title: s012: TNBC URMC-099 treated

city: CHICAGO

first: Ajay

last: Rana

state: ILLINOIS

address: 840 SOUTH WOOD ST.

department: SURGERY

institute: UNIV. OF ILLINOIS AT CHICAGO

data_processing:
The 3’RNAseq raw reads were mapped to human GRCh38 reference genome using bwa mem (arXiv:1303.3997 [q-bio.GN]). The raw count for each gene was quantified using featureCounts (PMID: 2422767) against Ensembl genes. We removed 3 outlier genes with much higher expression level than the next gene in several samples.   Batch effect correction was performed using edgeR (PMCID: Pmc3378882, Pmc2796818): batch A: samples 002, 007, 008, 009, 011, 013; batch B: samples 003, 004, 005, 006, 010, 012.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text tables

source_name: TNBC tumor

growth_protocol: The human patient derived xenograft tumor HCI-002 was implanted orthotropic (mammary fat pad) in NSG mice.

extract_protocol:
The treated tumor were removed from the mice after 21 days in a RNAse free work space and used for RNA seq. at the Genomic Core, Research Resourse Centre of Uiv. of illinois at Chicago
Purified RNA was provided to the UIC-Genome Research Core for RNA-seq analysis. Sequencing libraries were prepared using strand-specific QuantSeq 3’ RNAseq kit (Lexogen, FWD, Cat. No. 015). The QuantSeq protocol generates only one fragment per transcript, resulting in accurate gene expression values, and the sequences obtained are close to the 3’ end of the transcripts. Total RNA in the amount of 50 nanograms per sample was used as an input. Library construction was performed according to manufacturer’s protocol with all modifications recommended for samples with low RNA input. In brief, during the first strand cDNA synthesis an oligodT primer containing an Illumina-compatible sequence at its 5’ end was hybridized to mRNA and reverse transcription was performed. After that the RNA template was degraded, and during second strand synthesis the library was converted to dsDNA. Second strand synthesis was initiated by a random primer containing an Illumina-compatible linker sequence at its 5’ end. The  double-stranded  libraries were purified  by  using  magnetic  beads  to  remove  all  reaction  components. Next, the libraries were amplified to add the complete adapter sequences required for cluster generation and to generate sufficient material for quality control and sequencing. A number of PCR amplification cycles was 18, as determined by test qPCR using a small pre-amplification library aliquot for each individual sample. Final amplified libraries were purified, quantified and fragment sizes confirmed to be within 263-318 bp by gel electrophoresis using Agilent 4200 TapeStation (D1000 Screen Tape). Concentration of the final library pool was confirmed by qPCR. Sequencing was performed on NextSeq 500 (Illumina), high-output kit, 1x75 nt single-reads.

treatment_protocol: The HCI002 PDX tumor implanted in NSG mice after reaching tumor volume of 150mm3 were treated with Vehicle control, CEP-1347(1.5mg/kg b.w) and URMC-099(7.0mg/kg b.w) every day for 21 days.

value: TNBC tumor

value: URMC-099 treated


title: human liver sample A1034904

status: Public on Mar 01 2023

type: SRA

city: Durham

first: Anna Mae

last: Diehl

address: 905 S LaSalle St

country: USA

institute: Duke University

library_source: transcriptomic

data_processing:
Sequencing reads were trimmed using TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the mm10 reference genome using STAR
Gene expression counts were generated using HTSeq and DEseq2 was used to perform differential expression analyses (absolute log2FC >= 1 and q <0.05)
Assembly: hg39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: liver cells

extract_protocol:
Total RNAs were isolated from liver tissues or hepatocytes as previously described
Libraries were made with NEBNext Ultra RNA Library Prep Kit from Illumina. Sample qualities were assessed by Agilent RNA Bioanalyzer chip traces before pooled and sequenced with an Illumina HiSeq 2500

tag: cell type

value: liver cells

tag: fibrotic stage


title: human liver sample A1030578


title: human liver sample A1030526


title: s010: TNBC URMC-099 treated

tag: tissue

tag: treatment


title: human liver sample A1034979


title: MLB_R60_rep1

city: Daejeon

first: hanim

last: kim

address: Daehak-ro 291

department: biological science

country: South Korea

institute: KAIST

description:
Supplementary Data Set1_DEG. Xlsx
Supplementary Data Set2_DSG. Xlsx

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to TAIR10 Arabidopsis whole genome using Tophat v2.1.1 with parameters -p 8.
Mapped BAM files were processed with Aspli1.9 R package for the expression and the splicing analysis
Assembly: TAIR10
Supplementary files format and content: DEG analysis result including |log2(Fold-change)| value and FDR value for each genes.
Supplementary files format and content: DSG analysis result including |delta(PSI/PIR)| value and FDR value for each genes.

organism: Arabidopsis thaliana

source_name: Whole Seedling

growth_protocol: Seeds were spotted on 1/2MS plate and cold stratified for 2 days. After 6hr of white light (50 μmol/m2s, 4°C) treatment for germination induction, seeds were kept in either darkness (4°C) or under red-light (19 μmol/m2s, 4°C) for 60hr.

extract_protocol:
Total RNAs were extracted using the Spectrum Plant Total RNA Extraction Kit (Sigma-Aldrich).
RNA libraries were generated and sequenced on the Illumina NextSeq 500 platform.

tag: ecotype background

tag: age

value: Whole Seedling

tag: genotype

value: MLB

value: grown in continuous red light (19 μmol/m2s) for 60hr


title: C57BL/6J-3

type: RNA

city: Wuhan

first: Qiong

last: Yuan

address: Huangjiahu Road 2#

country: China

institute: Wuhan University of Science and Technology

description: C, healthy controls underwent physical examination who were matched with db/db mouse in age and gender

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing the slides, the arrays were scanned by the Agilent Scanner G2505C. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images.

data_processing:
Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.Quantile normalization and subsequent data processing were performed using the R software package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering.
In this research, there were only 792 circRNAs that can be detected in the heart tissue. The rest circRNAs that not be detected were not included.

organism: Mus musculus

label_protocol: The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA Array (8 x 15K, Arraystar).

growth_protocol: The mouse were fed until age 3 month.

extract_protocol: Total RNAs were digested with RNAse R (Epicentre, Inc.) to remove linear RNAs and enrich circRNAs. Then, the enriched circRNAs were amplified and transcribed into fluorescent cRNA by using a random priming method

treatment_protocol: Total RNA from each heart tissue sample was quantified using the NanoDrop ND-1000 system.

value: heart

tag: Sex

value: Male

tag: strain

tag: disease state

value: healthy control


title: Healthy_5d_RTD-1_Replicate_4

city: Los Angeles

first: Vasu

last: Punj

state: CA

address: Biggy Street

institute: USC

data_processing:
Illumina Casava1.7 software was used for basecalling.
Reads were trimmed for quality score and adaptor sequences were also removed. The high-quality reads (between 30-45 million) that passed quality filters were aligned to the rat reference genome (Rnor6) using HISAT aligner, allowing up to two mismatches in conjunction with the gene model from Ensemble 972. Reads were quantitated by counting the number of reads across exons.
A  gene was designated as "differentially expressed", if it  pass the FDR adjusted p < 0.05 in DEseq ( Anders and Huber 2010, Genome Biol., 11, R106 ) as well as in null model of hypothesis (Kani et al (2017, Mol. Cancer Ther., 16, 1645)
Genome_build: Rnor6

organism: Rattus norvegicus

source_name: Synovial tissue

growth_protocol: For pristane induced arthritis model in rat, Arthritis was induced in 6-8 week old female DA/OlaHsd rats by injection with 250 μl of Pristane and the disease was allowed to proceed untill a score of at least 3 was attained in each of the rear limbs and the day after was considered as time T=0.

extract_protocol:
Synovial tissue was isolated from rats and RNA was isolated using Zymo Mini RNA purification kit (ZymoResearch, Irvine, CA)  according to the manufacturer's instructions.
Strand specific library preparation was carried out using Clonetech SMARTer Stranded Total RNA-Seq (Pico) Kit.  Libraries were generated from total RNA for sequencing. Sequencing was performed on Illumina Nextseq500 with 1X 75 single end reads.

treatment_protocol: Rats were treated with either saline or 5 mg/kg RTD-1 in saline by subcutaneous injections for 1, 3 or 5 days.

value: Synovial tissue

tag: tag

value: Healthy_RTD_Treated-5 Day

value: healthy


title: Healthy_5d_RTD-1_Replicate_5


title: C57BL/6J-2


title: db/db-3

description: d, db/db mouse which is high glucose in the blood plasma

source_name: db/db mouse born at 3 month

value: db/db

value: model for type 2 diabetes


title: db/db-1


title: s009: TNBC URMC-099 treated


title: Healthy_5d_RTD-1_Replicate_3


title: Healthy_5d_RTD-1_Replicate_2


title: C57BL/6J-1


title: human liver sample A1029998


title: Healthy_5d_RTD-1_Replicate_1


title: human liver sample A1029942


title: human liver sample A1026809


title: Healthy_3d_RTD-1_Replicate_5

value: Healthy_RTD_Treated-3 Day


title: s008: TNBC CEP-1347 treated

value: CEP-1347 treated


title: s007: TNBC CEP-1347 treated


title: db/db-2


title: s011: TNBC URMC-099 treated


title: Healthy_3d_RTD-1_Replicate_4


title: Healthy_3d_RTD-1_Replicate_1


title: Healthy_3d_RTD-1_Replicate_3


title: Healthy_3d_RTD-1_Replicate_2


title: s005: TNBC CEP-1347 treated


title: human liver sample A1026810


title: PIA_5d_Saline_Replicate_7

value: Diseases_SalineTreated-5 Day

value: pristane induced arthritis (PIA)


title: PIA_5d_Saline_Replicate_6


title: s004: TNBC Vehicle Control

value: TNBC tumor

value: Vehicle Control


title: PIA_3d_Saline_Replicate_7

value: Diseases_SalineTreated-3 Day


title: s003: TNBC Vehicle Control


title: human liver sample A1026812

value: liver cells


title: human liver sample A1034964


title: PIA_3d_Saline_Replicate_8


title: PIA_3d_Saline_Replicate_6


title: s002: TNBC Vehicle Control


title: human liver sample A1030514


title: s001: TNBC Vehicle Control


title: s006: TNBC CEP-1347 treated


title: PIA_5d_Saline_Replicate_3


title: human liver sample A2010455


title: PIA_3d_Saline_Replicate_5


title: human liver sample A1026795


title: PIA_5d_Saline_Replicate_5


title: RNA_480_CD8_N

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the hg38 genome using STAR v.2.5.3 and the UCSC KnownGene reference transcriptome
Reads per kilobase per million (Rpkm) normalized gene expression counts were derived by analyzing coverage across all exons that fall within unique ENTREZ genes using the GenomicRanges package
Detected genes are defined as any gene with at least 3 rpm normalized expression counts in all replicates of any one sample group
Genome_build: hg38

molecule: polyA RNA

source_name: CD8 naive T cell

extract_protocol:
One thousand cells were sorted directly into RLT buffer (79216; Qiagen) containing 1% 2-Mercaptoethanol. RNA was isolated using the Quick-RNA Microprep kit (Zymo Research; R1050).
The SMART-Seq v4 Ultra Low Input RNA Kit (634894; Takara Bio) was used for synthesis of cRNA from isolated RNA, and 400 pg of cDNA was used as input for the NexteraXT kit (Illumina).

treatment_protocol: Collected cells were separated for either immediate flow sorting (resting cells) or incubated for 42-48 hours with anti-CD3/CD28 beads for ex-vivo stimulation. 1e6 cells were added to cell suspensions in a 2:1 bead-to-cell ratio before being removed prior to flow staining

tag: donor

value: blood

tag: stimulation

tag: sorting markers


title: Cytomatrix fraction 4, replicate [Ribo-seq]

city: Houston

first: Tattym

last: Shaiken

state: TX

address: One Baylor Plaza

department: Medicine

institute: Baylor College of Medicine

data_processing:
Library strategy: Ribo-seq
Fastqc (v0.11.8) was used for quality control and fastq files were trimmed using Trimmomatic (v0.38)
Bowtie aligner (v1.3.0) was used to remove rRNA sequences from the trimmed fastq files for only the Ribo-seq experiment
rRNA sequences used in the rRNA depletion step were downloaded from ensembl biomart
STAR aligner (v2.7.6a) was used to align and quantify gene expression for the trimmed and rRNA depleted Ribo-seq fastq files and the trimmed bulk RNA-seq fastq files
Features were quantified using featureCounts and the Gencode gene model
Assembly: GRCh38 p13 v35
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: HCT-15 cell

growth_protocol: HCT-15 cells were grown in DMEM enriched with 10% FBS

extract_protocol:
We extracted the cytosol with Buffer A (40 mM HEPES pH 7.4, 120 mM KCl, 0.5% Glycerol, and 0.5% NP-40. The CMX was isolated with buffer B (10 mM Tris-HCl pH 7.5, 1.5 mM KCl, 0.5% Triton X-100, 0.5% sodium deoxycholate, 2.5 mM MgCl2, 0.2 M LiCl) . Total RNA was isolated from the cytosol and CMX using RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCT-15 cells were  treated with 500 nM of pp242 for 24 hours

value: TOR-KI, pp242

tag: treatment time

value: 24 hours

tag: extraction buffer

value: Buffer B


title: PIA_5d_Saline_Replicate_2

value: Synovial tissue


title: PIA_5d_Saline_Replicate_1


title: human liver sample A1026750


title: RNA_398_CD8_N


title: human liver sample A1026753


title: PIA_5d_Saline_Replicate_8


title: PIA_3d_Saline_Replicate_3


title: RNA_253_CD8_N


title: human liver sample A1026733


title: PIA_3d_Saline_Replicate_1


title: PIA_3d_Saline_Replicate_2


title: human liver sample A1026718


title: PIA_1d_Saline_Replicate_3


title: PIA_1d_Saline_Replicate_2


title: RNA_480_CD8_NStim

source_name: CD8 naive T cell ex-vivo stimulated with anti-CD3/CD28 beads

value: anti-CD3/CD28 beads


title: PIA_1d_Saline_Replicate_4


title: PIA_5d_Saline_Replicate_4


title: human liver sample A1026713


title: PIA_5d_RTD-1_Replicate_8

value: Diseases_RTD_Treated-5 Day


title: RNA_398_CD8_NStim


title: PIA_1d_Saline_Replicate_1


title: human liver sample A1026711


title: PIA_5d_RTD-1_Replicate_5


title: PIA_3d_Saline_Replicate_4


title: RNA_253_CD8_NStim


title: PIA_5d_RTD-1_Replicate_6


title: PIA_3d_RTD-1_Replicate_8

value: Diseases_RTD_Treated-3 Day


title: RNA_125_CD8_NStim


title: PIA_3d_RTD-1_Replicate_7


title: PIA_5d_RTD-1_Replicate_7


title: PIA_3d_RTD-1_Replicate_6


title: human liver sample A1026708

value: Control


title: RNA_480_CD8_EMRA

source_name: CD8 EMRA T cell


title: human liver sample A1026706


title: RNA_125_CD8_N


title: PIA_3d_RTD-1_Replicate_5


title: PIA_5d_RTD-1_Replicate_4


title: RNA_253_CD8_EMRA


title: PIA_5d_RTD-1_Replicate_3


title: RNA_398_CD8_EMRA


title: human liver sample A1026700


title: RNA_125_CD8_EMRA


title: PIA_5d_RTD-1_Replicate_2


title: human liver sample A1026694


title: human liver sample A1026712


title: PIA_3d_RTD-1_Replicate_4


title: PIA_3d_RTD-1_Replicate_3


title: PIA_3d_RTD-1_Replicate_2


title: wt.P7.3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-Seq data from the first experiment to study effect of Nutlin in individuals with P47S and Y107H was aligned using STAR against hg19 version of human genome and RSEM was used for estimation of read counts and FPKM values using Ensemble transcriptome information
For the RNA-Seq experiment to identify a p53 hypomorph gene signature alignment was done using bowtie2 against hg19 version of human genome and Ensemble transcriptome information followed by RSEM to estimate read counts on gene level.
Assembly: hg19
Supplementary files format and content: RSEM raw gene counts

source_name: LCL

growth_protocol: LCLs were cultured in RPMI 1640 supplemented with 15% fetal bovine serum, 1% penicillin/streptomycin, and 2mM L-glutamine

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit (Qiagen) and on-column DNase digestions, according to the manufacturer’s protocol
Libraries were prepared using Quantseq 3’-mRNA kit (Lexogen) and sequencing was performed on Illumina Nextseq500 on high-output mode in a 75 bp single end run

treatment_protocol: Cells were treated with 10μM Nutlin-3a (Sigma-Aldrich)

value: LCL

tag: group

value: classifier

tag: set

value: training

tag: batch

tag: unique patient_id

tag: hypomorph

value: wt

value: untreated

tag: replicate


title: wt.P7.2

tag: cell type

tag: treatment


title: PIA_1d_RTD-1_Replicate_3

tag: tissue

value: pristane induced arthritis (PIA)


title: PIA_3d_RTD-1_Replicate_1


title: human liver sample A1026690

tag: fibrotic stage


title: human liver sample A1026691


title: wt.P7.1


title: PIA_1d_RTD-1_Replicate_4

tag: disease state


title: PIA_1d_RTD-1_Replicate_1

tag: tag


title: PIA_1d_RTD-1_Replicate_2


title: human liver sample A1026688


title: wt.P6.3


title: Naive_Replicate_3

value: naïve


title: PIA_5d_RTD-1_Replicate_1


title: Naive_Replicate_2


title: Naive_Replicate_1


title: wt.P6.2


title: human liver sample A1026686

value: liver cells


title: wt.P6.1


title: PIA_Replicate_4

value: Diseased


title: human liver sample A1026693


title: human liver sample A1026670


title: PIA_Replicate_3


title: PIA_Replicate_2


title: human liver sample A1026692


title: human liver sample A1026685


title: PIA_Replicate_1


title: wt.P5.1


title: human liver sample A1026657


title: Naive_Replicate_4


title: human liver sample A2002746


title: Caenorhabditis elegans-high glucose induce with naringin-rep1 [miRNA-seq]

city: Zhengzhou

first: Panpan

last: Wang

address: 郑州市高新区科学大道100号郑州大学

department: College of Public Health

institute: 郑州大学

data_processing:
After quality control by Solexa CHASTITY and discarding 3’ adapter and short fragments (＜17nt) in reads by Cutadapt (1.14), the mirdeep2 (0.0.8) was used to compared the trimmed data of miRNA with reference genome and  quantify its expression. The count per million value of miRNA was applied to conduct differentially expressed analysis using R package “edgeR”.
Assembly: WBcel235
Supplementary files format and content: tab-delimited text files include count values for each Sample.

organism: Caenorhabditis elegans

source_name: whole individual

growth_protocol: Wild type N2 nematodes grew in standard NGM medium.

extract_protocol:
For per 50-100mg tissue sample, 1ml TRI REAGENT was added and an electric homogenizer used to mix it. After that, the sample was incubated for 5 minutes at 15 to 30℃ to completely dissociate the nucleic acid protein complex. Add 0.2ml chloroform to 0.2ml chloroform was added in per 1ml mixture, and close the tube cap tightly. After shaking the tube vigorously by hand for 15 seconds, it was incubated at 15 to 30℃ for 2 to 3 minutes. Centrifuge at 12000xg for 15 minutes at 4℃. After that, the mixture will be divided into the lower red phenol-chloroform phase, the middle layer and the upper colorless water phase. The RNA is all distributed in the water phase. The volume of the water phase is approximately 60% of the TRI REAGENT reagent added during the homogenization. Transfer the aqueous phase to a new centrifuge tube. The aqueous phase is mixed with 0.5ml isopropanol to precipitate the RNA. After mixing, it was incubated at 15 to 30°C for 10 minutes, and centrifuged at 12000xg at 4℃ for 10 minutes. Remove the supernatant, and add at least 1ml 75% ethanol to every 1ml mixture to wash the RNA precipitate. After shaking, centrifuge at 7500xg at 4℃ for 5 minutes. Remove the ethanol solution and dry the RNA pellet in the air for 5-10 minutes. When dissolving RNA, add RNase-free water and pipe repeatedly with a gun several times, and then incubate at 55 to 60°C for 10 minutes. The obtained RNA solution was stored at -70℃.
1~2 μg total RNA of C. elegans was roughly extracted in each sample and prepared for library construction. The integrity of the total RNA of the samples was determined by agarose gel electrophoresis, and quantification and further quality control were performed using NanoDrop® (ND-1000, Thermo-Fisher, USA). The total RNA was firstly enriched by NEB Next® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Netherlands); and then,the library of miRNA was constructed using Multiplex Small RNA Library Prep Set for Illumina (E7508L, New England Biolabs, Netherlands). After degrading to ssDNA, it was captured in Illumina flow cell and conducted in situ amplification. Then, it was sequenced on the platform of Illumina NextSeq 500 (50 cycles).

treatment_protocol: Naringin was dissolved to 25μM, and the L4-larvae of C. elegans was exposed to 2% glucose, 2% glucose with DMSO and 2% glucose with naringin mixed with NGM and then added with OP50 at 20 °C.

tag: strain

tag: genotype

value: wild type

value: high glucose induce with naringin


title: human liver sample A1026656


title: Caenorhabditis elegans-high glucose induce with naringin-rep2 [miRNA-seq]

address: 郑州市高新区科学大道100号郑州大学


title: Caenorhabditis elegans-high glucose induce with DMSO-rep3 [miRNA-seq]

address: 郑州市高新区科学大道100号郑州大学

value: high glucose induce with DMSO


title: Caenorhabditis elegans-high glucose induce with DMSO-rep2 [miRNA-seq]

address: 郑州市高新区科学大道100号郑州大学


title: Caenorhabditis elegans-high glucose induce with naringin-rep3 [miRNA-seq]

address: 郑州市高新区科学大道100号郑州大学


title: wt.P4.2


title: human liver sample A1026652


title: Caenorhabditis elegans-high glucose induce with DMSO-rep1 [miRNA-seq]

address: 郑州市高新区科学大道100号郑州大学


title: wt.P4.1


title: Caenorhabditis elegans-high glucose induce-rep2 [miRNA-seq]

address: 郑州市高新区科学大道100号郑州大学

value: high glucose induce


title: Caenorhabditis elegans-high glucose induce-rep3 [miRNA-seq]

address: 郑州市高新区科学大道100号郑州大学


title: Caenorhabditis elegans-control-rep3 [miRNA-seq]

address: 郑州市高新区科学大道100号郑州大学


title: Caenorhabditis elegans-high glucose induce-rep1 [miRNA-seq]

address: 郑州市高新区科学大道100号郑州大学


title: Caenorhabditis elegans-control-rep2 [miRNA-seq]

address: 郑州市高新区科学大道100号郑州大学


title: wt.P3.3


title: human liver sample A1026676


title: wt.P3.2


title: wt.P5.3


title: human liver sample A1026641


title: wt.P5.2


title: wt.P4.3


title: human liver sample A1026645


title: wt.P3.1


title: human liver sample A1025470


title: H6

city: Guangzhou

first: Wenchao

last: Wu

state: Guangdong

address: 651 Dongfeng Road East, Yuexiu District,

institute: Sun Yat-sen University Cancer Center

description: gene.csv

data_processing:
Sequence reads were filtered with SOAPnuke software to remove read with adapters, unknown bases, and low-quality reads.
Genome mapping of filtered reads to reference genome GRCh38 was performed using HISAT2 and Bowtie2 software.
Raw data of RNA-seq were normalized and processed using R package DEseq2
Assembly: GRCh38
Supplementary files format and content: gene.csv include raw count values for all the samples

source_name: cell line

extract_protocol:
RNA extraction and sequencing were performed by NuoBiotech (Guangzhou) Co., Ltd, China.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations.

value: cell line

tag: cell line

value: Cutaneous T cell lymphoma


title: wt.P2.6


title: H2

description: gene.csv

value: Vehicle


title: H5

description: gene.csv


title: wt.P2.5


title: human liver sample A1025468


title: ZZH20220826-0, scRNAseq

first: Kuanhong

last: Xu

address: 1 Zhengdian Gold Industrial Park Road, Jiangxia District, Wuhan, China.

institute: Wuhan Institute of Biological Products

description: Singleron Matrix

library_source: transcriptomic single cell

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline.
Raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17 to trim poly-A tail and adapter sequences.
Cell barcode and UMI were extracted. After that, we used STAR v2.6.1a to map reads to the reference genome GRCh38.UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 software, and used to generate expression matrix files for subsequent analysis.
After visualizing the expression level of XXX cell Marker genes using FeaturePlot in the Seurat package v3.1.2, the result indicated substantial ambient RNA contamination. To solve this situation, ambient RNA removal was then performed using the decontX algorithm in the celda package v.1.3.8 . The decontX algorithm assumes that there are K cell populations and uses Bayesian variational inference to infer the ambient RNA contamination as a weighted combination of the XXX cell population distributions. This algorithm required the raw UMI counts and several cell populations calculated using FindClusters by Seurat package v3.1.2 as input, and the therefore derive a decontaminated count matrix from the raw data. A default random seed was used for reproducibility throughout the entire analysis.
Assembly: GRCh38
Supplementary files format and content: matrix files

source_name: blood

extract_protocol:
The PBMCs were isolated by density gradient centrifugation using Ficoll-Paque Plus medium (GE Healthcare) and washed with Ca/Mg-free PBS. To remove the red blood cells, 2 mL GEXSCOPE® red blood cell lysis buﬀer (RCLB, Singleron) was added at 25°C for 10 minutes. The solution was then centrifuged at 500 × g for 5 min and suspended in PBS. The blood samples were centrifuged at 400g for 5 min at 4°C, and the supernatant was discarded. After removed red blood cells, PBMCs were isolated by centrifuged at 400g for 10min at 4°C. The supernatant was discarded and the PBMCs were resuspended by phosphate buffered saline to obtain a single-cell suspension
Single-cell suspensions (2×105 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) (Ref). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: blood

value: PBMC

tag: time

value: preoperative

value: untreated control


title: ZZH20220901-7, scRNAseq

description: Singleron Matrix

value: treated with Porcine anti-human lymphocyte immunoglobulin


title: Radiorsensitive-3, 19T

city: Seoul

first: Kwang Seok

last: Kim

address: 75 Nowon-gil, Nowon-gu

department: Division of Fusion Radiology Research

institute: Korea Institute of Radiological and Medical Sciences

data_processing:
The data were normalised using quantile normalisation with IlluminaGUI in R
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include read count, FPKM and TPM values for each Sample

source_name: organoids

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

value: radio-sensitive

tag: disease

value: Locally Advanced Rectal Cancer

value: organoids


title: Radiorsensitive-2, 15T

tag: group


title: wt.P2.4

value: LCL

value: classifier

tag: set

value: training

value: wt

value: untreated


title: human liver sample A1025430

value: liver cells

value: Control


title: Caenorhabditis elegans-control-rep1 [miRNA-seq]

address: 郑州市高新区科学大道100号郑州大学

value: wild type


title: Radiorsensitive-1, 12T


title: Radioresistant-2, 18T

value: radio-resistant


title: Radioresistant-3, 22T


title: human liver sample A1025429


title: Y107H.P1.3

tag: batch


title: human liver sample A1034661


title: XAF1-ko+VSV - ATAC-seq

city: Beijing

first: Ming

last: Kuang

address: Xueyuan Road 38 #, Haidian District

institute: Peking University

description: XAF1 knockout HT29 cells were collected for total RNA extraction with VSV infection for 6h.

library_source: genomic

data_processing:
The raw data was generated by Illumina PE150 with 10G bases and 30M reads for each ATAC-seq sample.
Then the filtered reads were aligned and quantified to according genome, such as hg39, using aligner bowtie2, which would output the SAM or BAM files.
Then samtools were used to sort and index the SAM/BAM files. Peak calling was completed with Genrich, which produced the peak files with bed format for each sample.
In the downstream of ATAC-seq, the reads fall in peaks gap were normalized by RPKM firstly. The treatment samples were compared to their according Input sample data using bamCompare tool with the parameter firstly.
Then the R package ChIPseeker was used to annotate the identified peak files and the peaks were visualized by IGV software.
Assembly: hg19
Supplementary files format and content: bw file for Peak; csv file format for annotation

molecule: genomic DNA

growth_protocol: HT29 Cells were cultured in 1640 medium supplemented with 10% FBS (Gibco) and 100U/ml Penicillin-Streptomycin in a humidified incubator at 37 °C with 5% CO2..

extract_protocol:
Pellet 50,000 viable MSCs at 500 RCF at 4°C for 5 min. Aspirate all supernatant. Add 50 μL cold ATAC-Resuspension Buffer (RSB) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin into the cell pellet and pipette up and down 3 times. Incubate on ice for 3 minutes. Wash out lysis with 1 mL cold ATAC-RSB containing 0.1% Tween-20 but no NP40 or digitonin and invert tube 3 times to mix. Pellet nuclei at 500 RCF for 10 min at 4°C.
Aspirate all supernatant. Resuspend cell pellet in 50 μL of transposition mixture (25 μL 2x TD buffer, 2.5 μL transposase (100 nM final), 16.5 μL PBS, 0.5 μL 1% digitonin, 0.5 μL 10% Tween-20, 5 μL H2O) by pipetting up and down 6 times. Incubate reaction at 37°C for 30 minutes. Afterward, the DNA was purified with Magen DNA purify kit and amplified with primers containing barcodes by using the TruePrep DNA Library Prep Kit (TD501-01).

treatment_protocol: HT29 Cells were infected by VSV for 0 or 6 hours

value: Human epithelial cells

value: XAF1 knockout

value: VSV infection


title: Y107H.P1.2

tag: unique patient_id


title: human liver sample A1025354


title: Radioresistant-1, 14T


title: Y107H.P1.1

tag: hypomorph


title: Vec - ATAC-seq

description: HT29 cells were collected for total RNA extraction without VSV infection.

value: WT

value: no treatment


title: R273H.P1.3

tag: replicate


title: Vec+VSV - ATAC-seq

description: HT29 cells were collected for total RNA extraction with VSV infection for 6h.

tag: cell type


title: human liver sample A1030521


title: human liver sample A1025249


title: 280M

city: torrance

first: Omid

last: Khorram

address: 1124  w carson st

institute: The lundquist Institute at UCLA medical center

data_processing:
FastQC was used to check quality of reads
Hisat2 and featureCounts was used to align and count reads.
DeSeq2 was used for differential expression analysis.
Assembly: hg18
Supplementary files format and content: normalized read counts for DESeq2

source_name: Myometrium

extract_protocol:
TRIzol
mRNA-seq was performed by Novogene Corporation Inc.

value: Myometrium

tag: race

value: Caucasian


title: H1

description: gene.csv

tag: tissue

value: cell line

value: Cutaneous T cell lymphoma

tag: treatment

value: Vehicle


title: 280L

source_name: Leiomyoma

value: Leiomyoma

value: Mutant


title: 221M

value: African American


title: R273H.P1.1

value: LCL

value: classifier

value: training

value: untreated


title: 221L


title: 214L


title: human liver sample A1025243

value: liver cells

tag: fibrotic stage


title: human liver sample A1025239


title: R273H.P1.2


title: 233L


title: human liver sample A1025237


title: Y220H.P1.2


title: 214M


title: 263L


title: XAF1-ko - ATAC-seq

description: XAF1 knockout HT29 cells were collected for total RNA extraction without VSV infection.

value: Human epithelial cells

value: XAF1 knockout


title: human liver sample A1026819


title: 263M

value: WT


title: 339L


title: human liver sample A1025229

value: Control


title: Y220H.P1.1


title: 233M

value: Myometrium


title: R175C.P1.3


title: R175C.P1.2


title: 121M


title: human liver sample A1025440


title: R175C.P1.1


title: Y220H.P1.3


title: 121L


title: 131M


title: human liver sample A1025442


title: human liver sample A1025443


title: 90M


title: human liver sample A1025215


title: 295L


title: 295M


title: P47S.P5.3


title: 259L


title: 131L


title: P47S.P5.2


title: human liver sample A1025217


title: 259M


title: 339M

value: Caucasian


title: 8L


title: P47S.P5.1


title: P47S.P4.3


title: 32L


title: 8M


title: human liver sample A2001322


title: 90L


title: 32M


title: P47S.P4.2


title: 289L


title: 276L


title: P47S.P4.1


title: human liver sample A1024850


title: human liver sample A1024849


title: 276M


title: P47S.P3.3


title: 228L


title: P47S.P3.2


title: human liver sample A1024851


title: 228M


title: human liver sample A1024846


title: human liver sample A2001294


title: human liver sample A1024842


title: 293L


title: 314L


title: P47S.P3.1


title: 293M


title: 296L


title: 296M


title: P47S.P2.3


title: human liver sample A1024825


title: human liver sample A1024832


title: 143B cells, siCBX3, Day2, rep1

city: Shaoxing, China

first: Di

last: Qiao

address: Shaoxing , Zhejiang, China.

institute: School of Medicine, Shaoxing University

description: Si    2-1

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36)
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
Trimmed sequence reads were mapped to the reference genome of Homo sapiens from GRCh38 using STAR software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Assembly: GRCh38
Supplementary files format and content: excel spreadsheet file include reads counts values for all Sample
Supplementary files format and content: excel spreadsheet file include RPKM values for all Sample

growth_protocol: Cell lines were grown in DMEM supplemented with 10% fetal bovine serum (Gibco, Grand Island, NY, USA), 100 units of penicillin per milliliter, and 100 units of streptomycin per milliliter (Invitrogen, Carlsbad, CA, USA).

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNA from 143B cells at day 2 post-transfection.
Following the manufacturer's instructions, 2 g of total RNAs were utilized for stranded RNA sequencing library preparation using the KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog No. DR08502, Wuhan Seqhealth Co., Ltd., China).

treatment_protocol: Lipofectamine RNAiMAX Transfection Reagent (Invitrogen), Opti-MEM™ Reduced Serum Medium (Gibco, Grand Island, NY, USA), and siRNA were mixed to transfect osteosarcoma cell lines following the manufacturer’s protocol.

value: Osteosarcoma cell line

value: CBX3 knockdown


title: P47S.P2.2


title: 143B cells, siCBX3, Day2, rep2

description: Si    2-2


title: 143B cells, siNC, Day2, rep2

description: NC  1-2


title: 289M


title: human liver sample A1024817


title: 314M


title: P47S.P1.3


title: 143B cells, siNC, Day2, rep1

description: NC  1-1


title: P47S.P1.2


title: human liver sample A1024823


title: human liver sample A1024803


title: Patient31_Pre_WES

city: Grand Rapids

first: Hyo Sik

last: Jang

state: Michigan

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Whole Exome Sequencing

data_processing:
WES reads were trimmed with Trimmomatic to remove adapter sequences and aligned to the hg38 genome using bwa (bwa mem) . Somatic SNV and indel calling was performed using Mutect2 from GATK29 in Tumor-Only mode.
The reads from total RNA-seq libraries were trimmed for adapter sequences and aligned to the hg38 genome using HISAT2 with proper capture of RNA strand orientation. The bam files were normalized into CPM bedgraph files using deeptools "bamCoverage" command.
Assembly: hg38
Supplementary files format and content: Total RNAseq are processed and presented as CPM normalized bedgraph files. For WES, Mutation Annotation Format files are provided.

source_name: Tumor needle biospy

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen) followed by on-column DNase I digestion according to the manufacturer’s protocol. Genomic DNAs were purified from FFPE samples using AllPrep DNA/RNA FFPE kit (Qiagen).
Sequencing libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche, Cat# 08098140702). Whole exome sequencing libraries were constructed with Sure Select Human All Exon v6 (Agilent) and the Sure Select XT2 library prep kits (Agilent).
Total RNA-seq were sequenced as 50 bp paired-end. WES were sequenced as 75 bp or 150 bp paired-end

treatment_protocol: Clinical trial outlined in manuscript

tag: treatment timepoint

value: Pre-treatment


title: Patient28_Post_WES

description: Whole Exome Sequencing

value: Post-treatment


title: Patient28_Pre_WES

description: Whole Exome Sequencing


title: Patient27_Pre_WES

description: Whole Exome Sequencing


title: Patient24_Post_WES

description: Whole Exome Sequencing


title: Patient31_Post_WES

description: Whole Exome Sequencing


title: Patient25_Pre_WES

description: Whole Exome Sequencing


title: P47S.P1.1


title: human liver sample A1026673


title: P47S.P2.1


title: Patient21_Post_WES

description: Whole Exome Sequencing


title: Patient24_Pre_WES

description: Whole Exome Sequencing


title: Patient21_Pre_WES

description: Whole Exome Sequencing


title: wt.P2.2

value: wt


title: Patient20_Pre_WES

description: Whole Exome Sequencing


title: wt.P2.1


title: human liver sample A1020871


title: Y.nut.24.mut.3

value: nutlin


title: wt.P2.3

value: LCL


title: human liver sample A1024771


title: human liver sample A1024799


title: human liver sample A1025232


title: Patient19_Pre_WES

description: Whole Exome Sequencing


title: Patient18_Pre_WES

description: Whole Exome Sequencing


title: Patient16_Pre_WES

description: Whole Exome Sequencing


title: Y.nut.24.mut.2


title: human liver sample A1020862


title: human liver sample A1020857


title: Patient23_Pre_WES

description: Whole Exome Sequencing


title: human liver sample A1020854


title: Y.nut.24.mut.1


title: Patient7_Post_WES

description: Whole Exome Sequencing


title: Patient14_Pre_WES

description: Whole Exome Sequencing


title: Patient12_Pre_WES

description: Whole Exome Sequencing


title: Patient14_Post_WES

description: Whole Exome Sequencing


title: Y.unt.mut.2


title: Patient7_Pre_WES

description: Whole Exome Sequencing


title: human liver sample A1034654


title: human liver sample A1020840


title: Patient3_Post_WES

description: Whole Exome Sequencing


title: Y.unt.mut.1


title: Patient4_Pre_WES

description: Whole Exome Sequencing


title: Patient4_Post_WES

description: Whole Exome Sequencing


title: human liver sample A1020837


title: Patient3_Pre_WES

description: Whole Exome Sequencing


title: Patient2_Post_WES

description: Whole Exome Sequencing


title: Patient2_Pre_WES

description: Whole Exome Sequencing


title: Y.nut.24.wt.2


title: human liver sample A1020834


title: Patient14_EoT_WES

description: Whole Exome Sequencing

value: End-of-Treatment


title: human liver sample A1020787


title: Y.nut.24.wt.1


title: Patient1_Post_WES

description: Whole Exome Sequencing


title: Patient31_Pre_RNA

description: RNA-seq


title: Patient1_Pre_WES

description: Whole Exome Sequencing


title: Y.unt.mut.3


title: Y.unt.wt.3


title: human liver sample A1017423


title: Patient28_Post_RNA

description: RNA-seq


title: Y.nut.24.wt.3


title: Patient27_Pre_RNA

description: RNA-seq


title: human liver sample A1017408


title: Y.unt.wt.1


title: Patient24_Post_RNA

description: RNA-seq


title: Patient21_Post_RNA

description: RNA-seq


title: human liver sample A1017390


title: human liver sample A1017338


title: Patient24_Pre_RNA

description: RNA-seq


title: Y.unt.wt.2


title: human liver sample A1002594


title: Patient23_Pre_RNA

description: RNA-seq


title: P.nut.24.mut.3


title: P.nut.24.mut.2


title: Patient21_Pre_RNA

description: RNA-seq


title: P.nut.24.mut.1


title: human liver sample A1002590


title: Patient19_Pre_RNA

description: RNA-seq


title: P.unt.mut.3


title: human liver sample A1002580


title: Patient14_Post_RNA

description: RNA-seq


title: Patient16_Pre_RNA

description: RNA-seq


title: Patient20_Pre_RNA

description: RNA-seq


title: P.unt.mut.2


title: Patient25_Pre_RNA

description: RNA-seq


title: Patient14_Pre_RNA

description: RNA-seq


title: human liver sample A1002571


title: Patient4_Post_RNA

description: RNA-seq


title: human liver sample A1002568


title: Patient28_Pre_RNA

description: RNA-seq


title: P.unt.mut.1


title: Patient4_Pre_RNA

description: RNA-seq


title: P.nut.24.wt.3


title: Patient1_Post_RNA

description: RNA-seq


title: Patient3_Pre_RNA

description: RNA-seq


title: human liver sample A1002566


title: P.nut.24.wt.1


title: human liver sample A1002546


title: human liver sample A1002542


title: Patient18_Pre_RNA

description: RNA-seq


title: P.nut.24.wt.2


title: AP4KO_p53KO__DOX_2

city: Munich

first: Markus

last: Kaller

address: Thalkirchner Strasse 36

department: Institute of Pathology

country: Germany

institute: Ludwig-Maximilians-University Munich

data_processing:
alignment : RNA-Seq FASTQ files were processed using the RNA-Seq module implemented in the CLC Genomics Workbench v20.0.2 software (Qiagen Bioinformatics) and mapped to the GRCh38/hg38 human reference genome and its associated gene and transcript annotation (ENSEMBL) using the settings mismatch cost = 2, insertion cost = 2, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8
expression : RNA-Seq FASTQ files were processed using the RNA-Seq module implemented in the CLC Genomics Workbench v20.0.2 software (Qiagen Bioinformatics) and mapped to the GRCh38/hg38 human reference genome and its associated gene and transcript annotation (ENSEMBL) using the settings mismatch cost = 2, insertion cost = 2, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include raw gene counts for each sample

source_name: breast

growth_protocol: The human breast cancer cell line MCF-7 and its derivates generated here were grown in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS) (Invitrogen), 100 units/ml penicillin and 0.1 mg/ml streptomycin

extract_protocol:
Total RNA from MCF-7/pRTR-c-MYC cells was isolated using the High Pure RNA Isolation Kit (Roche) with an on-column DNase digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were pre-treated with ICI for 72 hours. Ectopic expression of c-MYC was induced with DOX for 48 hours in the presence of ICI.

value: breast

value: DOX


title: Patient3_Post_RNA

description: RNA-seq


title: P.unt.wt.3

value: untreated


title: AP4KO_p53KO__control_2

value: control


title: human liver sample A1034985

source_name: liver cells

value: liver cells


title: P.unt.wt.2


title: human liver sample A1002540


title: Patient1_Pre_RNA

description: RNA-seq


title: AP4KO_p53KO__control_1


title: p53_DOX_3


title: p53_DOX_2


title: human liver sample A1002534


title: P.unt.wt.1


title: human liver sample A1002531


title: p53_DOX_1


title: TRV:GhSP-GhPAN biol rep2

city: Denton

first: Roisin

middle: C

last: McGarry

address: 1511 West Sycamore

department: Dept. of Biological Sciences, BioDiscovery Institute

institute: University of North Texas

description: 75 cycles

data_processing:
Read quality was determined using FASTQC in the CyVerse Discovery Environment (Goff et al., 2011), with median quality scores ≥ 32 for 75 bp reads. The reads generated from four lanes for each sequenced library were concatenated.
Reads were mapped to the G. hirsutum v2.1 genome (Chen et al., 2020) and transcripts assembled using RMTA_v2.6.3 in the CyVerse Discovery Environment. Differential expression was determined using Cuffdiff2 (Trapnell et al., 2010). Normalized expression data was reported as fragments per kilobase of transcript per million mapped reads (FPKM).
Assembly: G. hirsutum v2.1. BioProject: PRJNA515894, BioProject: PRJNA713846
Supplementary files format and content: cds.fpkm_tracking file reports expression as FPKM for each mapped transcript
Supplementary files format and content: transcripts.sorted_by_expression.sig.txt reports pair-wise comparisons of signficantly differentially expressed genes.

organism: Gossypium hirsutum

source_name: isolated meristems

growth_protocol: Plants were grown in a growth chamber at 25°C (16 h light / 8 h dark) with balanced warm and cool white T5 fluorescent lights.

extract_protocol:
RNA was isolated by hot borate (Wan & Wilkins, 1994) followed by column clean-up (Zymo Research, Irvine, CA, USA). Total RNA concentration was determined by nanodrop.
20 ng was used to prepare libraries with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina. Library quality was assessed at the University of North Texas Health Science Center Genomics Core Facility (Fort Worth, TX, USA) by Agilent High Sensitivity D5000 Screen Tape assay (Agilent Technologies, Santa Clara, CA, USA). Libraries with concentrations ≥ 2 nM were sequenced for 75 cycles on an Illumina NextSeq 550 Sequencer (University of North Texas Health Science Center Genomics Core Facility).

treatment_protocol: At 4 days post-germination, plants were inoculated with virus via Agro-infiltration delivered to saturation into the cotyledons. At 15 days post-infection (19 days post-germination), apices from three replicate co-silenced plants and controls were harvested into acetone. Acetone was changed twice, and samples were stored at 4°C before processing. With the aid of a SMZ1500 stereomicroscope (Nikon, Melville, NY, USA), meristems were dissected from apices and returned to acetone. Acetone was removed and meristems were frozen in liquid nitrogen and homogenized using a Retsch mill (MM400).

value: isolated meristems

value: 15 days post-inoculation

value: meristem

value: Coker 312

value: infiltrated with Tobacco rattle virus (TRV) targeting SELF-PRUNING (GhSP) and PERIANTHIA (PAN) for co-silencing


title: TRV:GhSP-GhPAN biol rep1

description: 75 cycles


title: CRC2113LMO0B01004001R01000, LMO_BASALE, bio rep 1, QC ok

city: Candiolo

first: Livio

last: Trusolino

state: Turin

address: Strada Provinciale, 142 -KM 3.95

department: Oncology

country: Italy

institute: IRCCS Istituto Candiolo

data_processing:
Align with STAR on hybrid mm/hs genome
Assign counts to genes with FeatureCounts
Consider only human genes to normalize with DESeq2
QC based on evidence of lymphomatous infiltration
https://github.com/molinerisLab/StromaDistiller, https://github.com/vodkatad/RNASeq_biod_metadata
Assembly: GRCh38_GRCm38
Supplementary files format and content: merged_hs_mm.tsv.gz: raw counts for human and murine genes
Supplementary files format and content: vsd.tsv.gz: normalized expression values for human genes

source_name: Colorectal Cancer

growth_protocol: Please check the linked publication

extract_protocol:
total RNA extraction
PolyA enriched
Forward Stranded

treatment_protocol: Please check the linked publication

value: Colorectal Cancer

value: O

value: LM

value: WT


title: p53_control_3


title: AP4KO_p53KO__DOX_3


title: AP4KO_p53KO__DOX_1


title: CRC2041LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: TRV:GhSP-GhFIN biol rep2

description: 75 cycles

value: infiltrated with Tobacco rattle virus (TRV) targeting SELF-PRUNING (GhSP) and FIN for co-silencing


title: p53_control_2


title: AP4KO_p53KO__control_3


title: TRV:GhSP-GhFIN biol rep1

description: 75 cycles


title: CRC2041LMO0A01003001R01000, LMO_BASALE, bio rep 1, QC ok


title: human liver sample A1016494

city: Durham

first: Anna Mae

last: Diehl

address: 905 S LaSalle St

institute: Duke University

data_processing:
Sequencing reads were trimmed using TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the mm10 reference genome using STAR
Gene expression counts were generated using HTSeq and DEseq2 was used to perform differential expression analyses (absolute log2FC >= 1 and q <0.05)
Assembly: hg39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNAs were isolated from liver tissues or hepatocytes as previously described
Libraries were made with NEBNext Ultra RNA Library Prep Kit from Illumina. Sample qualities were assessed by Agilent RNA Bioanalyzer chip traces before pooled and sequenced with an Illumina HiSeq 2500

value: Control


title: TRV:GhSP-GhCLV3 biol rep3

description: 75 cycles

value: infiltrated with Tobacco rattle virus (TRV) targeting SELF-PRUNING (GhSP) and CLAVATA 3 (CLV3) for co-silencing


title: human liver sample A1025222


title: CRC2026LMO0A01004001R01000, LMO_BASALE, bio rep 1, QC ok


title: AP4_DOX_3

value: breast

value: DOX


title: TRV:GhSP-GhCLV3 biol rep2

description: 75 cycles


title: human liver sample A1016479


title: p53_control_1

value: control


title: human liver sample A1016477

value: liver cells


title: CRC1989LMO0A01005001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC2113LMX0B02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: TRV:GhSP-GhCLV3 biol rep1

description: 75 cycles

value: isolated meristems


title: AP4_DOX_1


title: CRC1979LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: AP4_DOX_2


title: human liver sample A1002557


title: TRV:GhSP-GhCLV2 biol rep3

description: 75 cycles

value: 15 days post-inoculation

value: infiltrated with Tobacco rattle virus (TRV) targeting SELF-PRUNING (GhSP) and CLAVATA 2 (CLV2) for co-silencing


title: AP4_control_3


title: human liver sample A1001176


title: human liver sample A1001173


title: AP4_control_2


title: TRV:GhSP-GhCLV2 biol rep1

description: 75 cycles

value: meristem

value: Coker 312


title: human liver sample A1001164


title: CRC1989LMX0B02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: TRV:GhSP-GhCLV1 biol rep3

description: 75 cycles

value: infiltrated with Tobacco rattle virus (TRV) targeting SELF-PRUNING (GhSP) and CLAVATA 1 (CLV1) for co-silencing


title: wildtype_DOX_3

value: wild-type


title: TRV:GhSP-GhCLV2 biol rep2

description: 75 cycles


title: CRC1979LMO0A01003001R01000, LMO_BASALE, bio rep 1, QC ok

value: O

value: LM

value: WT


title: CRC1917LMX0B02001TUMR05000, LMX_BASALE, bio rep 1, QC ok

value: X


title: human liver sample A1001157

value: Control


title: CRC1961LMX0A02003TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: human liver sample A1001155


title: wildtype_DOX_2

value: breast


title: AP4_control_1


title: CRC1917LMO0A01006001R01000, LMO_BASALE, bio rep 2, QC ok


title: human liver sample A1015497


title: TRV:GhSP-GhCLV1 biol rep1

description: 75 cycles


title: wildtype_DOX_1

value: DOX


title: CRC1917LMO0A01003001R01000, LMO_BASALE, bio rep 1, QC ok


title: TRV:GhSP biol rep2

description: 75 cycles

value: infiltrated with Tobacco rattle virus (TRV) targeting SELF-PRUNING (GhSP) for virus-induced gene silencing


title: human liver sample A1015495

value: liver cells


title: wildtype_control_3

value: control


title: CRC1917LMH0000000000R01000, LMH, bio rep 1, QC ok

value: H


title: wildtype_control_2


title: human liver sample A1015493


title: TRV:GhSP biol rep1

description: 75 cycles

value: isolated meristems

value: 15 days post-inoculation


title: CRC1961LMO0A01005001R01000, LMO_BASALE, bio rep 1, QC ok


title: TRV:GhSP-GhCLV1 biol rep2

description: 75 cycles

value: meristem

value: Coker 312


title: CRC1916LMX0B02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: human liver sample A1001156


title: CRC1903LMX0B02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: human liver sample A1013706


title: TRV biol rep2

description: 75 cycles

value: infiltrated with Tobacco rattle virus (TRV)


title: CRC1903LMO0B02006001R01000, LMO_BASALE, bio rep 2, QC ok

value: O


title: human liver sample A1013686


title: TRV biol rep1

description: 75 cycles


title: CRC1916LMO0B01009001R01000, LMO_BASALE, bio rep 1, QC ok

value: LM


title: Kasumi-1_SMARCA5FKBP12_24hdTAG47_2 [Mnase-Seq]

city: Nashville

first: Scott

middle: W

last: Hiebert

state: TN

address: 512 B Preston Research Building

department: Biochemistry

institute: Vanderbilt University

data_processing:
Adaptor trimming with Trimmomatic-0.32 PE ILLUMINACLIP:atac_adaptor.txt:2:30:7 MINLEN:15
alignment to hg19 genome with bowtie2
high quality reads (F4q10) were filtered using samtools
motifs from CTCF CUT&RUN deteremined by fimo
bam files were fltered with deepTools alignmentsieve
bigWig files around CTCF motifs with deepTools --MNase --minFragmentLength 130 --maxFragmentLength 210 --normalization CPM
Assembly: hg19
Supplementary files format and content: bigwig

source_name: Kasumi-1 cells

growth_protocol: Kasumi-1 cells were grown in RPMI +20% FBS +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine. CD34+ cells were cultured in IMDM + 20% FBS, 55 μM BME, 50 U/ml penicillin, 50 μg/ml streptomycin, 2mM L-glutamine, and 10 ng/mL SCF, Flt3-L, TPO, IL-3, and IL-6

extract_protocol:
followed MNase-seq protocol, isolated nuclei
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: cells were treated with 500 nM dTAG-47 for the indicated timepoints

value: Kasumi-1 cells


title: Kasumi-1_SMARCA5FKBP12_24hdTAG47_1 [Mnase-Seq]


title: human liver sample A1013681


title: Kasumi-1_SMARCA5FKBP12_6hdTAG47_2 [Mnase-Seq]


title: TRV:GhSP biol rep3

description: 75 cycles


title: human liver sample A1013680


title: CRC1900LMX0A01001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X

value: WT


title: CRC1900LMO0A04015001R01000, LMO_BASALE, bio rep 2, QC ok


title: human liver sample A1013673


title: human liver sample A1013709

value: Control


title: wildtype_control_1

value: breast

value: wild-type


title: human liver sample A2008241

value: liver cells


title: Kasumi-1_SMARCA5FKBP12_0hdTAG47_2 [Mnase-Seq]

value: untreated


title: CRC1897LMO0B01012001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC1903LMO0B01003001R01000, LMO_BASALE, bio rep 1, QC ok


title: human liver sample A1025446


title: Kasumi-1_SMARCA5FKBP12_6hdTAG47_1 [Mnase-Seq]


title: CRC1895LMX0B02003TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: Kasumi-1_SMARCA5FKBP12_2hdTAG47_2 [Mnase-Seq]


title: Kasumi-1_SMARCA5FKBP12_2hdTAG47_1 [Mnase-Seq]


title: human liver sample A1013664


title: CRC1900LMO0A01010001R01000, LMO_BASALE, bio rep 1, QC ok


title: OCI-LY1_SMARCA5-FKBP12_24hdTAG_antiCTCF_1 [CUT&RUN]

data_processing:
For Cut&Run: adaptor trimming with Trimmomatic-0.32
alignment to hg19+scer genome with bowtie2
high quality reads (F4q10) were filtered using samtools
peaks called with MACS2 (( anti-flag: narrowPeak, q=0.001),(anti-CTCF, anti-RUNX1, anti-ETOZnf, anti-H2AZ: narrowPeak, q=0.01), (anti-H3K27me3: broadPeak, q=0.01))
CUT&RUN +/-dTAG at indicated time points, differential peaks were identified by Diffbind/DESeq2 using total counts for normalization
Assembly: hg19
bigwig files were generated using deepTools
Supplementary files format and content: bigWigs, narrowPeak, broadPeaks, counts tables with differential analysis
Library strategy: Cut&Run

source_name: OCI-LY1 SMARCA5-FKBP12-1xFLAG cells

extract_protocol:
For Cut&Run anti-flag, released DNA fragments were extracted using phenol:chloroform:IAA and ethanol precipitation. For Cut&Run anti-CTCF, released DNA fragments were extracted using NEB Monarch Nucleic Acid Purification Kits.
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit

value: OCI-LY1 SMARCA5-FKBP12-1xFLAG cells

tag: assay

value: CUT&RUN

tag: antibody

value: anti-CTCF (Millipore, 07-729)

tag: secondary antibody

value: anti-rabbit (Invitrogen, 31238)


title: OCI-LY1_SMARCA5-FKBP12_24hdTAG_antiCTCF_2 [CUT&RUN]

tag: cell line


title: LHS-T-lncRNA-mRNA-circRNA

city: BEIJING

first: Ben

last: Wan

state: 北京

address: Xinjiekou street No.31

institute: Beijing Research Institute of Traumatology and Orthopaedics

hyb_protocol: The labeled cRNAs were hybridized onto the microarray.

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

data_processing:
Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data.Genespring (version 14.8,Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm.
The probes that at least 1 conditions out of 2 conditions have flags in “Detected” were chosen for further data analysis.

source_name: tumor tissues

label_protocol: Total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

extract_protocol: Total RNA was extracted from Trizol reagent.Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies). The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols

tag: metastasis

value: No Metastasis

tag: gender

value: Male

tag: outcome

value: No Evidence of Disease

tag: enneking   stage

value: IIB

tag: position

value: Distal of femur

tag: age


title: CRC1895LMO0B01006001R01000, LMO_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: O

value: LM

tag: genotype


title: CRC1897LMX0B02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X

tag: cell type

value: WT


title: human liver sample A1013649


title: WHS-T-lncRNA-mRNA-circRNA

value: Proximal of tibia


title: Kasumi-1_SMARCA5FKBP12_0hdTAG47_1 [Mnase-Seq]

value: Kasumi-1 cells


title: LHS-C-lncRNA-mRNA-circRNA

source_name: adjacent tissues


title: WHS-C-lncRNA-mRNA-circRNA


title: CRC1888LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: human liver sample A1002230

value: liver cells


title: human liver sample A1002228


title: OCI-LY1_SMARCA5-FKBP12_2hdTAG_antiCTCF_2 [CUT&RUN]

value: OCI-LY1 SMARCA5-FKBP12-1xFLAG cells


title: human liver sample A1013634


title: CRC1895LMO0B04011001R01000, LMO_BASALE, bio rep 2, QC ok


title: OCI-LY1_SMARCA5-FKBP12_6hdTAG_antiCTCF_2 [CUT&RUN]

value: CUT&RUN


title: GCZ-T-lncRNA-mRNA-circRNA


title: GCZ-C-lncRNA-mRNA-circRNA


title: human liver sample A1013631

value: Control


title: OCI-LY1_SMARCA5-FKBP12_6hdTAG_antiCTCF_1 [CUT&RUN]

value: anti-CTCF (Millipore, 07-729)

value: anti-rabbit (Invitrogen, 31238)


title: WT-C-lncRNA-mRNA-circRNA

value: Lung

value: Male

value: Survival With Tumor

value: III


title: Δcdc50 cells rep2

city: Shanghai

first: Ke-Zhi

last: Chen

address: 197 Ruijin 2nd Road

department: Department of laboratory medicine

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters.
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: Candida glabrata CBS 138
Supplementary files format and content: Excel files include RPKM values for each Sample

organism: Nakaseomyces glabratus CBS 138

source_name: yeast cells

extract_protocol:
Total RNA was extracted from the tissue using TRIzol Reagent and genomic DNA was removed using DNase I.
RNA-seq transcriptome library was prepared following TruSeq RNA sample preparation Kit from Illumina using 1μg of total RNA.

value: yeast cells

value: Cdc50 knockout


title: Δcdc50 cells rep1


title: OCI-LY1_SMARCA5-FKBP12_2hdTAG_antiCTCF_1 [CUT&RUN]


title: OCI-LY1_SMARCA5-FKBP12_0hdTAG_antiCTCF_1 [CUT&RUN]

value: untreated


title: Δcdc50 cells rep3


title: CRC1888LMO0A02005001R01000, LMO_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: O

value: LM


title: human liver sample A1002224


title: ATCC2001 cells rep3

value: WT


title: OCI-LY1_SMARCA5-FKBP12(+)dTAG_antiFlag_2 [CUT&RUN]

value: anti-flag (Sigma, F1804)

value: anti-mouse (abcam, ab46540)


title: human liver sample A1002210

value: liver cells


title: PBW-C-lncRNA-mRNA-circRNA

value: Female

value: Dead of Disease

value: Proximal of tibia


title: OCI-LY1_SMARCA5-FKBP12(-)dTAG_antiFlag_2 [CUT&RUN]

value: OCI-LY1 SMARCA5-FKBP12-1xFLAG cells

value: CUT&RUN


title: WT-T-lncRNA-mRNA-circRNA

value: Lung

value: Male

value: Survival With Tumor


title: PBW-T-lncRNA-mRNA-circRNA

value: III


title: GZH-T-lncRNA-mRNA-circRNA

value: Lung,soft tissue

value: Dorsal metastases


title: CRC1779LMO0A02008001R01000, LMO_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: O


title: human liver sample A1002223


title: CRC1883LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X

value: LM

value: WT


title: CRC1883LMO0A01013001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC1875LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC1774LMX0A02003TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: human liver sample A1025455

value: liver cells


title: OCI-LY1_SMARCA5-FKBP12(-)dTAG_antiFlag_1 [CUT&RUN]

value: untreated

value: anti-flag (Sigma, F1804)

value: anti-mouse (abcam, ab46540)


title: BES1_Input, His, rep1

city: Xian

first: Liping

last: Zhu

address: Guodu street

institute: Shaanxi Normal University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis.
The MACS2 software（Version 2.1.1）was used for peak calling.
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: bigWig

source_name: fiber

extract_protocol:
fibers were fixed with 1% formaldehyde for 10 minutes. Chromatin was extracted, and sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: fiber

value: 5 day

tag: purification tag

value: His

tag: chip antibody


title: ATCC2001 cells rep2

tag: tissue

value: yeast cells


title: OCI-LY1_SMARCA5-FKBP12(+)dTAG_antiFlag_1 [CUT&RUN]

value: OCI-LY1 SMARCA5-FKBP12-1xFLAG cells

tag: treatment

value: CUT&RUN


title: human liver sample A1002167

tag: fibrotic stage


title: HEL_SMARCA5-FKBP12_24hdTAG_antiCTCF_2 [CUT&RUN]

source_name: HEL SMARCA5-FKBP12-1xFLAG cells

value: HEL SMARCA5-FKBP12-1xFLAG cells

tag: assay

value: anti-CTCF (Millipore, 07-729)

value: anti-rabbit (Invitrogen, 31238)


title: BES1, His, rep1

value: anti-His antibody (Mouse monoclonal anti-His, Abcam, Cat# ab18184)


title: CRC1774LMO0A01009001R02000, LMO_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: O


title: CRC1779LMX0B02003TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X

value: LM

value: WT


title: human liver sample A2010443

value: liver cells


title: human liver sample A1002188


title: CRC1757LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: RNAseq_SK6

city: Dallas

first: Jialiang

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Sequenced libraries were evaluated with FastQC.
Sequencing reads were mapped to the mouse reference genome (mm10) using STAR v.2.7.2b.
Gene expression counts were calculated using RSEM v.1.3.0.
Differential expression analysis was performed using DESeq2 package based on the criteria of more than two-fold change in expression value versus control and false discovery rates (FDR) <0.05.
Assembly: mm10
Supplementary files format and content: txt files include read counts, TPM, FPKM for each sample

source_name: whole kidney

extract_protocol:
Trizol/Chloroform protocol
mRNAs were isolated by PAGE, followed by adaptor ligation and RT with PCR amplification. PCR products were again purified by PAGE and dissolved in EB solution. Double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The ssCir DNA was formatted as the final sequencing library. The library was amplified with phi29 to general DNA nanoballs (DNBs) which were loaded into the patterned nanoarray. Libraries were sequenced on the BGISEQ500 platform.

value: whole kidney

tag: strain

tag: Sex

value: male


title: CRC1757LMO0A02005001R01000, LMO_BASALE, bio rep 1, QC ok

tag: cell line


title: GZH-C-lncRNA-mRNA-circRNA

tag: metastasis

value: Lung,soft tissue

value: Female

value: Dead of Disease

value: III

value: Dorsal metastases


title: ATCC2001 cells rep1

value: yeast cells


title: RNAseq_SK4


title: human liver sample A1002150


title: HEL_SMARCA5-FKBP12_24hdTAG_antiCTCF_1 [CUT&RUN]

value: HEL SMARCA5-FKBP12-1xFLAG cells

value: CUT&RUN

tag: antibody

value: anti-CTCF (Millipore, 07-729)

tag: secondary antibody


title: human liver sample A1002170


title: human liver sample A1002152


title: HEL_SMARCA5-FKBP12_6hdTAG_antiCTCF_2 [CUT&RUN]

value: anti-rabbit (Invitrogen, 31238)


title: human liver sample A1002164


title: OCI-LY1_SMARCA5-FKBP12_0hdTAG_antiCTCF_2 [CUT&RUN]

value: OCI-LY1 SMARCA5-FKBP12-1xFLAG cells

value: untreated


title: CRC1750LMX0B01001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X

value: LM


title: RNAseq_SK3

value: whole kidney


title: CRC1745LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: WT


title: human liver sample A1002149

value: liver cells

value: Control


title: RNAseq_SK2

value: male


title: HEL_SMARCA5-FKBP12_2hdTAG_antiCTCF_1 [CUT&RUN]


title: CRC1745LMO0B04009001R01000, LMO_BASALE, bio rep 2, QC ok

value: O


title: human liver sample A1019649


title: CRC1745LMO0B04008001R01000, LMO_BASALE, bio rep 1, QC ok


title: RNAseq_SK5


title: HEL_SMARCA5-FKBP12_6hdTAG_antiCTCF_1 [CUT&RUN]


title: HEL_SMARCA5-FKBP12_0hdTAG_antiCTCF_2 [CUT&RUN]


title: HEL_SMARCA5-FKBP12_0hdTAG_antiCTCF_1 [CUT&RUN]


title: human liver sample A1019669


title: human liver sample A1019659


title: human liver sample A1002146


title: CRC1744LMX0B02003TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: RNAseq_SK_Ctrl6

value: vehicle


title: HEL_SMARCA5-FKBP12(+)dTAG_antiFlag_2 [CUT&RUN]

value: anti-flag (Sigma, F1804)

value: anti-mouse (abcam, ab46540)


title: HEL_SMARCA5-FKBP12(+)dTAG_antiFlag_1 [CUT&RUN]

value: HEL SMARCA5-FKBP12-1xFLAG cells

value: CUT&RUN


title: RNAseq_SK_Ctrl5


title: RNAseq_SK_Ctrl4


title: CRC1744LMO0A02006001R01000, LMO_BASALE, bio rep 1, QC ok


title: human liver sample A1019655


title: CRC1737LMX0B02004TUMR01000, LMX_BASALE, bio rep 1, QC failed


title: HEL_SMARCA5-FKBP12_2hdTAG_antiCTCF_2 [CUT&RUN]

value: anti-CTCF (Millipore, 07-729)

value: anti-rabbit (Invitrogen, 31238)


title: human liver sample A1019650


title: HEL_SMARCA5-FKBP12(-)dTAG_antiFlag_2 [CUT&RUN]

value: untreated


title: CRC1731PMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: PM


title: RNAseq_SK_Ctrl3


title: HEL_SMARCA5-FKBP12(-)dTAG_antiFlag_1 [CUT&RUN]


title: CRC1729LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X

value: LM


title: human liver sample A1019644


title: RNAseq_SIK_KO3

value: whole kidney


title: RNAseq_SK1


title: Kasumi-1_SMARCA5-FKBP12_antiH2AZ_1 [CUT&RUN]

source_name: Kasumi-1 SMARCA5-FKBP12-1xFLAG cells

value: Kasumi-1 SMARCA5-FKBP12-1xFLAG cells

value: anti-H2AZ (Abcam, ab4174)


title: human liver sample A1019646

value: liver cells

value: Control


title: RNAseq_SK_Ctrl1

value: male

value: vehicle


title: RNAseq_SK_Ctrl2


title: Kasumi-1_SMARCA5-FKBP12_antiH3K27me3_2 [CUT&RUN]


title: CRC1729LMO0A02007001R01000, LMO_BASALE, bio rep 1, QC ok

value: O

value: WT


title: Kasumi-1_SMARCA5-FKBP12_antiH3K27me3_1 [CUT&RUN]

value: CUT&RUN


title: human liver sample A1019637


title: CRC1729LMO0A04011001R01000, LMO_BASALE, bio rep 2, QC ok


title: CRC1723LMO0A04011001R01000, LMO_BASALE, bio rep 2, QC ok


title: Kasumi-1_SMARCA5-FKBP12_antiH2AZ_2 [CUT&RUN]


title: RNAseq_SIK_KO2


title: RNAseq_SIK_KO4


title: CRC1723LMX0A02002TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: human liver sample A1019639


title: Kasumi-1_SMARCA5-FKBP12_24hdTAG_antiRUNX1_2 [CUT&RUN]

value: anti-RUNX1( SantaCruz, sc-365644)

value: anti-mouse (abcam, ab46540)


title: RNAseq_SIK_KO1


title: human liver sample A1019633


title: Kasumi-1_SMARCA5-FKBP12_24hdTAG_antiRUNX1_1 [CUT&RUN]


title: CRC1723LMO0A02007001R02000, LMO_BASALE, bio rep 1, QC ok


title: CRC1722PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: human liver sample A1019629


title: RNAseq_SIK_Ctrl4


title: human liver sample A1019647


title: Kasumi-1_SMARCA5-FKBP12_0hdTAG_antiRUNX1_2 [CUT&RUN]

value: untreated


title: RNAseq_SIK_Ctrl3


title: CRC1721PRX0A01001TUMR09000, PRX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: CRC1713PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: X


title: human liver sample A1019596


title: CRC1681LMO0A02011002R01000, LMO_BASALE, bio rep 1, QC ok

value: LM


title: human liver sample A1019586


title: Kasumi-1_SMARCA5-FKBP12_0hdTAG_antiRUNX1_1 [CUT&RUN]


title: human liver sample A1019588


title: RNAseq_SIK_Ctrl1

value: whole kidney


title: human liver sample A1019609


title: RNAseq_SIK_Ctrl2


title: CRC1681LMX0B02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: Kasumi-1_SMARCA5-FKBP12_24hdTAG_antiETOZnf_1 [CUT&RUN]

value: Kasumi-1 SMARCA5-FKBP12-1xFLAG cells

value: anti-ETOZnf(in house)

value: anti-rabbit (Invitrogen, 31238)


title: RNA-seq St_M28

first: Yan

last: Jiang

address: 131 Dongan rd

department: Institutes of Brain Science

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence (--quality 20 --phred33 --stringency 1 --length 20 --paired), then mapped to mm10 whole genome using Tophat2 v2.1.1 with parameters --max-multihits 20 --transcriptome-max-hits 60
The number of reads falling in the exons were counted by FeatureCounts v1.6.3 with GTF file (gencode.vM20.annotation.gtf).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample.

source_name: Brain

extract_protocol:
Brains were removed, flash frozen on dry ice, and RNA was harvested using  RNeasy Lipid Tissue Mini Kit (Qiagen Cat#74804), and total RNA was used for the construction of sequencing libraries.
mRNA was captured by Oligo (dT) magnetic beads and the quality was evaluated on Agilent 2100 Bioanalyzer.

value: Brain

tag: condition

value: Stress

value: wild type

tag: gender

value: Male


title: Kasumi-1_SMARCA5-FKBP12_0hdTAG_antiETOZnf_2 [CUT&RUN]


title: human liver sample A1000952

value: liver cells


title: human liver sample A1019583

value: Control


title: RNA-seq St_F35

value: Female

tag: age


title: Kasumi-1_SMARCA5-FKBP12_0hdTAG_antiETOZnf_1 [CUT&RUN]

value: CUT&RUN


title: CRC1675LMX0A02003TUMR01000, LMX_BASALE, bio rep 1, QC ok

tag: genotype

value: WT


title: Kasumi-1_SMARCA5FKBP12_T12hRelease_6hdTAG47_4 [ATAC-Seq]

description:
6954-12.withdup.j.r.Eblacklist.q0.05.narrowPeak
6954-MB-12

data_processing:
Adaptor trimming with Trimmomatic-0.32 PE ILLUMINACLIP:atac_adaptor.txt:2:30:7 MINLEN:15
alignment to hg19+dm3 genome with bowtie2
high quality reads (F4q10) were filtered using samtools
peaks called with Genrich (q 0.05 -j -r -E ; v. 0.6 )
for ATAC-seq +/-dTAG, differential peaks were identified by Diffbind/DESeq2, using 0h as a negative control
Assembly: hg19
Supplementary files format and content: Genrich peak files, differential peak files generated by Diffbind+DESeq2

growth_protocol: Kasumi-1 cells were grown in RPMI +20% FBS +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine. OCI-LY1 cells were grown in IMDM +10% FetalPlex +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine. HEL cells were grown in RPMI +10% FetalPlex +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine.

extract_protocol:
followed ATAC-seq protocol, isolated nuclei
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit or Active Motif Kit

treatment_protocol: Cells were treated with 500 nM dTAG-47 for the indicated timepoints

value: Kasumi-1 cells

tag: time

value: Synchronized cells_T12hRelease


title: human liver sample A1000947

tag: cell type


title: CRC1675LMO0A04008001R01000, LMO_BASALE, bio rep 2, QC ok

value: Colorectal Cancer

value: O


title: CRC1709LMX0A02004TUMR09000, LMX_BASALE, bio rep 1, QC failed

value: X

value: LM


title: Kasumi-1_SMARCA5FKBP12_T12hRelease_6hdTAG47_3 [ATAC-Seq]

description:
6954-11.withdup.j.r.Eblacklist.q0.05.narrowPeak
6954-MB-11


title: RNA-seq St_M29


title: human liver sample A1000943


title: Kasumi-1_SMARCA5-FKBP12_24hdTAG_antiETOZnf_2 [CUT&RUN]

value: Kasumi-1 SMARCA5-FKBP12-1xFLAG cells

value: anti-ETOZnf(in house)


title: RNA-seq Co_M30

value: Brain

value: control


title: RNA-seq Co_M31

value: wild type


title: CRC1675LMO0A02005001R01000, LMO_BASALE, bio rep 1, QC ok


title: Kasumi-1_SMARCA5FKBP12_T12hRelease_6hdTAG47_2 [ATAC-Seq]

description:
7189-11-12.withdup.j.r.Eblacklist.q0.05.narrowPeak
7189-MB-12


title: Kasumi-1_SMARCA5FKBP12_T12hRelease_6hdTAG47_1 [ATAC-Seq]

description:
7189-11-12.withdup.j.r.Eblacklist.q0.05.narrowPeak
7189-MB-11


title: human liver sample A1000930


title: CRC1647PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: RNA-seq Co_F37


title: CRC1634LMO0A03014002R01000, LMO_BASALE, bio rep 1, QC ok


title: human liver sample A1000927

value: liver cells


title: Kasumi-1_SMARCA5FKBP12_T12hRelease_0hdTAG47_4 [ATAC-Seq]

description:
6954-10.withdup.j.r.Eblacklist.q0.05.narrowPeak
6954-MB-10

value: untreated


title: RNA-seq St_F34

value: Stress

value: Female


title: CRC1629LMO0A04015001R01000, LMO_BASALE, bio rep 2, QC ok

value: WT


title: Kasumi-1_SMARCA5FKBP12_T12hRelease_0hdTAG47_2 [ATAC-Seq]

description:
7189-9-10.withdup.j.r.Eblacklist.q0.05.narrowPeak
7189-MB-10

value: Kasumi-1 cells


title: human liver sample A1000921

value: Control


title: Kasumi-1_SMARCA5FKBP12_T6hRelease_6hdTAG47_4 [ATAC-Seq]

description:
6954-8.withdup.j.r.Eblacklist.q0.05.narrowPeak
6954-MB-8

value: Synchronized cells_T6hRelease


title: Water-stressed 48 h maize primary root tip replicate 1

city: Columbia

first: Sidharth

last: Sen

state: Missouri

address: Agriculture Bldg, University of Missouri

department: The Division of Plant Sciences and Technology

institute: University of Missouri

data_processing:
Sequencing were performed by GENEWIZ Inc.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Zea mays AGPv4 (FR697 specific assembly) whole genome using Hisat2 (v1.0).
Read counts were calculated using Htseq-count (v0.6.1), counting how many aligned reads overlap the exon of each gene (Anders et al., 2015).
Assembly: Zea mays AGPv4 (FR697 specific assembly)
Supplementary files format and content: Matrix tables for raw counts for all samples

organism: Zea mays

source_name: Maize Primary Root Tip

growth_protocol: Maize (cv. FR697) seedlings were cultivated in a vermiculite culture system at well-watered (WW) and water-stressed (WS) treatments. Seedlings were grown at 29 oC and near-saturation humidity in a dark growth chamber until harvest. The root tips of maize were harvested at 24 h and 48 h after transplanting to well-watered or water-stressed media. Transplanting and harvesting were performed using a green ‘safe’ light. Root tips containing the whole elongation zones of maize (12 mm for WW; 7 mm for WS) primary roots were collected.

extract_protocol:
Maize root tip samples (12 mm for WW; 7 mm for WS) were collected from seedlings and immediately frozen in liquid nitrogen and pooled to generate 50-100 mg FW per sample. Total RNA was isolated using Qigen Plant RNeasy mini kit.
RNA libraries for sequencing were prepared using standard Illumina protocols.

treatment_protocol: The media were set at water potentials of -0.02 MPa (well-watered treatments, WW), -1.6 MPa (water-stressed treatments, WS), which were obtained by mixing with certain amounts of 1 mM CaSO4. No further water supplies were added after the transplanting.

value: Root


title: CRC1629LMX0B02004TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X


title: human liver sample A1000919


title: human liver sample A1000906


title: Kasumi-1_SMARCA5FKBP12_T12hRelease_0hdTAG47_3 [ATAC-Seq]

description:
6954-9.withdup.j.r.Eblacklist.q0.05.narrowPeak
6954-MB-9

value: Synchronized cells_T12hRelease


title: CRC1628LMO0A04010001R01000, LMO_BASALE, bio rep 1, QC ok

value: O

value: LM


title: human liver sample A1000915


title: human liver sample Z0175720


title: RNA-seq Co_F36

value: Brain

value: control


title: human liver sample Z0175713


title: Kasumi-1_SMARCA5FKBP12_T6hRelease_6hdTAG47_2 [ATAC-Seq]

description:
7189-7-8.withdup.j.r.Eblacklist.q0.05.narrowPeak
7189-MB-8


title: Water-stressed 48 h maize primary root tip replicate 3


title: Water-stressed 48 h maize primary root tip replicate 2


title: Water-stressed 24 h maize primary root tip replicate 3


title: CRC1629LMO0A04014001R01000, LMO_BASALE, bio rep 1, QC ok


title: Kasumi-1_SMARCA5FKBP12_T12hRelease_0hdTAG47_1 [ATAC-Seq]

description:
7189-9-10.withdup.j.r.Eblacklist.q0.05.narrowPeak
7189-MB-9


title: CRC1629LMH0000000000R01000, LMH, bio rep 1, QC ok

value: H


title: human liver sample A1000981

value: liver cells


title: Kasumi-1_SMARCA5FKBP12_T6hRelease_6hdTAG47_3 [ATAC-Seq]

description:
6954-7.withdup.j.r.Eblacklist.q0.05.narrowPeak
6954-MB-7


title: CRC1624PRX0B02001TUMR09000, PRX_BASALE, bio rep 2, QC ok

value: PR


title: CRC1624LMX0B02003TUMR01000, LMX_BASALE, bio rep 2, QC ok


title: Water-stressed 24 h maize primary root tip replicate 2


title: human liver sample Z0175698


title: CRC1624PRX0A02002TUMR09000, PRX_BASALE, bio rep 1, QC ok


title: human liver sample Z0175703


title: Kasumi-1_SMARCA5FKBP12_T6hRelease_0hdTAG47_4 [ATAC-Seq]

description:
6954-6.withdup.j.r.Eblacklist.q0.05.narrowPeak
6954-MB-6

value: untreated


title: CRC1624PRH0000000000R05000, PRH, bio rep 1, QC ok


title: Kasumi-1_SMARCA5FKBP12_T6hRelease_6hdTAG47_1 [ATAC-Seq]

description:
7189-7-8.withdup.j.r.Eblacklist.q0.05.narrowPeak
7189-MB-7


title: CRC1624LMH0000000000R01000, LMH, bio rep 1, QC ok


title: Well-watered 48 h maize primary root tip replicate 2


title: Kasumi-1_SMARCA5FKBP12_T6hRelease_0hdTAG47_2 [ATAC-Seq]

description:
7189-5-6.withdup.j.r.Eblacklist.q0.05.narrowPeak
7189-MB-6


title: Well-watered 48 h maize primary root tip replicate 3


title: Kasumi-1_SMARCA5FKBP12_T6hRelease_0hdTAG47_3 [ATAC-Seq]

description:
6954-5.withdup.j.r.Eblacklist.q0.05.narrowPeak
6954-MB-5


title: human liver sample Z0175700


title: Water-stressed 24 h maize primary root tip replicate 1


title: CRC1620LMX0A02003TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: Kasumi-1_SMARCA5FKBP12_T6hRelease_0hdTAG47_1 [ATAC-Seq]

description:
7189-5-6.withdup.j.r.Eblacklist.q0.05.narrowPeak
7189-MB-5


title: Well-watered 48 h maize primary root tip replicate 1


title: human liver sample Z0175675


title: CRC1624LMX0A01001TUMR09000, LMX_BASALE, bio rep 1, QC ok


title: human liver sample Z0175694


title: Well-watered 24 h maize primary root tip replicate 2


title: Well-watered 24 h maize primary root tip replicate 3


title: CRC1621LMX0B02001TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC1620LMO0B04011001R01000.2, LMO_BASALE, bio rep 2, QC ok


title: human liver sample Z0175662


title: human liver sample Z0175665


title: Kasumi-1_SMARCA5FKBP12_G1_6hdTAG47_5 [ATAC-Seq]

description:
8364-3-4.withdup.j.r.Eblacklist.q0.05.narrowPeak
8364-MB-4

value: Synchronized cells_G1


title: Kasumi-1_SMARCA5FKBP12_G1_6hdTAG47_2 [ATAC-Seq]

description:
7189-3-4.withdup.j.r.Eblacklist.q0.05.narrowPeak
7189-MB-4


title: Well-watered 24 h maize primary root tip replicate 1


title: B16F10_IL2-IL12_TwoDose_2d_B

city: Cambridge

first: K

middle: Dane

last: Wittrup

state: Massachusetts

department: Koch Institute for Integrative Cancer Research

institute: Massachusetts Institute of Technology

description: Nanostring Mouse PanCancer Immune Profiling Panel (XT-CSO-MIP1-12)

hyb_protocol: Hybridization of RNA to the Mouse PanCancer Immune Profiler nCounter panel probe set (Nanostring) was performed according to manufacturer's instructions for 22 hours at 65C. Hybridized RNA was loaded into the analysis cartridge using Nanostring PrepStation.

scan_protocol: Scanning of analysis cartridge was performed on Nanostring Digital Analyzer under maximum resolution.

data_processing: Nanostring nSolver software was used to process count data. Background thresholding was performed using the mean of 8 negative control probes. Normalization was performed in nSolver prior to analysis of differential gene expression and pathway analysis between cohorts.

source_name: Tumor

growth_protocol: B16F10 cells (ATCC) were maintained in 5% CO2 at 37C and tested negative for mycoplasma and rodent pathogens (IMPACT I test, IDEXX) prior to tumor inoculation of 1M cells into the right flank of C57BL/6 mice.

extract_protocol: RNA was extracted from FFPE tissue scrolls (3x10um) using Qiagen FFPE RNEasy kit following manufacturer's protocol. Samples were QC'd for concentration and fragment analysis on Bioanalyzer (Agilent) prior to hybridization to the nCounter panel probe set.

treatment_protocol: C57BL/6 mice bearing B16F10 tumors (day 6, ~30mm^2) were randomly assigned into three treatment cohorts to receive intratumoral collagen-binding cytokines IL-2 and IL-12 two days prior to tumor collection (cohort 1; n=3), eight days prior to collection (cohort 2; n=3), or two doses of cytokines (day 0 and day 6) with tumor collection two days after the second dose (cohort 3; n=3). Three mice also had tumors treated with saline as controls, with tumors removed two days after injection.

tag: tumor model

value: Intratumoral IL-2 and IL-12

tag: cohort

value: Cohort 3


title: B16F10_IL2-IL12_TwoDose_2d_C

tag: treatment


title: Kasumi-1_SMARCA5FKBP12_G1_6hdTAG47_3 [ATAC-Seq]

description:
6954-3.withdup.j.r.Eblacklist.q0.05.narrowPeak
6954-MB-3

value: Kasumi-1 cells


title: human liver sample Z0175661

tag: fibrotic stage


title: CRC1620LMO0B04010001R01000, LMO_BASALE, bio rep 1, QC ok

tag: tissue

value: WT


title: CRC1620LMH0000000000R02000, LMH, bio rep 1, QC ok


title: Kasumi-1_SMARCA5FKBP12_G1_6hdTAG47_4 [ATAC-Seq]

description:
8364-3-4.withdup.j.r.Eblacklist.q0.05.narrowPeak
8364-MB-3


title: human liver sample Z0175659

value: Control


title: Kasumi-1_SMARCA5FKBP12_G1_0hdTAG47_5 [ATAC-Seq]

description:
8364-1-2.withdup.j.r.Eblacklist.q0.05.narrowPeak
8364-MB-2


title: Kasumi-1_SMARCA5FKBP12_G1_6hdTAG47_1 [ATAC-Seq]

description:
7189-3-4.withdup.j.r.Eblacklist.q0.05.narrowPeak
7189-MB-3


title: B16F10_IL2-IL12_OneDose_8d_C

value: Cohort 2


title: B16F10_IL2-IL12_TwoDose_2d_A


title: CRC1888LMO0A04009001R01000, LMO_BASALE, bio rep 2, QC ok

value: Colorectal Cancer


title: human liver sample Z0175649


title: CRC1614LMO0B05015002R01000, LMO_BASALE, bio rep 2, QC ok


title: human liver sample Z0175421


title: human liver sample Z0175420


title: Kasumi-1_SMARCA5FKBP12_G1_0hdTAG47_3 [ATAC-Seq]

description:
6954-1.withdup.j.r.Eblacklist.q0.05.narrowPeak
6954-MB-1


title: human liver sample Z0175418


title: CRC1614LMX0A02003TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: Kasumi-1_SMARCA5FKBP12_G1_0hdTAG47_4 [ATAC-Seq]

description:
8364-1-2.withdup.j.r.Eblacklist.q0.05.narrowPeak
8364-MB-1


title: CRC1605LMX0B04011TUMR01000, LMX_cetux_6w, bio rep 2, QC ok

value: CET


title: CRC1605LMX0B04005TUMR01000, LMX_cetux_6w, bio rep 1, QC ok

value: LM


title: B16F10_IL2-IL12_OneDose_2d_C

value: Cohort 1


title: B16F10_IL2-IL12_OneDose_8d_A


title: CRC1614LMO0B05015001R01000, LMO_BASALE, bio rep 1, QC ok

value: O


title: B16F10_IL2-IL12_OneDose_8d_B


title: human liver sample Z0175415


title: human liver sample A1026665


title: CRC1605LMX0B04001TUMR01000, LMX_cetux_6w_NT, bio rep 1, QC ok

value: NT


title: Kasumi-1_SMARCA5FKBP12_G1_0hdTAG47_1 [ATAC-Seq]

description:
7189-1-2.withdup.j.r.Eblacklist.q0.05.narrowPeak
7189-MB-1


title: OCILY1_SMARCA5FKBP12_6hdTAG47_2 [ATAC-Seq]

description:
7018-7-8.withdup.j.r.Eblacklist.q0.05.narrowPeak
7018-MB-8

source_name: OCILY1 cells

value: OCILY1 cells

value: Asychronous cells


title: CRC1605LMH0000000000R01000, LMH, bio rep 1, QC ok

value: H


title: human liver sample 200807682

value: liver cells


title: human liver sample Z0175410


title: human liver sample Z0175409


title: B16F10_IL2-IL12_OneDose_2d_A

value: Intratumoral IL-2 and IL-12


title: Kasumi-1_SMARCA5FKBP12_G1_0hdTAG47_2 [ATAC-Seq]

description:
7189-1-2.withdup.j.r.Eblacklist.q0.05.narrowPeak
7189-MB-2

value: untreated

value: Synchronized cells_G1


title: OCILY1_SMARCA5FKBP12_0hdTAG47_1 [ATAC-Seq]

description:
7018-5-6.withdup.j.r.Eblacklist.q0.05.narrowPeak
7018-MB-5


title: CRC1599LMO0A03009001R01000, LMO_BASALE, bio rep 2, QC ok

value: WT


title: human liver sample Z0175405

value: Control


title: B16F10_Saline_2d_C

value: Saline


title: B16F10_IL2-IL12_OneDose_2d_B


title: B16F10_Saline_2d_A


title: HEL_SMARCA5FKBP12_6hdTAG47_2 [ATAC-Seq]

description:
7018-3-4.withdup.j.r.Eblacklist.q0.05.narrowPeak
7018-MB-4

source_name: HEL cells

value: HEL cells


title: ANF_ID40

type: genomic

city: Hamburg

first: Catena

last: Kresbach

address: Martinistrasse 52

institute: Research Institute Children‘s Cancer Center Hamburg

description: Sample 40

hyb_protocol: 100-500 ng DNA were used for bisulfite conversion with the EZ DNA Methylation Kit (Zymo Research). Afterwards, the DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were used to clean and restore the converted DNA.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
R (v4.1.2)
Average Beta

label: Cy5 and Cy3

source_name: biopsy, Peripheral

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated from FFPE tissue using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions.

tag: material

value: FFPE

tag: array type

value: female

tag: clinical nf1 syndrome

value: sporadic

tag: initial histological diagnosis

value: Low grade MPNST

tag: revised histological diagnosis (who 2021)

value: PN


title: ANF_ID39

description: Sample 39

tag: Sex

value: ANNUBP


title: human liver sample 200806674

source_name: liver cells


title: HEL_SMARCA5FKBP12_6hdTAG47_1 [ATAC-Seq]

description:
7018-3-4.withdup.j.r.Eblacklist.q0.05.narrowPeak
7018-MB-3

tag: cell line


title: HEL_SMARCA5FKBP12_0hdTAG47_2 [ATAC-Seq]

description:
7018-1-2.withdup.j.r.Eblacklist.q0.05.narrowPeak
7018-MB-2


title: human liver sample 200806169


title: ANF_ID37

description: Sample 37

source_name: biopsy, Spinal/paravertebral

value: male


title: ANF_ID38

description: Sample 38


title: CRC1599LMH0000000000R05000, LMH, bio rep 1, QC ok

source_name: Colorectal Cancer

value: Colorectal Cancer

value: LM


title: CRC1598LMX0B02003TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: OCILY1_SMARCA5FKBP12_6hdTAG47_1 [ATAC-Seq]

description:
7018-7-8.withdup.j.r.Eblacklist.q0.05.narrowPeak
7018-MB-7

value: OCILY1 cells

value: Asychronous cells


title: CRC1599LMX0A02002TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC1589LMX0B02003TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: human liver sample 200804730

value: liver cells


title: HEL_SMARCA5FKBP12_0hdTAG47_1 [ATAC-Seq]

description:
7018-1-2.withdup.j.r.Eblacklist.q0.05.narrowPeak
7018-MB-1

value: untreated


title: CRC1599LMO0A03008001R01000, LMO_BASALE, bio rep 1, QC ok

value: O

value: WT


title: human liver sample 200804834

value: Control


title: human liver sample 200802499


title: B16F10_Saline_2d_B

value: Saline


title: ANF_ID32

description: Sample 32

source_name: biopsy, arm

value: FFPE

value: female

value: Atypical neurofibroma


title: CRC1589LMO0B06057001R01000, LMO_BASALE, bio rep 2, QC ok


title: Kasumi-1_SMARCA5FKBP12_24hdTAG47_3 [ATAC-Seq]

description:
7567-7-8.withdup.j.r.Eblacklist.q0.05.narrowPeak
7567-MB-7

source_name: Kasumi-1 cells

value: Kasumi-1 cells


title: OCILY1_SMARCA5FKBP12_0hdTAG47_2 [ATAC-Seq]

description:
7018-5-6.withdup.j.r.Eblacklist.q0.05.narrowPeak
7018-MB-6


title: ANF_ID23

description: Sample 23

value: PN


title: ANF_ID22

description: Sample 22

value: male


title: CRC1598LMO0A04011001R01000, LMO_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: ANF_ID21

description: Sample 21


title: Kasumi-1_SMARCA5FKBP12_6hdTAG47_4 [ATAC-Seq]

description:
7567-5-6.withdup.j.r.Eblacklist.q0.05.narrowPeak
7567-MB-6


title: Kasumi-1_SMARCA5FKBP12_2hdTAG47_4 [ATAC-Seq]

description:
7567-3-4.withdup.j.r.Eblacklist.q0.05.narrowPeak
7567-MB-4


title: CRC1589LMO0B04015001R01000, LMO_BASALE, bio rep 1, QC ok

value: LM


title: CRC1586LMX0B02001TUMR01000, LMX_BASALE, bio rep 2, QC ok

value: X


title: CRC1588LMO0A04008001R01000, LMO_BASALE, bio rep 1, QC ok


title: human liver sample 200802372


title: Kasumi-1_SMARCA5FKBP12_6hdTAG47_3 [ATAC-Seq]

description:
7567-5-6.withdup.j.r.Eblacklist.q0.05.narrowPeak
7567-MB-5


title: CRC1588LMX0B02003TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: human liver sample 200801437


title: Kasumi-1_SMARCA5FKBP12_0hdTAG47_4 [ATAC-Seq]

description:
7567-1-2.withdup.j.r.Eblacklist.q0.05.narrowPeak
7567-MB-2


title: ANF_ID20

description: Sample 20


title: ANF_ID18

description: Sample 18

value: ANNUBP


title: human liver sample 200801265


title: CRC1586LMH0000000000R01000, LMH, bio rep 1, QC ok

value: H


title: Kasumi-1_SMARCA5FKBP12_24hdTAG47_4 [ATAC-Seq]

description:
7567-7-8.withdup.j.r.Eblacklist.q0.05.narrowPeak
7567-MB-8

value: Asychronous cells


title: Kasumi-1_SMARCA5FKBP12_0hdTAG47_3 [ATAC-Seq]

description:
7567-1-2.withdup.j.r.Eblacklist.q0.05.narrowPeak
7567-MB-1

value: untreated


title: Kasumi-1_SMARCA5FKBP12_2hdTAG47_3 [ATAC-Seq]

description:
7567-3-4.withdup.j.r.Eblacklist.q0.05.narrowPeak
7567-MB-3


title: human liver sample 200806721

value: liver cells


title: CRC1586LMX0A01001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: WT


title: human liver sample 200801190

value: Control


title: CRC1579LMO0B05013001R01000, LMO_BASALE, bio rep 1, QC ok

value: O


title: human liver sample 200802272


title: GFPCNO Rep 2

city: Saarbrücken

first: Kathrin

last: Kattler-Lackes

state: non-US Resident

address: Campus A2.4 Raum 0.13

department: Epigenetics

institute: Saarland University

data_processing:
Raw reads were subjected to quality control and then trimmed for library adapters and low-quality tails.
Trimmed reads were mapped to the mouse reference genome (mm10) using STAR (version v2.6.1d).
The quantification of read numbers mapped of each gene was performed by FeatureCounts.
Raw counts were normalized as FPKM values.
Assembly: mm10
Supplementary files format and content: FPKM gene count matrix

source_name: brain - tanycytes

extract_protocol:
Dissociation was performed using a Papain dissociation system (Worthington) as described previously73. The dissociated cells were then sorted using FACS (Sony SH800). Cells were sorted by fluorescence (endogenously expressed GFP and virally expressed mCherry) with excitation at 488 nm and 560 nm and emission detected at 508 nm and 600/60 nm.
Smart-seq2

treatment_protocol: M5-GFP and M5-DREADD-GFP mice were i.c.v. injected with 2 ml AAV2/1+2-CAGS-mCherry virus three weeks before cell sorting. The basal hypothalamus from adult male M5-GFP mice, which either underwent 14 hours of fasting (8 mice) or normal diet feeding (6 mice) or from 6 adult male M5-DREADD-GFP mice (M5-GFP mice were used as control (6 mice), animals were injected with 2 µg CNO i.c.v. and sacrificed after 3 hours) were dissected and pooled from 2 mice.

value: brain - tanycytes

value: >12 weeks


title: CRC1575LMO0A04019001R01000, LMO_BASALE, bio rep 1, QC ok


title: ANF_ID19

description: Sample 19

value: FFPE

value: Atypical neurofibroma


title: GFPCNO Rep 3


title: c-Kit+ selected

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

institute: UNIVERSITA' DI PADOVA

data_processing:
NovaSeqTM 6000 (Illumina, San Diego, CA, USA) running in a 50-bp pair-end mode.
Reads were mapped an counted on human genome using STAR aligner
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: amniotic fluid stem cells

growth_protocol: hAFSCs were grown in culture medium (αMEM) supplemented with 20% foetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following manufacture's instructions.
RNA Truseq Stranded Total
Bead-based rRNA depletion, cDNA synthesis, and PCR

value: amniotic fluid stem cells

value: immunomagnetic c-kit selection


title: human liver sample 200800442


title: GFPCNO Rep 1

value: male


title: CRC1568LMO0A04009001R01000, LMO_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: LM


title: Fed Rep 3

value: fed


title: Fed Rep 4


title: human liver sample 200801636


title: CRC1568LMX0B02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: Fed Rep 1


title: Total [scRNA-Seq]

description: 10x Genomics

data_processing:
Alignment and count matrix generation was performed using Cell Ranger v6.0.1
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
5000 cells were isolated using Chromium 10 x genimic platform
and Libraries were prepared using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1

value: no-treatment


title: human liver sample 200714241


title: c-Kit+ selected [scRNA-Seq]

description: 10x Genomics


title: LT_CTN_20μM_rep2

city: Taipei

first: Jui-Feng

last: Tsai

address: No. 1, Sec. 1, Ren'Ai Rd,

department: Graduate Institute of Toxicology

country: Taiwan

institute: National Taiwan University

data_processing:
Fastqc for reads quality check
Cutadapt for adaptor trimming
STAR for alignment to human reference genome
RSeQC for post-alignment quality control
edgeR for normalization to CPM
Assembly: Homo sapiens GRCh38.107
Supplementary files format and content: Tab-delimited TXT file containing raw read counts of each gene for each sample
Supplementary files format and content: CSV file containing log2CPM values of each gene for all the samples

growth_protocol: HEK293 cells were regularly cultured in MEM containing 10% FBS.

extract_protocol:
RNA extraction was performed with TRIzol reagent according to manufacturer’s instruction (Invitrogen, Waltham, MA). RNA quality assessment was performed by Azenta Life Sciences, Inc. (Chelmsford, MA) according to manufacturers’ protocol.
cDNA library construction was performed by Azenta Life Sciences, Inc. (Chelmsford, MA) according to manufacturers’ protocol.

treatment_protocol: HEK293 cells were treated with 20 μM CTN for 3 days (short-term, ST) and 30 days (long-term, LT). Colony formation assay was performed at day 30 and the colonies formed were picked up for RNA-seq analysis. HEK293 cells treated with vehicle for 30 days were served as control (CTRL).

value: Embryonic kidney epithelium

value: CTN 20 microM

tag: time point

value: 30 day CTN treatment


title: human liver sample 200714376

value: liver cells


title: Fed Rep 2

tag: age