

value: kidney

value: offspring exposure to maternal low protein diet during fetal life

tag: age

value: offspring on postnatal day 28


title: pup (D28) kidney, maternal protein restriction sample for biological rep3


title: pup (D28) kidney, maternal protein restriction sample for biological rep4


title: pup (D28) kidney, control sample for biological rep3

description: Gene expression data from the kidneys of pups exposed to a control diet throughout their fetal life

source_name: pup (D28) kidney of fetal exposure to maternal control diet

value: offspring exposure to maternal control diet during fetal life


title: pup (D28) kidney, maternal protein restriction sample for biological rep1


title: pup (D28) kidney, control sample for biological rep2


title: pup (D10) kidney, maternal protein restriction sample for biological rep3

source_name: pup (D10) kidney of fetal exposure to maternal low-protein diet

value: offspring on postnatal day 10


title: pup (D10) kidney, maternal protein restriction sample for biological rep4


title: pup (D28) kidney, control sample for biological rep5


title: pup (D10) kidney, control sample for biological rep3

source_name: pup (D10) kidney of fetal exposure to maternal control diet


title: pup (D10) kidney, control sample for biological rep1


title: pup (D10) kidney, control sample for biological rep5


title: pup (D28) kidney, control sample for biological rep1


title: pup (D10) kidney, maternal protein restriction sample for biological rep2


title: pup (D5) kidney, control sample for biological rep5

source_name: pup (D5) kidney of fetal exposure to maternal control diet

value: offspring on postnatal day 5


title: pup (D5) kidney, maternal protein restriction sample for biological rep3

source_name: pup (D5) kidney of fetal exposure to maternal low-protein diet


title: pup (D28) kidney, control sample for biological rep4


title: pup (D5) kidney, maternal protein restriction sample for biological rep2


title: pup (D10) kidney, maternal protein restriction sample for biological rep5


title: pup (D10) kidney, control sample for biological rep2


title: pup (D10) kidney, control sample for biological rep4


title: pup (D10) kidney, maternal protein restriction sample for biological rep1


title: pup (D5) kidney, maternal protein restriction sample for biological rep5


title: pup (D5) kidney, maternal protein restriction sample for biological rep4


title: pup (D28) kidney, maternal protein restriction sample for biological rep2


title: pup (D5) kidney, maternal protein restriction sample for biological rep1


title: pup (D5) kidney, control sample for biological rep4


title: HUVEC donor 7 TNF removal 12 hr

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 15, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: HUVEC

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Cells were grown on gelatin coated flask until P2 in endothlial cell growth medium advanced

extract_protocol: Trizol

treatment_protocol: Basal (normal cell growth medium), TNF stimulation (25 ng/ml for 24 hr), TNF stimulation (25 ng/ml for 24 hrs) followed by removal and culture in normal cell growth medium for 12 or 24 hrs

value: Umbilical cord

value: TNF removal 12hr


title: HUVEC donor 7 TNF removal 24 hr

value: TNF removal 24hr


title: pup (D5) kidney, control sample for biological rep1


title: RNA-Seq of Sorghum bicolor: Btx623 Root lateral replicate 1 under low phosphorous condition

city: Cold Spring Harbor

first: Nicholas

last: Gladman

state: NY

address: 1 Bungtown Rd

department: ARS

institute: USDA

data_processing:
RNA-seq: Paired-end fastq files were trimmed for quality with Trimmomatic and then merged with Samtools before aligning to the v3.4.1 S. bicolor genome with Kallisto package in rStudio v3.6.1. Differential gene expression was deter- mined through DESeq2 after importing Kallisto abundance files with tximport package. Dimensional analysis was performed using the factoextra package. Heatmaps and hierarchical clustering were per- formed with the heatmpap.2 package in rStudio.
ChIP-seq: Paired-end fastq files were trimmed for quality with Trimmomatic and then mapped to the v3.4.1 S. bicolor genome with BWA (bwa mem -q 30, -f 2 -ubhS). Sorted bam files were marked for duplicates with Picard and then merged with Samtools. Tag directories creation and peak calling, peak enrichment comparison was performed through the Homer package. Overlapped peaks were identified through Bedtools (intersectBed). Peak annotation was performed using the annotatePeaks module of the Homer software. Samtools was used to obtain flagstat metrics and perform various file conversion and handling. Various visualization and file creation was performed using the deepTools package (Ramírez et al., 2016); aligned bam files (that were input-controlled) were converted to bigWig format for generating computeMatrix files for plotHeatmap and plotEnrichment outputs. k-means cluster number was determined by selecting the result that generated the distinct read coverage within and around gene models while minimizing clus- ter overlap.
Bisulphite-Seq: Reads were trimmed and quality controlled using Trim Galore and FASTQC respectively (http://www.bioinformatics.babraham.ac.uk/projects/index.html). Reads were aligned and extracted with Bismark (Krueger & Andrews, 2011). Differential methylation quantification and visualiza- tions were done with MethylKit (Akalin et al., 2012). Additional visual- izations were performed with deepTools (Ramírez et al., 2016) after converting Bismark-aligned bam files to bigWig and then generating computeMatrix files for plotHeatmap and plotEnrichment outputs.
Assembly: Sorghum Bicolor BTx623 v 3.1
Supplementary files format and content: RNA-seq: abundance files (*_abundance.tsv) from a kallisto quant run of trimmomatic-trimmed fastq files. These files are used for input into a differential expression analysis program (DESeq2 or edgeR).
Supplementary files format and content: ChIP-seq: these are bigwig files after processing with the Homer package. Aligned read files were marked for duplicates with Picard and then merged with Samtools. Subsequently, tag directories, peak calling, and peak enrichment were performed with Homer. These files are those outputs using the 'genomic DNA as control' samples as input controls for the calling.
Supplementary files format and content: Bisulphite-Seq: the *_all_differential_methylated_regions.csv files were generated from the MethylKit package after aligning the fastq files with Bismark. These files contain differential methylated sites for CPG, CHG, and CHH methylation using normal phosphorus growth conditions as the control. Statistical values for each call are included in the .csv files as well as a MethylKit score.

organism: Sorghum bicolor

source_name: Root lateral

extract_protocol:
RNA-seq: Root tissue samples were ground in liquid nitrogen and then the RNA was isolated in Trizol reagent (ThermoFisher) followed by purifica- tion using Zymo-spin columns (Directzol RNA kit; Zymo Research). Column-bound RNA was treated with DNase 1 and finally eluted with 50 μl of DNase/RNase-free water. RNA quality was determined using the Bioanalyzer hardware with the Agilent RNA 6000 Nano Kit (Agilent). Poly-A RNA was isolated from total RNA using Dynabeads (ThermoFisher). Libraries for sequencing were created using the ScriptSeq RNA-seq prep kit (Illumina) following manufacturer protocols. Final libraries were amplified with 17 cycles of PCR and assessed on the Bioanalyzer with the High Sensitivity DNA kit (Agilent). Bisulphite-seq: Bisulfite-sequencing was done as described in (Li et al., 2014). The root apices (first two cm) of all primary and lateral roots were excised from plants grown as described above after 10 days of growth on SP and LP media. The root samples from 10 plants constituted one bio- logical replicate. DNA was isolated from root sections and sheared into fragments between 200 and 300 bp in length. These fragments underwent end repair, dA tailing, and ligation to methylated adaptors for subsequent bisulfite conversion. Libraries were PCR amplified, purified, and qual- ity controlled via Agilent DNA 1000 chip. Sequencing was done on a HiSeq 2500 v4 with 125 bp paired-end reads. ChIP-seq: The entire root systems were harvested for ChIP-seq library prepara- tion. The root tissue was cut into sections and fixed in 10-mM dimethyl adipimate (DMA; Sigma-Aldrich) while applying a vacuum. Samples were ground in liquid nitrogen and then placed in extraction buffer, filtered through miracloth and then a 30-mm CellTrics filter (CellTrics). Nuclei were isolated and then chromatin was sheared in 130-ml tubes (Covaris). Shearing was performed on a Covaris S220 sonicator for 5 min at a cycle/burst of 200, peak power of 175, and duty factor of 10. Immunoprecipitation was performed with anti- bodies for H3K27me3 (Millipore), H3K4me3 (Abcam), H3 (Abacam) for input control, and Protein A Dynabeads (ThermoFisher) for input control. Crosslinking was reversed and samples were purified using Chip DNA Clean and Concentrator Kit (Zymo Research).
RNA-seq: Libraries for sequencing were created using the ScriptSeq RNA-seq prep kit (Illumina) following manufacturer protocols. Final libraries were amplified with 17 cycles of PCR and assessed on the Bioanalyzer with the High Sensitivity DNA kit (Agilent). All root tis- sue libraries that were sequenced comprised two biological replicates. Bisulphite-seq: DNA was isolated from root sections and sheared into fragments between 200 and 300 bp in length. These fragments underwent end repair, dA tailing, and ligation to methylated adaptors for subsequent bisulfite conversion. Libraries were PCR amplified, purified, and qual- ity controlled via Agilent DNA 1000 chip. Chip-seq: Libraries were created using the Nextflex ChIP-Seq library prep kit (Bioo Scien- tific) with the NextFlex ChIP-seq Barcodes. Sequencing was done on a HiSeq 2500 v4 with 125 bp paired-end reads

value: Root lateral

value: low phosphorus


title: HUVEC donor 7 basal

value: basal


title: pup (D5) kidney, control sample for biological rep2


title: HUVEC donor 4 TNF removal 12 hr


title: HUAEC donor 7 TNF removal 24 hr

source_name: HUAEC


title: HUAEC donor 4 TNF removal 12 hr


title: HUAEC donor 4 basal


title: HUVEC donor 1 TNF

value: TNF stimulated


title: HUAEC donor 1 TNF removal 24 hr


title: HUVEC donor 4 TNF


title: HUAEC donor 7 basal


title: RNA-Seq of Sorghum bicolor: Btx623 Root lateral replicate 1 under high phosphorous condition

value: normal phosphorus


title: HUVEC donor 1 TNF removal 12 hr


title: HUVEC donor 1 basal


title: HUVEC donor 4 basal


title: HUVEC donor 7 TNF


title: HUAEC donor 1 TNF removal 12 hr


title: HUAEC donor 4 TNF removal 24 hr


title: HUAEC donor 7 TNF removal 12 hr


title: HUAEC donor 1 basal


title: HUVEC donor 1 TNF removal 24 hr


title: HUVEC donor 4 TNF removal 24 hr


title: HUAEC donor 1 TNF


title: HUAEC donor 7 TNF


title: RNA-Seq of Sorghum bicolor: Btx623 Root intermediate  replicate 2 under high phosphorous condition

source_name: Root intermediate

value: Root intermediate


title: HUAEC donor 4 TNF


title: RNA-Seq of Sorghum bicolor: Btx623 Root intermediate  replicate 1 under low phosphorous condition


title: RNA-Seq of Sorghum bicolor: Btx623 Root intermediate  replicate 2 under low phosphorous condition


title: RNA-Seq of Sorghum bicolor: Btx623 Root apex replicate 2 under low phosphorous condition

source_name: whole root

value: whole root


title: pup (D5) kidney, control sample for biological rep3


title: RNA-Seq of Sorghum bicolor: Btx623 Root apex replicate 2 under high phosphorous condition

source_name: Root apex

value: Root apex


title: RNA-Seq of Sorghum bicolor: Btx623 Root intermediate  replicate 1 under high phosphorous condition


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 2 under low phosphorous condition and K27me3 antibody

description:
G3_noP_K27me3_rep1_tagDir_inp_controlled.HisBroad.bw
G3_noP_K27me3_rep2_tagDir_inp_controlled.HisBroad.bw

library_source: genomic


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 2 under low phosphorous condition and K4me3 antibody

description:
G3_noP_K4me3_rep1_tagDir_inp_controlled.HisTight.bw
G3_noP_K4me3_rep2_tagDir_inp_controlled.HisTight.bw


title: RNA-Seq of Sorghum bicolor: Btx623 Root apex replicate 1 under high phosphorous condition


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 2 under low phosphorous condition and H3 antibody

description:
G3_noP_H3_rep1_tagDir_inp_controlled.HisBroad.bw
G3_noP_H3_rep1_tagDir_inp_controlled.HisTight.bw
G3_noP_H3_rep2_tagDir_inp_controlled.HisBroad.bw
G3_noP_H3_rep2_tagDir_inp_controlled.HisTight.bw


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 2 under low phosphorous condition and genomic DNA as control


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 2 under high phosphorous condition and K27Ac antibody

description:
G3_P_K27Ac_rep1_tagDir_inp_controlled.HisTight.bw
G3_P_K27Ac_rep2_tagDir_inp_controlled.HisTight.bw


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 2 under high phosphorous condition and K27me3 antibody

description:
G3_P_K27me3_rep1_tagDir_inp_controlled.HisBroad.bw
G3_P_K27me3_rep2_tagDir_inp_controlled.HisBroad.bw


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 2 under high phosphorous condition and genomic DNA as control

description:
G3_P_H3_rep1_tagDir_inp_controlled.HisBroad.bw
G3_P_H3_rep1_tagDir_inp_controlled.HisTight.bw
G3_P_H3_rep2_tagDir_inp_controlled.HisBroad.bw
G3_P_H3_rep2_tagDir_inp_controlled.HisTight.bw


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 2 under high phosphorous condition and H3 antibody


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 1 under low phosphorous condition and K4me3 antibody


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 1 under low phosphorous condition and K27me3 antibody


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 1 under low phosphorous condition and genomic DNA as control


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 1 under low phosphorous condition and H3 antibody


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 1 under low phosphorous condition and K27Ac antibody

description:
G3_noP_K27Ac_rep1_tagDir_inp_controlled.HisTight.bw
G3_noP_K27Ac_rep2_tagDir_inp_controlled.HisTight.bw


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 1 under high phosphorous condition and H3 antibody


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 1 under high phosphorous condition and K27me3 antibody


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 1 under high phosphorous condition and K27Ac antibody


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 1 under high phosphorous condition and genomic DNA as control


title: Barcoded samples of neurotypical and ASD diagnosed individuals

city: Safed

first: Evan

last: Elliott

address: Henrietta Szold Street, P.O. Box 1589

department: The Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

data_processing:
Microbial diversity and composition were assessed using QIIME2 version 2019.4. First, singleend sequences were imported (qiime import) and demultiplexed (qiime demux) with golay error correction.
sequences were denoised using DADA2 (qiime dada2 denoise-single), trimming the first 5 bases and truncating each sequence at position 215
A phylogenetic tree was constructed using the fragment-insertion method (qiime fragment-insertion sepp).
Taxonomic classification was done using a naïve-based classifier trained on the 99% Greengenes 13_8 V4 reference set (qiime feature-classifier classify-sklearn).
In order to remove low-confidence features, only features with a frequency higher than 50 reads in at least 5 samples were kept. Differences in relative abundances of bacterial taxa between groups were identified using the ANOVA-like differential expression tool (ALDEx2). Sex and gender were defined as covariates in this analysis of the human cohort.

source_name: stool

extract_protocol:
Genomic DNA extracted from stool samples, using the PureLinkTM Microbiome DNA Purification Kit (ThermoFisher, Waltham, MA, USA) according to the manufacturer's instructions and following a 2-minute bead beating step (BioSpec, Bartlesville, OK, USA). Purified DNA was used for PCR amplification of the variable V4 region using the 515F and 806R barcoded primers following the Earth Microbiome Project protocol (Human Microbiome Project Consortium, 2012).
equimolar amounts of DNA were pooled and sequenced using the Illumina MiSeq platform and MiSeq Reagent Kit V2 (500 cycles)

treatment_protocol: Human stool samples

value: stool


title: RNA-Seq of Sorghum bicolor: Btx623 Root apex replicate 1 under low phosphorous condition


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 2 under low phosphorous condition and K27Ac antibody


title: mPFC_58_Cast_VTX

city: San Antonio

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: gene expression with medial prefrontal cortex tissue with castration and with vortioxetine chow

hyb_protocol: According to Agilent microarray protocol

scan_protocol: Agilent SureScan G2600D Microarray Scanner, scanning protocol GE 11.05

data_processing: Agilent expression data were processed with LIMMA R package (v3.46.0), with background correction, normalized between arrays, and averaged over irregular replicate probes.

source_name: medial prefrontal cortex

label_protocol: 100-200 ng of RNA were used to create cyanine 3-labeled cRNA probes (Low Input Quick Amp Labeling kit, Agilent).

growth_protocol: Young adult male Sprague-Dawley rats (Envigo, USA) were approximately 60 days old and weighed 225-250g upon arrival. For ADT treatment, animals were surgically castrated or received sham surgery and were separated into single housing 7-10 days before initiating treatment with drug-infused diet on experimental day 0

extract_protocol: A separate cohort of animals were sacrificed on day 17, and the hippocampus or mPFC was bluntly dissected on ice.  The tissues were then separated for region specificity, and flash frozen in 2-methylbutane on dry ice. Samples were stored at -80°C until use. Qiazol lysis buffer (Qiagen, Hilden, Germany) and Direct-zol miniprep RNA isolation kit (Zymo Research, Irvine, CA) were used to isolate RNA. Samples with an RNA integrity number >7 were used for the assay, as determined using an Agilent Bioanalyzer (Agilent, Santa Clara, CA)

treatment_protocol: Drug was administered in the diet beginning 7-10 days after ADT surgery, and animals remained on diet for 17 days (up to 28 days total). Vortioxetine was obtained from H. Lundbeck A/S. Drug-infused chow containing 0.6 g vortioxetine per kg chow and control chow (Purina #5001) were prepared by Research Diets, Inc.  Free-feeding animals consumed 12-16 g of food per day, corresponding to a dose of 28 mg/kg/day for an average 300 g rat at the time of testing

tag: castration

value: Castration

value: vortioxetine

value: medial prefrontal cortex

value: male

tag: strain

value: Sprague-Dawley


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 1 under high phosphorous condition and K4me3 antibody

description:
G3_P_K4me3_rep1_tagDir_inp_controlled.HisTight.bw
G3_P_K4me3_rep2_tagDir_inp_controlled.HisTight.bw

tag: tissue


title: ChIP-Seq Sorghum bicolor: Btx623 whole root replicate 2 under high phosphorous condition and K4me3 antibody


title: mPFC_42_Intact_CNTL

description: gene expression with medial prefrontal cortex tissue without castration and with control chow

value: Sham

value: control


title: mPFC_45_Cast_CNTL

description: gene expression with medial prefrontal cortex tissue with castration and with control chow


title: mPFC_52_Cast_VTX


title: mPFC_61_Intact_VTX


title: mPFC_46_Cast_CNTL


title: mPFC_67_Intact_VTX

description: gene expression with medial prefrontal cortex tissue without castration and with vortioxetine chow


title: mPFC_38_Intact_CNTL

value: Control


title: dHipp_C20R_Cast_VTX

description: gene expression with dorsal hippocampus tissue with castration and with vortioxetine chow

source_name: dorsal hippocampus

value: dorsal hippocampus


title: mPFC_64_Cast_VTX


title: dHipp_C4L_Cast_VTX


title: dHipp_C13L_Cast_Ctrl

description: gene expression with dorsal hippocampus tissue with castration and with control chow


title: dHipp_C2R_Cast_VTX


title: mPFC_43_Intact_CNTL


title: dHipp_C16R_Cast_VTX


title: dHipp_S16L_Sham_VTX

description: gene expression with dorsal hippocampus tissue without castration and with with vortioxetine chow


title: dHipp_C12L_Cast_Ctrl


title: dHipp_C17L_Cast_VTX


title: dHipp_C7R_Cast_Ctrl


title: dHipp_C6R_Cast_Ctrl


title: mPFC_35_Cast_CNTL


title: dHipp_C11L_Cast_VTX


title: dHipp_C18R_Cast_Ctrl


title: dHipp_S17L_Sham_VTX

description: gene expression with dorsal hippocampus tissue without castration and with vortioxetine chow


title: sin-3(tm1276)_rep3

city: Lyon

first: Cecile

last: Bedet

address: 46 allée d'Italie

department: Bilogie

institute: ENS de Lyon

data_processing:
quality control, adapter trimming, quality filtering with fastp (Version 0.20.1)
mapping with RNA-STAR (Version 2.7.3a) on genome WS278
reads count was performed with htseq-count (Version 0.7.2)
differential expression was calculated with DESeq2 (Version 1.36.0) using a homemade R script (Rversion 4.2.2)
Assembly: WS278
Supplementary files format and content: raw read count table (.tsv)
Supplementary files format and content: diff expression file (.csv)

organism: Caenorhabditis elegans

source_name: germline

extract_protocol:
Gonad dissections and extractions were performed as in Herbette et al, Cells. 2020 ,doi: 10.3390/cells9092049. Briefly, gonads of 5 to 7 young adults at the L4 stage + 12 h were dissected in dissection buffer (Egg Buffer1.1 × (HEPES pH 7.3 25 mM, NaCl 118 mM, KCL 48 mM, CaCl2 2 mM, 2 mM MgCl2), 0.5 mM Levamisole, 0.1% Tween 20) on slides. Extruded gonads were cut at the elbow and the distal part recovered using a drawn capillary and transferred to 30 µL of ×B extraction buffer (Kit Picopure, Life Technology, # 12204-01, Carlsbad, MA, USA), frozen in liquid nitrogen and stored at −80 °C. For RNA preparation tubes were thawed, the volume of XB extraction buffer adjusted to 100 μL, and RNA purified using the PicoPure kit (Life Technology, # 12204-01) according to the manufacturer’s instructions. Elution was in 13 μL of nuclease-free water. The integrity of RNA was evaluated using Tape Station 4200 (Agilent, Santa Clara, CA, USA), and the concentration of RNA measured using DropSense 96 (Unchained Labs, Pleasanton, CA, USA).
Librairies were generated using the Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit (Illumina) and sequenced using the Illumina Hiseq 4000 technology (1x50 bases)

value: germline


title: dHipp_C8L_Cast_Ctrl


title: dHipp_S15R_Sham_VTX


title: sin-3(tm1276)_rep2


title: dHipp_S11R_Sham_VTX


title: dHipp_S19R_Sham_Ctrl

description: gene expression with dorsal hippocampus tissue without castration and with control chow


title: sin-3(tm1276)_rep1


title: smartseq2_Mature_LA_161517

city: Vienna

first: Jingkui

last: Wang

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

description: RNA- expression for Differential Gene expression analysis regrading mature arm vs hand as different limb positions (intact Hand CT cells).

data_processing:
Smart-seq2 processing pipeline was adapted for axolotl genome from nf-core/rnaseq.
The raw reads were trimmed with trim_galore (v0.6.2) and mapped to axolotl genome (AmexG_v6,  Schloissnig et al., 2021) using hisat2 (v2.1.0).
Read counts at gene levels were quantified by featureCounts in subread (v2.0.1).
To identify segment-specific genes in mature samples, the read counts were normalized and pairwise comparisons were done with DESeq2 (v1.26.0)
Bigwig files were made with deeptools (v3.1.2)
Assembly: AmexG_6
Supplementary files format and content: bigwigs and genomic tracks

organism: Ambystoma mexicanum

source_name: Connective tissue cells

extract_protocol:
RNA was harvested using a total RNA isolation kit (in-house kit provided by Molecular Biology Services in Vienna BioCenter). Sequencing libraries were prepared by VBC NGS-Facility.
Smart-seq version 2

value: Connective tissue cells


title: wild-type_rep3

value: wild-type


title: wild-type_rep2


title: iFoxL2, mES+24hrs, ATAC-seq, rep2

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

data_processing:
Basecalls were performed using using bcl-convert verison 00.000.000.3.8.2-12-g85770e0b
BWA mem (version 0.7.17-r1188) was used to align paired-end ATAC-seq reads against the mm10 reference genome using the following arguments: “-t 8 -v 1 -T 30 -h 5”.
Picard MarkDuplicates (version 2.7.1) was used to mark duplicate read pair alignments and then samtools view with arguments “-h -b -f 0x1 -F 0x404” was used to filter out duplicated read pairs.
ATAC-seq heatmaps and profile plots were created using DeepTools (version 3.5.1)
Assembly: mm10
Supplementary files format and content: bw: bigwig format files with read coverage of mapped ATAC-seq data

growth_protocol: Generation of the mES transgenic cell lines used in this study is described in [PMID: 19796622]. These cell lines were part of NIA (National Institute on Aging/NIH) mouse ES cell collection. Cell lines are derived from MC1 mouse ES cells (129S6/SvEvTac). Doxycycline-repressible expression constructs containing the relevant TF ORF, C-terminally tagged with His6-FLAG, and a puromycin resistance gene were inserted into the expression-competent Rosa26 locus. ES cells were cultured in a gelatin-coated dish with DMEM medium containing 15% FBS, 1000 U/ml LIF, 1 mM sodium pyruvate, 0.1 mM MEM non-essential amino acids, 2 mM glutamate, 0.1 mM ß-mercaptoethanol, 0.2µg/ml Doxycycline and 1.0μg/ml puromycin.

extract_protocol:
ATAC-seq experiments followed the Omni-ATAC-seq protocol [PMID: 28846090].  For each experiment, 50,000 cells were harvested. Cells were dissociated in 50 μl ATAC-Resuspension Buffer (10 mM Tris (pH 7.4), 10 mM NaCl, 3 mM MgCl2) with 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin, incubated on ice for 3 mins, and then suspended in 1 mL ATAC-Resuspension Buffer with 0.1% Tween-20 and centrifuged for 10 min at 4°C and 500g. The pellet was resuspended in transposition mixture (25 μl 2x TD buffer, 2.5 μl transposome (Tn5 + oligo DNA), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, 5 μl H2O), followed by incubation at 37°C for 30mins. The reaction was cleaned up with AMPure XP beads. Transposed fragments were PCR amplified for a number of PCR cycles determined from one-third of the maximum fluorescence measured by quantitative PCR reaction with 1 × SYBR Green (Invitrogen), custom-designed primers [PMID: 30194434], and 2 × NEB MasterMix (New England Labs, M0541).
The library was cleaned up with AMPure XP beads and the fragment length distribution of the library was determined using a Bioanalyzer High Sensitivity chip. The libraries were sequenced on an Illumina NextSeq 2000.

treatment_protocol: To induce transgene TFs, Dox was removed by washing three times with PBS at 3 hr intervals and cells were grown in DMEM differentiation medium containing 10% FBS for the stated amount of time.

value: embryonic stem cells

value: Dox removal +24hrs


title: iFoxP3, mES+24hrs, ATAC-seq, rep1


title: iFoxP3, mES+24hrs, ATAC-seq, rep2


title: dHipp_S4L_Sham_VTX


title: dHipp_S2R_Sham_VTX


title: dHipp_S18L_Sham_Ctrl


title: sin3_rep5

extract_protocol:
Gonads from 9-12 young adults were dissected in UltraPure water on microscope slides at 4°C to immobilize worms without use of anesthetic. RNA was isolated, reverse-transcribed, amplified and clean up following the Smart-seq2 protocol described by Serra et al. (Serra et al., 2018). Three independent biological replicates were performed for each strain
Librairies were generated using the SMART-Seq v4 UltraLow Input RNA kit (Clontech) followed by the Nextera XT DNA sample preparation Kit (Illumina) and sequenced using the Illumina Hiseq 4000 technology (1x50 bases)


title: dHipp_S7R_Sham_Ctrl


title: iFoxL2, mES+24hrs, ATAC-seq, rep1


title: dHipp_S12L_Sham_Ctrl


title: dHipp_S8R_Sham_Ctrl


title: dHipp_S6L_Sham_Ctrl


title: iFoxG1, mES+24hrs, ATAC-seq, rep2


title: iFoxG1, mES+24hrs, ATAC-seq, rep1


title: smartseq2_Mature_LA_161514


title: wild-type_rep1


title: hda3_rep5


title: hda3_rep4


title: wt_rep5


title: iFoxA1, mES+24hrs, ATAC-seq, rep2


title: iFoxC1, mES+24hrs, ATAC-seq, rep2


title: iFoxA1, mES+24hrs, ATAC-seq, rep1


title: wt_rep3


title: EmptyControl, mES+24hrs, ATAC-seq, rep1


title: EmptyControl, mES+24hrs, ATAC-seq, rep2


title: snATAC-seq of homo sapiens adult brain: Sub from donor 2

city: La Jolla

first: Yang

address: 9500 Gilman Dr

institute: University of California San Diego

data_processing:
Keep only fragments quality score MAPQ > 30
Keep only the properly paired fragments with length <1000 bp
Remove PCR duplicates
Peak calling using MACS2
Count cell-by-bin accessibility matrix, cell-by-peak matrix, cell-by-gene matrix
Assembly: hg38
Supplementary files format and content: bedpe format, the fragments after quality control
Supplementary files format and content: HDF5 format, cell-by-bin accessibility matrix, cell-by-peak matrix, cell-by-gene matrix, and barcode

source_name: Sub

extract_protocol:
https://www.protocols.io/view/sequencing-open-chromatin-of-single-cell-nuclei-sn-5jyl8756g2wp/v2
Single nucleus ATAC-seq was performed as described with steps optimized for automation and modifications in permeabilization and sort buffers (PMID: 29434377). A step-by-step-protocol for library preparation is available here: https://www.protocols.io/view/sequencing-open-chromatin-of-single-cell-nuclei-sn-pjudknw/abstract.
Brain nuclei were pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4  C; 5920R, Eppendorf). Nuclei pellets were resuspended in 1 ml nuclei permeabilization buffer (10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sigma), 0.1% IGEPAL-CA630 (Sigma), 0.01% Digitonin (Promega) and 1% BSA (Proliant 7500804) in molecular biology-grade water) and pelleted again (500 x g, 5 min, 4  C; 5920R, Eppendorf). Nuclei were resuspended in 1 mL high salt tagmentation buffer (36.3 mM Tris-acetate (pH = 7.8), 72.6 mM potassium-acetate, 11 mM Mg-acetate, 17.6% DMF) and counted using a hemocytometer. Concentration was adjusted to 2,000 nuclei/9   l, and 2,000 nuclei were dispensed into each well of a 96-well plate. For tagmentation, 1   L barcoded Tn5 transposomes were added using a BenchSmart    96 (Mettler Toledo), mixed five times, and incubated for 60 min at 37   C with shaking (500 rpm). To inhibit the Tn5 reaction, 10   L of 40 mM EDTA was added to each well with a BenchSmart    96 (Mettler Toledo), mixed 10 times, and the plate was incubated at 37   C for 15 min with shaking (500 rpm). Next, 10   L 3 x sort buffer (3 % BSA, 3 mM EDTA in PBS) was added using a BenchSmart    96 (Mettler Toledo). If processing two or more samples per day, tagmentation was performed with different sets of barcodes in separate 96 well plates. After tagmentation nuclei from individual plates were pooled together, added to a FACS tube and stained with 3   M Draq7 (Cell Signaling). Using a SH800 (Sony), 20 nuclei per sample were sorted per well into eight 96-well plates (total of 768 wells, 15,360 nuclei per sample) containing 10.5   L EB (25 pmol primer i7, 25 pmol primer i5, 200 ng BSA (Sigma). Preparation of sort plates and alldownstream pipetting steps were performed on a Biomek i7 Automated Workstation (Beckman Coulter). After addition of 1   L 0.2% SDS, samples were incubated at 55   C for 7 min with shaking (500 rpm). 1   L 12.5% Triton-X was added to each well to quench the SDS. Next, 12.5   L NEBNext High-Fidelity 2   PCR Master Mix (NEB) were added and samples were PCR-amplified (72   C 5 min, 98   C 30 s, (98   C 10 s, 63   C 30 s, 72  C 60 s)    12 cycles, held at 12   C). After PCR, all wells were combined. Libraries were purified according to the MinElute PCR Purification Kit manual (Qiagen) using a vacuum manifold (QIAvac 24 plus, Qiagen) and size selection was performed with SPRI Beads (Beckmann Coulter, 0.55x and 1.5x). Libraries were purified one more time with SPRI Beads (Beckmann Coulter, 1.5x). Libraries were quantified using a Qubit fluorimeter (Life technologies) and the nucleosomal pattern was verified using a Tapestation (High Sensitivity D1000, Agilent). Libraries generated were sequenced on NovaSeq6000 (Illumina) using custom sequencing primers with following read lengths: 50 + 10 + 12 + 50 (Read1 + Index1 + Index2 + Read2).

value: Sub

value: Donor 2

value: neurotypical adult male'


title: sin3_rep4


title: snATAC-seq of homo sapiens adult brain: Sub from donor 1

value: Donor 1


title: snATAC-seq of homo sapiens adult brain: HiB from donor 4 rep 1

source_name: HiB

value: HiB

value: Donor 4


title: snATAC-seq of homo sapiens adult brain: HiT from donor 4

source_name: HiT

value: HiT


title: snATAC-seq of homo sapiens adult brain: HiB from donor 1


title: snATAC-seq of homo sapiens adult brain: HiT from donor 1


title: snATAC-seq of homo sapiens adult brain: HiB from donor 2 rep 1


title: snATAC-seq of homo sapiens adult brain: AMY from donor 4

source_name: AMY

value: AMY


title: snATAC-seq of homo sapiens adult brain: HiB from donor 2 rep 2


title: snATAC-seq of homo sapiens adult brain: HiB from donor 4 rep 2


title: sin3_rep3


title: snATAC-seq of homo sapiens adult brain: AMY from donor 2


title: snATAC-seq of homo sapiens adult brain: AMY from donor 1


title: iFoxC1, mES+24hrs, ATAC-seq, rep1


title: snATAC-seq of homo sapiens adult brain: BL-La from donor 4

source_name: BL-La

value: BL-La


title: snATAC-seq of homo sapiens adult brain: BL-La from donor 2


title: snATAC-seq of homo sapiens adult brain: BL-La from donor 1


title: snATAC-seq of homo sapiens adult brain: Sub from donor 4


title: snATAC-seq of homo sapiens adult brain: CMN-CN from donor 4

source_name: CMN-CN

value: CMN-CN


title: wt_rep4


title: snATAC-seq of homo sapiens adult brain: CMN from donor 2

source_name: CMN

value: CMN


title: snATAC-seq of homo sapiens adult brain: CMN from donor 1


title: snATAC-seq of homo sapiens adult brain: BNST from donor 4

source_name: BNST

value: BNST


title: snATAC-seq of homo sapiens adult brain: BNST from donor 1


title: snATAC-seq of homo sapiens adult brain: SI from donor 2

source_name: SI

value: SI


title: snATAC-seq of homo sapiens adult brain: BNST from donor 2


title: snATAC-seq of homo sapiens adult brain: SI from donor 1


title: snATAC-seq of homo sapiens adult brain: SI from donor 4


title: snATAC-seq of homo sapiens adult brain: SEP from donor 4

source_name: SEP

value: SEP


title: snATAC-seq of homo sapiens adult brain: HiT from donor 2


title: snATAC-seq of homo sapiens adult brain: SEP from donor 2


title: snATAC-seq of homo sapiens adult brain: CaB from donor 1

source_name: CaB

value: CaB


title: snATAC-seq of homo sapiens adult brain: SEP from donor 1


title: snATAC-seq of homo sapiens adult brain: GPe from donor 2

source_name: GPe

value: GPe


title: snATAC-seq of homo sapiens adult brain: CaB from donor 4


title: snATAC-seq of homo sapiens adult brain: GPe from donor 4


title: snATAC-seq of homo sapiens adult brain: Pu from donor 1

source_name: Pu

value: Pu


title: snATAC-seq of homo sapiens adult brain: CaB from donor 2


title: snATAC-seq of homo sapiens adult brain: NAC from donor 2

source_name: NAC

value: NAC


title: snATAC-seq of homo sapiens adult brain: NAC from donor 4


title: snATAC-seq of homo sapiens adult brain: Pu from donor 2

value: Donor 2


title: snATAC-seq of homo sapiens adult brain: Pu from donor 4

value: neurotypical adult male'


title: snATAC-seq of homo sapiens adult brain: GPe from donor 1

value: Donor 1


title: snATAC-seq of homo sapiens adult brain: NAC from donor 1


title: snATAC-seq of homo sapiens adult brain: Cla from donor 2

source_name: Cla

value: Cla


title: snATAC-seq of homo sapiens adult brain: Cla from donor 4

value: Donor 4


title: snATAC-seq of homo sapiens adult brain: PN from donor 4

source_name: PN

value: PN


title: snATAC-seq of homo sapiens adult brain: Cla from donor 1


title: snATAC-seq of homo sapiens adult brain: PN from donor 2


title: snATAC-seq of homo sapiens adult brain: PN from donor 1


title: snATAC-seq of homo sapiens adult brain: CBL from donor 4

source_name: CBL

value: CBL


title: snATAC-seq of homo sapiens adult brain: CBL from donor 2


title: snATAC-seq of homo sapiens adult brain: CBL from donor 1


title: snATAC-seq of homo sapiens adult brain: CBV from donor 2

source_name: CBV

value: CBV


title: snATAC-seq of homo sapiens adult brain: CBV from donor 4


title: snATAC-seq of homo sapiens adult brain: MD from donor 4

source_name: MD

value: MD


title: snATAC-seq of homo sapiens adult brain: CBV from donor 1


title: snATAC-seq of homo sapiens adult brain: MD from donor 2


title: snATAC-seq of homo sapiens adult brain: MD from donor 1


title: snATAC-seq of homo sapiens adult brain: Pul from donor 4

source_name: Pul

value: Pul


title: snATAC-seq of homo sapiens adult brain: Pul from donor 2


title: snATAC-seq of homo sapiens adult brain: Pul from donor 1


title: snATAC-seq of homo sapiens adult brain: IC from donor 2

source_name: IC

value: IC


title: snATAC-seq of homo sapiens adult brain: A25 from donor 2


title: snATAC-seq of homo sapiens adult brain: A25 from donor 1


title: snATAC-seq of homo sapiens adult brain: IC from donor 4


title: snATAC-seq of homo sapiens adult brain: A25 from donor 4


title: snATAC-seq of homo sapiens adult brain: A38 from donor 2


title: snATAC-seq of homo sapiens adult brain: A38 from donor 4


title: snATAC-seq of homo sapiens adult brain: A38 from donor 1


title: snATAC-seq of homo sapiens adult brain: Idg from donor 4

source_name: Idg

value: Idg


title: snATAC-seq of homo sapiens adult brain: Idg from donor 2


title: snATAC-seq of homo sapiens adult brain: ITG from donor 2

source_name: ITG

value: ITG


title: snATAC-seq of homo sapiens adult brain: ITG from donor 1


title: snATAC-seq of homo sapiens adult brain: MEC from donor 4

source_name: MEC

value: MEC


title: snATAC-seq of homo sapiens adult brain: Idg from donor 1


title: snATAC-seq of homo sapiens adult brain: MEC from donor 1


title: snATAC-seq of homo sapiens adult brain: ITG from donor 4


title: snATAC-seq of homo sapiens adult brain: TH-TL from donor 4

source_name: TH-TL

value: TH-TL


title: snATAC-seq of homo sapiens adult brain: MEC from donor 2


title: snATAC-seq of homo sapiens adult brain: TH-TL from donor 1


title: snATAC-seq of homo sapiens adult brain: A19 from donor 2


title: snATAC-seq of homo sapiens adult brain: LEC from donor 4

source_name: LEC

value: LEC


title: snATAC-seq of homo sapiens adult brain: TH-TL from donor 2


title: snATAC-seq of homo sapiens adult brain: A19 from donor 1


title: snATAC-seq of homo sapiens adult brain: A19 from donor 4


title: snATAC-seq of homo sapiens adult brain: LEC from donor 2


title: snATAC-seq of homo sapiens adult brain: LEC from donor 1


title: snATAC-seq of homo sapiens adult brain: IC from donor 1


title: snATAC-seq of homo sapiens adult brain: Pir from donor 2

source_name: Pir

value: Pir


title: snATAC-seq of homo sapiens adult brain: Pro from donor 4

source_name: Pro

value: Pro


title: snATAC-seq of homo sapiens adult brain: Pir from donor 1

value: neurotypical adult male'


title: snATAC-seq of homo sapiens adult brain: Pro from donor 2

value: Donor 2


title: snATAC-seq of homo sapiens adult brain: Ig from donor 2

source_name: Ig

value: Ig


title: snATAC-seq of homo sapiens adult brain: Ig from donor 4

value: Donor 4


title: snATAC-seq of homo sapiens adult brain: Ig from donor 1

value: Donor 1


title: snATAC-seq of homo sapiens adult brain: S1C from donor 2


title: snATAC-seq of homo sapiens adult brain: S1C from donor 1


title: snATAC-seq of homo sapiens adult brain: A5-A7 from donor 1


title: snATAC-seq of homo sapiens adult brain: A5-A7 from donor 2


title: snATAC-seq of homo sapiens adult brain: A5-A7 from donor 4


title: snATAC-seq of homo sapiens adult brain: Pro from donor 1


title: snATAC-seq of homo sapiens adult brain: A44-A45 from donor 4


title: snATAC-seq of homo sapiens adult brain: A44-A45 from donor 2


title: snATAC-seq of homo sapiens adult brain: A1C from donor 4


title: snATAC-seq of homo sapiens adult brain: A1C from donor 2


title: snATAC-seq of homo sapiens adult brain: A44-A45 from donor 1


title: snATAC-seq of homo sapiens adult brain: A1C from donor 1


title: snATAC-seq of homo sapiens adult brain: V1C from donor 2


title: snATAC-seq of homo sapiens adult brain: V1C from donor 1


title: snATAC-seq of homo sapiens adult brain: V1C from donor 4


title: snATAC-seq of homo sapiens adult brain: ACC from donor 2

source_name: ACC

value: ACC


title: snATAC-seq of homo sapiens adult brain: A46 from donor 4


title: snATAC-seq of homo sapiens adult brain: ACC from donor 1


title: snATAC-seq of homo sapiens adult brain: Pir from donor 4


title: snATAC-seq of homo sapiens adult brain: A46 from donor 2


title: snATAC-seq of homo sapiens adult brain: A46 from donor 1


title: snATAC-seq of homo sapiens adult brain: FI from donor 4

source_name: FI

value: FI


title: snATAC-seq of homo sapiens adult brain: S1C from donor 4


title: snATAC-seq of homo sapiens adult brain: FI from donor 1


title: snATAC-seq of homo sapiens adult brain: V2 from donor 2


title: snATAC-seq of homo sapiens adult brain: V2 from donor 4


title: snATAC-seq of homo sapiens adult brain: M1C from donor 4


title: snATAC-seq of homo sapiens adult brain: MTG from donor 4

source_name: MTG

value: MTG


title: snATAC-seq of homo sapiens adult brain: M1C from donor 1


title: snATAC-seq of homo sapiens adult brain: MTG from donor 1


title: snATAC-seq of homo sapiens adult brain: M1C from donor 2


title: snATAC-seq of homo sapiens adult brain: ACC from donor 4


title: G3458, Enzalutamide, breast tumor

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

description: counts.xlsx

data_processing:
Data was aligned using hg38 and STAR 2.0
Assembly: hg38
Supplementary files format and content: Excel table with raw counts

molecule: polyA RNA

source_name: breast tumor

extract_protocol: RNA was extracted using Rneasy plus kit (Qiagen). 1.5ug of RNA was used for the construction of sequencing libraries.

value: breast cancer

value: Enzalutamide

value: breast tumor


title: G3470, Enzalutamide, breast tumor

description: counts.xlsx


title: G3486, Enzalutamide, breast tumor

description: counts.xlsx


title: snATAC-seq of homo sapiens adult brain: MTG from donor 2


title: G2473, UT-105, breast tumor

description: counts.xlsx


title: G2460, UT-105, breast tumor

description: counts.xlsx


title: G1481, Vehicle, breast tumor

description: counts.xlsx

value: Vehicle


title: G1472, Vehicle, breast tumor

description: counts.xlsx


title: G1366, Vehicle, breast tumor

description: counts.xlsx


title: G2454, UT-105, breast tumor

description: counts.xlsx


title: snATAC-seq of homo sapiens adult brain: FI from donor 2


title: G1360, Vehicle, breast tumor

description: counts.xlsx


title: HBRT1279

data_processing:
Data was aligned using hg38 and STAR 2.0
Counts were normalized using CPM
Assembly: hg38

source_name: breast

value: breast

tag: ar expression based on histology 10% cutoff


title: HBRT1323


title: HBRT1258


title: snATAC-seq of homo sapiens adult brain: V2 from donor 1


title: HBRT1186


title: HBRT1140


title: HBRT1357


title: HBRT1378


title: HBRT1114


title: HBRT1295


title: HBRT1288


title: HBRT1342


title: HBRT1125


title: HBRT1289


title: HBRT1213


title: HBRT1109


title: G1484, Vehicle, breast tumor

description: counts.xlsx


title: HBRT1094


title: HBRT1150


title: HBRT1188


title: HBRT1129


title: DOD 0013


title: CHTN 019


title: DOD 0003


title: CHTN 017


title: CHTN 018


title: HBRT1375


title: DOD 0004


title: HBRT1386


title: HBRT1351


title: HBRT1355


title: HBRT1223


title: HBRT1130


title: HBRT1135


title: HBRT1115


title: HBRT1082


title: HBRT1098


title: CHTN 020


title: HBRT1012


title: HBRT1049


title: DOD 0014


title: HBRT1071


title: pat_79_T

city: Milan,

first: Raffaella

last: Pini

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

data_processing:
The 100-bp single-end reads were aligned to the reference human genome GRCh38 using STAR aligner (version 2.5.3a)
Only uniquely mapped reads were retained. At the gene level, expression counts were estimated using featureCounts (version1.6.3), and annotated according to Gencode basic annotations (Gencode version 28)
Reads per kilobase of transcript per million reads  (RPKM) were computed with edgeR rpkm function
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample

source_name: tumor

growth_protocol: Not applicable

extract_protocol:
RNA was extracted using the Rneasy Plus Mini (Quiagen).
RNA libraries fro RNA-seq were prepared using the TruSeq Stranded mRNA (Illumina) protocol, following manufacturer's instructions

treatment_protocol: Not applicable

value: tumor

value: FOLFIRINOX


title: pat_78_T


title: pat_75_T


title: pat_77_T


title: pat_73_T


title: pat_68_T


title: pat_69_T


title: pat_67_T


title: HBRT1302


title: pat_66_T


title: pat_65_T


title: pat_64_T


title: pat_63_T


title: pat_74_T


title: pat_72_T


title: pat_76_T


title: pat_71_T


title: pat_52_T

value: gemcitabine + nab-paclitaxel


title: pat_55_T


title: pat_59_T


title: pat_61_T


title: pat_57_T


title: pat_50_T


title: pat_70_T


title: pat_56_T


title: pat_49_T


title: pat_53_T


title: pat_47_T


title: pat_54_T


title: pat_58_T


title: pat_45_T


title: pat_48_T


title: pat_51_T


title: pat_44_T


title: pat_43_T


title: pat_46_T


title: pat_42_T


title: pat_62_T


title: pat_24_TDRL

source_name: tumor-draining lymph nodes

value: tumor-draining lymph nodes

value: Chemo-naive


title: pat_19_TDRL


title: pat_60_T


title: pat_21_TDRL


title: pat_17_TDRL


title: pat_16_TDRL


title: pat_15_TDRL


title: pat_14_TDRL


title: pat_13_TDRL


title: pat_11_TDRL


title: pat_03_TDRL


title: pat_06_TDRL


title: pat_04_TDRL


title: pat_20_T


title: pat_23_TDRL


title: pat_07_TDRL


title: pat_19_T


title: pat_01_TDRL


title: pat_09_TDRL


title: pat_14_T


title: pat_22_TDRL


title: pat_02_TDRL


title: pat_18_T


title: pat_21_T


title: pat_16_T


title: pat_17_T


title: pat_10_T


title: pat_13_T


title: pat_11_T


title: pat_09_T


title: pat_08_T


title: pat_06_T


title: pat_15_T


title: pat_05_TDRL


title: pat_05_T


title: pat_12_T


title: pat_02_T


title: pat_08_TDRL


title: NF12

city: Aurora

first: Vladimir

last: Amani

state: CO

address: 12800 East 19th Avenue, Building: RC-1 North; Room: P184402A

institute: University of Colorado Anschutz Medical Campus

description:
single_nuclei_features.tsv.gz
single_nuclei_barcodes.tsv.gz
single_nuclei_matrix.mtx.gz
single_nuclei_metadata.csv.gz

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed using CellRanger (10× Genomics) and Seurat 3.1.0.C Cells from individual subpopulations were reanalyzed separately using Harmony alignment [13]. Presto was used for determining differential expression and marker gene identification.
Assembly: GRCh38
Supplementary files format and content: scRNA-seq: UMI counts, barcodes, and genes in sparseMatrix format, and cell metadata in CSV format.
Supplementary files format and content: Spatial Transcriptomics: UMI counts, barcodes, and genes in sparseMatrix format, spot metadata in CSV format, and image file in JPEG format.

source_name: Plexiform Neurofibroma

extract_protocol:
Human NF1-associated plexiform neurofibroma samples were collected from surgeries at Children’s Hospital Colorado (COM-IRB-13-1672). Bulk frozen samples were processed using CHAPS-based buffer as previously described by Slyper et al.  that provided nuclei that were not only high in membrane integrity, but also nuclear yield [12].  An additional wash step was utilized to prevent the presence of cell-free RNA that has been shown to confound downstream snRNA-sequencing. Bright field microscopy was employed to determine yield, quality and membrane integrity of single-nuclei. Single-nuclei generated from PN were analyzed using the 10xGenomics Chromium drop-seq platform. The snRNA-seq was performed at the UC Cancer Center Microarray and Genomics Core, where 4000 nuclei per sample were captured and barcoded to generate cDNA libraries. Libraries will subsequently be sequenced using the Illumina NovaSeq6000 platform at approximately 50,000 reads per nuclei.
Chromium Single Cell V2 and V3 Chemistry Library Kits, Gel Bead & Multiplex Kit and Chip Kit (10X Genomics)

value: Plexiform Neurofibroma


title: NF15


title: NF15_spatial

description:
spatial_features.tsv.gz
spatial_barcodes.tsv.gz
spatial_matrix.mtx.gz
spatial_metadata.csv.gz

data_processing:
library strategy: Spatial Transcriptomics
Sequencing data were processed with Space Ranger (10x genomics, v1.2.1), followed by analysis in R using the Seurat (v4.0.1) tool suite. To ensure the number of genes detected were between 50 and 15000 and less than 50% of UMIs mapped to mitochondrial genes, spots were filtered. SCTransform normalization on each sample and principal component analysis on merged data was conducted, followed by sample integration with Harmony (v1.0) using 30 principal components and theta= 2. UMAP dimension reduction and shared nearest neighbor clustering were conducted on 30 principal components. Clustering results at different resolution settings were evaluated through Clustree (v0.4.3) visualizations. Space Ranger (10× Genomics), Seurat, Harmony and Clustree packages were utilized to cluster, process, filter and integrate newly generated ST data. The Wilcoxon test was used to determine differential gene expression within ST gene clusters. Cell types were defined by (1) Jaccard index calculation of ST cluster marker gene overlap with snRNA-seq markers as conducted previously (2) manual interpretation of ST cluster markers, and (3) ontological analysis using DAVID (Database for Annotation, Visualization, and Integrated Discovery: https://david.ncifcrf.gov; version 6.8). Enrichment of GOterm Direct gene-sets in ST cluster signatures was established. ST cluster overlays on H&E image were produced in the Loupe Browser (10× Genomics).
Assembly: GRCh38
Supplementary files format and content: scRNA-seq: UMI counts, barcodes, and genes in sparseMatrix format, and cell metadata in CSV format.
Supplementary files format and content: Spatial Transcriptomics: UMI counts, barcodes, and genes in sparseMatrix format, spot metadata in CSV format, and image file in JPEG format.

extract_protocol:
OCT embedded frozen primary PN samples were sectioned on a Cryostar NX70 cryostat (Thermo Fisher Scientific) at 10 μm sections and mounted on ST capture slides (Visium, 10× Genomics). The optimal tissue section permeabilization time (18 minutes) was established using test section preliminary analysis. 4 PN sections were then permeabilized and resulting capture sections underwent methanol fixation and were stained with H&E and imaged on an Evos M7000 (ThermoFisher) with brightfield settings. RNA libraries were generated and subsequently sequenced at 70 000 read pairs per spot (Novaseq6000, Illumina) with 151x151 bp runs.
10x Genomics Visium protocol


title: NF13


title: pat_04_T


title: NF12_spatial


title: NF32


title: Kasumi-1_m6A-input

city: Shanghai

first: Jiaying

address: 320 Yue Yang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

data_processing:
Raw reads were filtered by fastp(0.22.0) with default set, clean sequenced reads were alignmented to hg38 by hisat2(2.2.1), suppress unpaired alignments for paired reads,suppress discordant alignments for paired reads.(RNA-seq)
Aligned reads were extracted by featureCounts(2.0.1) with default parameters and normalized by DEseq2(1.32.0).(RNA-seq)
Raw reads were filtered by fastp(0.22.0) with default set, clean sequenced reads were alignmented to hg38 by hisat2(2.2.1), suppress unpaired alignments for paired reads,suppress discordant alignments for paired reads.(RIP-seq)
Peaks were called by macs2(2.2.6) callpeaks algorithm with default set.(RIP-seq)
fastp software were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter，used HISAT2 to map reads to the reference genome Homo sapiens (GRCh38)，Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software
Assembly: hg38 for RNA-seq,RIP-seq and m6A seq.
Supplementary files format and content: normalized files were calculated by DEseq2(1.32.0).(RNA-seq)
Supplementary files format and content: BigWig files were generated by deeptools(3.5.1) bamCoverge and normalized with BPM(Bins Per Million mapped reads)method .(RIP-seq)
Supplementary files format and content: StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM(m6A-seq)
Library strategy: m6A-seq

source_name: Peripheral blood

growth_protocol: Kasumi-1 were cultured in RPMI 1640 Medium (Gibco) supplemented with 10% fetal bovine serum (FBS), 50 U/ml penicillin and 50 μg/ml streptomycin.

extract_protocol:
After infection by  shCtrl and shRBPMS lenti-virus for 48h, Kasumi-1 cells were selected by puromycine for 48h and then harvested for RNA extraction with TRIzol Reagent (Invitrogen).Kasumi-1 cells were treated with RB98# and then harvested for RNA extraction with TRIzol Reagent (Invitrogen) (RNA-seq)
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. (m6A-seq)
Libraries were generated using the NR605-02 V8 RNA-seq Library Prep Kit for Illumina and sequenced with Illumina NovaSeq6000.(RNA-seq)
Libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina and sequenced with Illumina NovaSeq6000.(RIP-seq)
The poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs withE. coliDNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average  size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.(m6A-seq)

value: Peripheral blood

value: myeloblast

value: leukemic cell line with an 8;21 chromosome translocation

value: endogenous m6A


title: NF16_spatial


title: pat_07_T


title: NF09_spatial


title: NF09


title: NF16


title: NF02


title: Kasumi-1_RIP-input

data_processing:
Raw reads were filtered by fastp(0.22.0) with default set, clean sequenced reads were alignmented to hg38 by hisat2(2.2.1), suppress unpaired alignments for paired reads,suppress discordant alignments for paired reads.(RNA-seq)
Aligned reads were extracted by featureCounts(2.0.1) with default parameters and normalized by DEseq2(1.32.0).(RNA-seq)
Raw reads were filtered by fastp(0.22.0) with default set, clean sequenced reads were alignmented to hg38 by hisat2(2.2.1), suppress unpaired alignments for paired reads,suppress discordant alignments for paired reads.(RIP-seq)
Peaks were called by macs2(2.2.6) callpeaks algorithm with default set.(RIP-seq)
fastp software were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter，used HISAT2 to map reads to the reference genome Homo sapiens (GRCh38)，Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software
Assembly: hg38 for RNA-seq,RIP-seq and m6A seq.
Supplementary files format and content: normalized files were calculated by DEseq2(1.32.0).(RNA-seq)
Supplementary files format and content: BigWig files were generated by deeptools(3.5.1) bamCoverge and normalized with BPM(Bins Per Million mapped reads)method .(RIP-seq)
Supplementary files format and content: StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM(m6A-seq)

value: HA RBPMS Kasumi-1

value: exogenous RIP-seq


title: Kasumi-1_m6A-IP


title: Kasumi-1_RIP-IP


title: Kasumi-1_RB98-2

description:
5_2
Kasumi-1_RB98.csv


title: pat_01_T