title: H1092 cells,treated with 2 μM BafA1, rep2

city: Tianjin

first: Yujie

last: Hao

address: 22 Qixiangtai Road

institute: Tianjin Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

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

value: SCLC cells

value: treated with 2 μM BafA1 for 24 hours


title: ODD replicate 1

status: Public on Oct 02 2025

type: SRA

city: Rome

first: Alessandro

last: Palma

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

library_source: transcriptomic

data_processing:
Adaptors were removed with fastp tool and roaw reads in FASTQ format aligned to the reference genome using STAR tool. Gene loci fragment quantification was performed using a customized genome annotation file (GRCh38_primary.86_LNCMB3.gtf). Read counts with "reverse" configuration were used as quantifcation of genes.
Assembly: GRCh38.p13, Gencode Release 38, GRCh38.primary_assembly.genome.fa
Supplementary files format and content: tab-delimited text files include rounded row counts values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: D283 Med cells

growth_protocol: Rea J, Carissimo A, Trisciuoglio D, Illi B, Picard D, Remke M, Laneve P, Caffarelli E. Identification and Functional Characterization of Novel MYC-Regulated Long Noncoding RNAs in Group 3 Medulloblastoma. Cancers (Basel). 2021 Jul 30;13(15):3853. doi: 10.3390/cancers13153853. PMID: 34359754; PMCID: PMC8345409.

extract_protocol:
miRNeasy Micro Kit (Qiagen)
TruSeq Stranded mRNA Library

treatment_protocol: Tollis P, Vitiello E, Migliaccio F, D'Ambra E, Rocchegiani A, Garone MG, Bozzoni I, Rosa A, Carissimo A, Laneve P, Caffarelli E. The long noncoding RNA nHOTAIRM1 is necessary for differentiation and activity of iPSC-derived spinal motor neurons. Cell Death Dis. 2023 Nov 14;14(11):741. doi: 10.1038/s41419-023-06196-y. PMID: 37963881; PMCID: PMC10646148.

tag: cell line

value: D283 Med cells

tag: cell type

value: G3 Medulloblastoma

tag: genotype

value: WT

tag: treatment

value: Native RNA Pulldown


title: H1092 cells,treated with 2 μM BafA1, rep1

country: China


title: H1092 cells,treated with 5 μL DMSO, rep3

value: treated with 5 μL DMSO for 24 hours


title: H1092 cells,treated with 5 μL DMSO, rep2


title: H1092 cells,treated with 5 μL DMSO, rep1


title: 14_KMM1_edit_ctr2

city: Nantes

first: David

last: Chiron

address: 8 quai Moncousu

country: France

institute: CRCI2NA, INSERM_U1307, CNRS_6075, Nantes_Université

data_processing:
Samples demultiplexing is performed with a python script. It will transform the raw paired-end fastq files into a single-end fastq file for each sample
Alignment on refseq reference transcriptome is performed using bwa
Aligned reads are parsed and UMI are counted for each gene in each sample to create an expression matrix
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was extracted with RNeasy Mini Kit (Qiagen) and sequenced on 3’ends
The libraries are prepared from 10 ng of total RNA in 4µl. The mRNA poly(A) tails are tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse transcriptase. Barcoded cDNAs from multiple samples are then pooled, amplified and tagmented using a transposon-fragmentation approach which enriches for 3′ends of cDNA. A library of 350–800 bp length is run on an Illumina NovaSeq 6000 using NovaSeq 6000 SP Reagent Kit 100 cycles (ref #20027464)
RNA-Seq (3'SRP)

value: myeloma cell

tag: group

tag: replicate


title: DMS114 cells,treated with 200 mM trehalose, rep2

value: treated with 200 mM trehalose for 12 hours


title: DMS114 cells,treated with 200 mM trehalose, rep1


title: 9_KMM1_edit_ctr3


title: DMS114 cells,treated with 200 mM trehalose, rep3


title: DMS114 cells, control, rep3


title: 8_KMM1_edit_ctr2


title: DMS114 cells, control, rep2


title: 2_KMM1_edit_ctr2


title: SK-N-SH Over Expression YAP1, rep1

city: Vienna

first: CCRI

last: BiCU

address: Zimmermannpl. 10

department: Bioinformatics Core Unit

country: Austria

institute: St. Anna Children's Cancer Research Institute

data_processing:
Illumina HiSeq Control Software (HCS) HD was used for the data acquisition on the sequencing instrument
On-instrument base-calling performed by the Illumina Real-Time Analysis
BCL to BAM file conversion and demultiplexing
Conversion of Bam files to FASTQ with samtools (v1.17)
Processing of the data with Nextflow/rna-seq pipeline (v3.14)
Assembly: GRCh38/hg38
Supplementary files format and content: RDS/RData file with raw gene counts

extract_protocol:
Cells were detached and dissociated using accutase and washed 1x with DPBS before RNA isolation using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions, including homogenization with QIAshredder columns (Qiagen) and on-column DNAse digest with RNase-free DNase set (Qiagen). The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific) and the RNA integrity number (RIN) was determined using the 2100 Bioanalyzer instrument (Agilent).
RNA-seq libraries were prepared with the NEBNext® Ultra™ II Directional RNA sample preparation kit (New England Biolabs) according to manufacturer’s instructions. NGS library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the 2100 Bioanalyzer instrument (Agilent).


title: DMS114 cells, control, rep1


title: SK-N-SH Over Expression WWTR1, rep1


title: SK-N-SH Over Expression Empty Vector, rep1


title: CLB-Ma Over Expression WWTR1, rep1


title: CLB-Ma Over Expression YAP1, rep1


title: SK-N-SH Adrenergic, rep1

source_name: SK-N-SH

value: SK-N-SH

value: Adrenergic


title: H1092 cells,treated with 2 μM BafA1, rep3


title: STA-NB-10 Adrenergic, rep1


title: STA-NB-10 Mesenchymal, rep1

value: Mesenchymal


title: STA-NB-8 Adrenergic, rep1


title: STA-NB-8 Mesenchymal, rep1


title: SK-N-SH-A TAZ rep2

description: IG Control: SK-N-SH-A_IgG_rep2

library_source: genomic

data_processing:
Illumina HiSeq Control Software (HCS) HD was used for the data acquisition on the sequencing instrument
On-instrument base-calling performed by the Illumina Real-Time Analysis
BCL to BAM file conversion and demultiplexing
Conversion of Bam files to FASTQ with samtools (v1.17)
Obtained raw fastq data were processed with nf-core/cutandrun framework v3.2.2 with default settings
Assembly: GRCh38/hg38
Supplementary files format and content: bigWig files containting track information for genome browser
Supplementary files format and content: narrowPeak fies that provide called peaks of signal enrichment by MACS2
Library strategy: Cut&Run

molecule: genomic DNA

extract_protocol:
250k cells per sample were dissociated, collected and washed once with DPBS. For nuclear isolation, cell pellets, after centrifugation at 400 g for 3 min, were resuspended in 100 µl nuclear extraction buffer (20 mM HEPES, pH 7.9, 10 mM KCl, 0.1 % Triton X-100, 20 % glycerol, 1 mM MnCl2, 0.5 mM Spermidine, 1x cOmplete protease inhibitor cocktail (Roche)) and lysed at 4 °C for 10 min. Then, nuclei were pelleted at 400 g for 3 min and resuspended in 100 µl nuclear extraction buffer. 10 µl of Concanavalin A beads (Polysciences) were washed twice with 100 µl bead activation buffer (20 mM HEPES, pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) and resuspended in 10 µl of bead activation buffer.  Following, 100 µl nuclei were immobilized by incubation with 10 µl activated Concanavalin A beads (Polysciences) for 10 min at RT. Upon incubation of the nuclei-bead complex, the supernatant was removed and the beads were resuspended in 50 µl antibody buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x cOmplete protease inhibitor cocktail (Roche), 0.01 % digitonin, 2 mM EDTA) containing the antibodies and incubated at 4 °C while nutating overnight. Antibodies were used diluted as follows: 1:50 anti-YAP1 (Cell Signaling Technology, D8H1X, #14074), 1:25 anti-WWTR1 (Sigma-Aldrich, #HPA00741), 1:50 anti-JUN (Cell Signaling Technology, 60A8, #9165), 1:50 anti-H3K27Ac (Active Motif, #39133), 1:50 anti-H3K4me1 (Diagenode, #C15410194), 1:50 normal IgG (Cell Signaling Technology, #2729). Afterwards, the beads were washed twice with digitonin buffer (20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x cOmplete protease inhibitor cocktail (Roche), 0.01 % digitonin), and incubated with 700 ng/ml protein A/G-conjugated micrococcal nuclease (pAG-MNAse - kind gift from Joris van der Veeken, IMP) in 50 µl digitonin buffer at RT for 30 min. After two washes with digitonin buffer, the beads were resuspended in 50 µl digitonin buffer and digestion started by addition of 1 µl 100 mM CaCl2 and incubation at 4 °C for 90 min. The reaction was stopped by addition of 33 µl stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 µg/mL RNase A, 50 µg/mL glycogen), followed by incubation at 37 °C for 10 min to release cleaved chromatin. DNA was extracted from the supernatant using Monarch DNA and PCR cleanup kit (New England Biolabs) according to manufacturer’s instructions.
2 ng of DNA were used for library preparation using the NEBNext ultra II DNA library Prep kit (New England Biolabs).


title: SK-N-SH-A Jun rep2

description: IG Control: SK-N-SH-A_IgG_rep2


title: SK-N-SH-A YAP rep2

description: IG Control: SK-N-SH-A_IgG_rep2


title: SK-N-SH-A Jun rep1

description: IG Control: SK-N-SH-A_IgG_rep1


title: SK-N-SH-A IgG rep2

description: Control sample


title: SK-N-SH-A YAP rep1

description: IG Control: SK-N-SH-A_IgG_rep1


title: SK-N-SH-M TAZ rep1

description: IG Control: SK-N-SH-M_IgG_rep1


title: SK-N-SH-M YAP rep2

description: IG Control: SK-N-SH-M_IgG_rep2


title: SK-N-SH-M TAZ rep2

description: IG Control: SK-N-SH-M_IgG_rep2


title: SK-N-SH-A TAZ rep1

description: IG Control: SK-N-SH-A_IgG_rep1


title: SK-N-SH-M Jun rep1

description: IG Control: SK-N-SH-M_IgG_rep1


title: CLB-Ma-A TAZ rep2

description: IG Control: CLB-Ma-A_IgG_rep2

source_name: CLB-Ma

value: CLB-Ma


title: CLB-Ma Over Expression Empty Vector, rep1


title: SK-N-SH-M IgG rep2

description: Control sample


title: CLB-Ma-A Jun rep2

description: IG Control: CLB-Ma-A_IgG_rep2


title: CLB-Ma Adrenergic, rep1


title: CLB-Ma-A IgG rep2

description: Control sample


title: CLB-Ma-M Jun rep2

description: IG Control: CLB-Ma-M_IgG_rep2


title: CLB-Ma-A YAP rep2

description: IG Control: CLB-Ma-A_IgG_rep2


title: CLB-Ma Mesenchymal, rep1


title: SK-N-SH Mesenchymal, rep1


title: CLB-Ma-M IgG rep2

description: Control sample


title: CLB-Ma-A Jun rep1

description: IG Control: CLB-Ma-A_IgG_rep1


title: CLB-Ma-M Jun rep1

description: IG Control: CLB-Ma-M_IgG_rep1


title: SK-N-SH-A H3K4me1 rep2

description: IG Control: SK-N-SH-A_IgG_rep2


title: CLB-Ma-M YAP rep1

description: IG Control: CLB-Ma-M_IgG_rep1


title: SK-N-SH-A H3K27ac rep1

description: IG Control: SK-N-SH-A_IgG_rep1


title: SK-N-SH-A H3K4me1 rep1

description: IG Control: SK-N-SH-A_IgG_rep1


title: SK-N-SH-A H3K27ac rep2

description: IG Control: SK-N-SH-A_IgG_rep2


title: SK-N-SH-A IgG rep1

description: Control sample


title: SK-N-SH-M H3K4me1 rep2

description: IG Control: SK-N-SH-M_IgG_rep2


title: SK-N-SH-M H3K4me1 rep1

description: IG Control: SK-N-SH-M_IgG_rep1


title: SK-N-SH-M H3K27ac rep1

description: IG Control: SK-N-SH-M_IgG_rep1


title: SK-N-SH-M IgG rep1

description: Control sample


title: CLB-Ma-A H3K27ac rep2

description: IG Control: CLB-Ma-A_IgG_rep2


title: CLB-Ma-A H3K4me1 rep1

description: IG Control: CLB-Ma-A_IgG_rep1


title: CLB-Ma-A H3K4me1 rep2

description: IG Control: CLB-Ma-A_IgG_rep2


title: CLB-Ma-A H3K27ac rep1

description: IG Control: CLB-Ma-A_IgG_rep1


title: CLB-Ma-M YAP rep2

description: IG Control: CLB-Ma-M_IgG_rep2


title: CLB-Ma-M H3K4me1 rep2

description: IG Control: CLB-Ma-M_IgG_rep2


title: CLB-Ma-A IgG rep1

description: Control sample


title: CLB-Ma-M TAZ rep2

description: IG Control: CLB-Ma-M_IgG_rep2


title: STA-NB-8 Mesenchymal rep1

data_processing:
Illumina HiSeq Control Software (HCS) HD was used for the data acquisition on the sequencing instrument
On-instrument base-calling performed by the Illumina Real-Time Analysis
BCL to BAM file conversion and demultiplexing
Conversion of Bam files to FASTQ with samtools (v1.17)
Processing with a pipeline that includes mapping reads with STAR (v2.7.10a), identification of duplicates with Picard (v2.27.4),  peak calling with MACS2 (v2.2.7.1), annotation of peaks with HOMER (v4.11), identification of consensus peaks with BEDTools (v2.30.0) and counting reads in peaks with featureCOunts (v2.0.1)
Assembly: GRCh38/hg38
Supplementary files format and content: csv tables with read counts and annotations for consensus peaks performed by HOMER
Supplementary files format and content: bigWig files containting track information for genome browser

extract_protocol:
50 000 cells were detached and dissociated using accutase and washed 1x with DPBS. Cell pellets were lysed in 25 µl Tagment DNA Enzyme and Buffer (Illumina), supplemented with 0.01% digitonin (Promega) and 2x cOmplete, EDTA-free protease inhibitor cocktail (Roche). Samples were incubated at 37 °C for 30 min before placing on ice and subsequent purification using MinElute PCR purification kit (Qiagen) according to manufacturer’s instructions, with elution in 12 µl.
1 μl of eluted DNA was used in a quantitative PCR (qPCR) reaction to estimate the optimum number of amplification cycles. The remaining 10 μl of each library were amplified for the number of cycles corresponding to the Cqvalue (that is, the cycle number at which fluorescence has increased above background levels) from the qPCR. Library amplification was followed by SPRI (Beckman Coulter) size selection to exclude fragments larger than 1,200 bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies). Library amplification was performed using custom Nextera primers.


title: SK-N-SH Mesenchymal rep1


title: CLB-Ma-M H3K27ac rep1

description: IG Control: CLB-Ma-M_IgG_rep1


title: CLB-Ma-M TAZ rep1

description: IG Control: CLB-Ma-M_IgG_rep1


title: CLB-Ma-M H3K4me1 rep1

description: IG Control: CLB-Ma-M_IgG_rep1


title: STA-NB-10 Mesenchymal rep1


title: STA-NB-8 Adrenergic rep1


title: STA-NB-10 Adrenergic rep1


title: CLB-Ma Mesenchymal rep1


title: ATAC_TALL_T_7

city: Memphis

first: Daniel

last: Savic

state: Tennessee

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

country: USA

institute: St. Jude Children's Research Hospital

data_processing:
Reads were mapped to the human genome using bowtie2
Peak calling was performed using MACS2 using the default q value of 0.05
Assembly: hg19
Supplementary files format and content: narrowPeak files for each experimental sample

source_name: ALL

extract_protocol:
Cells were transposed following to the Fast-ATAC protocol from the Greenleaf Lab
Libraries were prepared for sequencing using standard Illumina protocols for Nextera adapters

tag: disease state

value: T-ALL

value: ALL


title: CLB-Ma Adrenergic rep1


title: ATAC_TALL_T_6


title: ATAC_TALL_T_4


title: ATAC_TALL_T_5


title: 786-O cells,siMITD1_3

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Library qualty assessement
illumina sequencing
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: kidney

growth_protocol: 786-O cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

tag: tissue

value: kidney

value: 786-O cells

value: renal cancer cells

value: case


title: 786-O cells,siMITD1_2


title: 786-O cells,sicontrol_for_siMITD1_1

value: control

value: sicontrol


title: 786-O cells,sicontrol_for_siMITD1_3


title: 786-O cells,sicontrol_for_siMITD1_2


title: 786-O cells, siANKRD35_2


title: 786-O cells, siANKRD35_1


title: 786-O cells, siANKRD35_3


title: 786-O cells,sicontrol_for_siANKRD35_1


title: 786-O cells, shRBCK1_3


title: SK-N-SH Adrenergic rep1


title: 786-O cells,sicontrol_for_siANKRD35_2


title: 786-O cells, shRBCK1_1


title: 786-O cells, shcontrol_3

value: shcontrol


title: CLB-Ma-M H3K27ac rep2

description: IG Control: CLB-Ma-M_IgG_rep2


title: 786-O cells,sicontrol_for_siANKRD35_3


title: Control-4.Input

city: Beijing

first: Dong

last: Han

address: 28 Fuxing street

institute: Chinese PLA general hospital

data_processing:
Briefly, Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
Clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps.
For input RNA-seq, The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA and mRNA were identified.
Assembly: hg19
Supplementary files format and content: Excel table files include RPKM values for each Sample
Supplementary files format and content: Excel table files include m6A peaks calling results for each Sample

source_name: human valvular interstitial cells

growth_protocol: Primary hVICs were isolated from human aortic valves and cultured in high glucose Dulbecco’s modified Eagle’s medium

extract_protocol:
Briefly, m6A RNA immunoprecipitation was performed with the GenSeqTM m6A RNA IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions.
Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA).

treatment_protocol: Human valvular interstitial cells from calcific aortic valve disease patients were transfected with piRNA AVCAPIR mimic or negative control (NC) mimic. Following the confirmation of overexpression, cells were sent for m6A methylated RNA immunoprecipitation sequencing (MeRIP-seq) combined with input RNA sequencing (RNA-seq).

value: calcific aortic valve disease

tag: fraction

value: Input

value: human valvular interstitial cells

value: negative control (NC) mimic

value: negative control (NC) mimic transfection


title: 786-O cells, shRBCK1_2


title: 786-O cells, shcontrol_2


title: Control-3.Input


title: Control-3.IP

value: IP


title: Control-4.IP


title: Control-2.Input


title: Control-1.Input


title: 786-O cells, shcontrol_1


title: 786-O cells,siMITD1_1


title: CAV-4.Input

value: AVCAPIR overexpression

value: AVCAPIR transfection


title: Control-1.IP


title: Control-2.IP


title: CAV-3.Input


title: CAV-4.IP


title: CAV-3.IP


title: CAV-1.Input


title: CAV-2.Input


title: CAV-1.IP


title: OS_Patient tumor-SJOS013768_D2-FFPE

type: genomic

first: Gang

last: Wu

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina EPIC v1 (850K) array following Illumina standard protocol

scan_protocol: Standard Illumina protocol

data_processing:
Methylation Analysis: Raw data files generated by the iScan array scanner were read and preprocessed by using 'minfi' Bioconductor package.
processed value definition: Average beta value

label: Cy3 and Cy5

source_name: Femur

label_protocol: Standard Illumina protocol

extract_protocol: Genomics DNA was extracted from froze tumor tissues using  Qiagen kit (catalog #65904) or FFPE tumors using Promega Maxwell DNA FFPE Kit according to standard instructions recommended by the kit

tag: Sex

value: F

value: OS

value: Femur

value: Y

tag: sample type

value: Patient tumor

tag: tumor group

tag: age at collection (yr)


title: OS_Xenograft-SJOS013768_X3-frozen

source_name: Lung

value: Lung

value: Xenograft


title: OS_Xenograft-SJOS001112_X1-frozen

value: M

value: N


title: OS_Patient tumor-SJOS030441_R1-FFPE


title: OS_Patient tumor-SJOS013768_R1-FFPE


title: OS_Patient tumor-SJOS001127_M1-FFPE


title: OS_Xenograft-SJOS046149_X1-frozen

source_name: Back

value: Back


title: OS_Patient tumor-SJOS001132_R1-FFPE


title: OS_Patient tumor-SJOS001121_R2-FFPE

source_name: Thigh

value: Thigh


title: OS_Xenograft-SJOS013768_X1-frozen_rep2


title: OS_Patient tumor-SJOS010929_D3-FFPE


title: OS_Patient tumor-SJOS030605_R2-frozen


title: OS_Xenograft-SJOS013769_X1-frozen

source_name: Tibia

value: Tibia


title: OS_Xenograft-SJOS016016_X1-frozen


title: OS_Patient tumor-SJOS063819_D1-FFPE


title: CAV-2.IP

value: calcific aortic valve disease

value: human valvular interstitial cells


title: OS_Xenograft-SJOS016015_X1-frozen


title: OS_Xenograft-SJOS013768_X1-frozen_rep1


title: OS_Patient tumor-SJOS030605_R1-frozen

source_name: Chest

value: Chest


title: OS_Xenograft-SJOS001121_X-frozen


title: OS_Patient tumor-SJOS030645_D2-frozen


title: OS_Xenograft-SJOS063822_X1-FFPE


title: OS_Patient tumor-SJOS063833_D1-frozen_rep2


title: OS_Patient tumor-SJOS031478_D6-frozen


title: OS_Xenograft-SJOS001108_X1-FFPE


title: OS_Xenograft-SJOS030566_X1-frozen


title: OS_Xenograft-SJOS030441_X1-frozen


title: OS_Xenograft-SJOS063833_X1-frozen


title: OS_Xenograft-SJOS030605_X2-frozen


title: OS_Xenograft-SJOS030272_X1-frozen


title: OS_Xenograft-SJOS003939_X1-frozen

source_name: Humerus

value: Humerus


title: OS_Xenograft-SJOS030648_X1-frozen


title: OS_Xenograft-SJOS063819_X1-frozen


title: OS_Xenograft-SJOS030589_X3-frozen


title: OS_Patient tumor-SJOS030101_D3-frozen


title: OS_Xenograft-SJOS046149_X2-frozen


title: OS_Xenograft-SJOS063833_X2-frozen


title: OS_Xenograft-SJOS071776_X1-frozen


title: OS_Xenograft-SJOS030645_X1-frozen


title: OS_Xenograft-SJOS030589_X1-frozen


title: OS_Xenograft-SJOS030589_X5-frozen


title: OS_Xenograft-SJOS001116_X2-frozen


title: OS_Xenograft-SJOS030589_X4-frozen


title: OS_Xenograft-SJOS030759_X1-frozen


title: OS_Xenograft-SJOS030589_X2-frozen


title: OS_Xenograft-SJOS030876_X2-frozen


title: OS_Xenograft-SJOS001107_X3-FFPE


title: OS_Xenograft-SJOS071782_X1-frozen


title: OS_Xenograft-SJOS031782_X1-frozen


title: OS_Xenograft-SJOS030876_X1-frozen


title: OS_Xenograft-SJOS030645_X3-frozen


title: OS_Xenograft-SJOS071781_X1-frozen


title: OS_Xenograft-SJOS071776_X3-frozen


title: OS_Xenograft-SJOS003939_X2-frozen


title: OS_Xenograft-SJOS030422_X1-frozen


title: OS_Xenograft-SJOS031130_X1-frozen


title: OS_Patient tumor-SJOS030759_D1-frozen


title: OS_Xenograft-SJOS071776_X2-frozen


title: OS_Patient tumor-SJOS001107_R1-frozen


title: OS_Patient tumor-SJOS031478_D7-frozen


title: OS_Patient tumor-SJOS030422_M1-frozen


title: OS_Patient tumor-SJOS071776_M2-frozen


title: OS_Patient tumor-SJOS071776_M4-frozen


title: OS_Patient tumor-SJOS046149_R1-frozen


title: OS_Patient tumor-SJOS071776_M1-frozen


title: OS_Patient tumor-SJOS030876_R2-frozen_rep1


title: OS_Patient tumor-SJOS046149_M1-FFPE


title: OS_Patient tumor-SJOS031125_D2-frozen


title: OS_Patient tumor-SJOS031130_D2-frozen


title: OS_Patient tumor-SJOS012409_D1-frozen


title: OS_Patient tumor-SJOS030589_M3-frozen


title: OS_Xenograft-SJOS031125_X1-frozen


title: OS_Patient tumor-SJOS030589_M1-frozen

source_name: Pleura

value: Pleura


title: OS_Patient tumor-SJOS031782_D1-frozen


title: OS_Patient tumor-SJOS063833_D1-frozen_rep1


title: OS_Patient tumor-SJOS030589_D4-frozen

value: F


title: OS_Patient tumor-SJOS071781_D1-frozen

value: OS


title: OS_Patient tumor-SJOS030279_D3-frozen

value: Femur


title: OS_Patient tumor-SJOS030589_D3-frozen

value: Y


title: OS_Patient tumor-SJOS030597_D1-frozen

value: Patient tumor


title: OS_Patient tumor-SJOS030566_D2-frozen


title: OS_Patient tumor-SJOS030272_R1-frozen


title: OS_Patient tumor-SJOS046149_M2-frozen

value: Lung


title: OS_Patient tumor-SJOS001107_D1-frozen


title: OS_Patient tumor-SJOS016016_D1-frozen


title: OS_Patient tumor-SJOS001105_R1-frozen


title: OS_Patient tumor-SJOS016015_D1-frozen


title: NB_Xenograft-SJNBL013763_X1-FFPE

source_name: Adrenal

value: NB

value: Adrenal

value: Xenograft


title: ATAC_TALL_T_8

value: T-ALL

value: ALL


title: NB_Xenograft-SJNBL046_X-frozen

value: M


title: NB_Xenograft-SJNBL015724_X1-FFPE


title: NB_Patient tumor-SJNBL030721_A2-FFPE

source_name: Thoracic

value: Thoracic


title: NB_Patient tumor-SJNBL030721_A1-FFPE

source_name: Rib

value: Rib


title: NB_Patient tumor-SJNBL030721_D6-FFPE

source_name: Retroperitoneum

value: Retroperitoneum


title: NB_Xenograft-SJNBL030721_X1-frozen


title: NB_Patient tumor-SJNBL031239_D3-FFPE

value: N


title: NB_Xenograft-SJNBL030339_X1-frozen


title: NB_Patient tumor-SJNBL030721_D2-FFPE


title: NB_Xenograft-SJNBL031239_X1-frozen


title: NB_Xenograft-SJNBL031232_X1-frozen


title: NB_Xenograft-SJNBL063821_X1-frozen

source_name: Mediastinum

value: Mediastinum


title: NB_Xenograft-SJNBL031239_X2-frozen

value: F


title: NB_Xenograft-SJNBL030721_X5-frozen

source_name: Paravertebrate

value: Paravertebrate


title: NB_Xenograft-SJNBL030721_X6-frozen


title: OS_Patient tumor-SJOS030589_D2-frozen

value: OS

value: Femur


title: NB_Xenograft-SJNBL031668_X1-frozen

value: Y


title: NB_Patient tumor-SJNBL013763_D3-FFPE

value: Patient tumor


title: NB_Xenograft-SJNBL030721_X7-frozen

value: NB


title: NB_Xenograft-SJNBL030824_X2-frozen

source_name: Pelvis

value: Pelvis


title: NB_Xenograft-SJNBL030824_X1-frozen

value: Xenograft


title: NB_Patient tumor-SJNBL013762_D2-FFPE

value: Adrenal


title: NB_Patient tumor-SJNBL031232_D2-FFPE


title: NB_Xenograft-SJNBL030721_X4-frozen


title: NB_Patient tumor-SJNBL047443_R2-FFPE_rep2

source_name: Spine

value: Spine


title: NB_Patient tumor-SJNBL030721_D3-FFPE

value: M


title: NB_Patient tumor-SJNBL105_D-FFPE


title: NB_Patient tumor-SJNBL031668_M1-FFPE

value: Lung


title: NB_Patient tumor-SJNBL071354_D1-FFPE


title: NB_Patient tumor-SJNBL013763_D4-FFPE


title: NB_Patient tumor-SJNBL063820_D1-FFPE_rep2


title: NB_Patient tumor-SJNBL030721_D5-FFPE


title: NB_Patient tumor-SJNBL031239_D2-FFPE


title: NB_Patient tumor-SJNBL030513_D2-FFPE


title: NB_Patient tumor-SJNBL063820_D1-FFPE_rep1


title: NB_Patient tumor-SJNBL046145_M1-FFPE


title: NB_Patient tumor-SJNBL015724_D3-FFPE_rep2


title: NB_Patient tumor-SJNBL030339_D2-FFPE


title: NB_Patient tumor-SJNBL030721_D4-FFPE


title: NB_Patient tumor-SJNBL015724_D3-FFPE_rep1


title: NB_Patient tumor-SJNBL046148_D3-FFPE


title: NB_Xenograft-SJNBL071354_X1-frozen


title: NB_Patient tumor-SJNBL030721_R1-frozen


title: NB_Patient tumor-SJNBL013761_D4-FFPE


title: NB_Patient tumor-SJNBL015724_D1-frozen


title: NB_Patient tumor-SJNBL030824_R1-FFPE


title: NB_Patient tumor-SJNBL046148_D2-FFPE


title: NB_Xenograft-SJNBL012407_X1-frozen


title: NB_Xenograft-SJNBL013761_X1-frozen


title: NB_Xenograft-SJNBL030721_X3-frozen

source_name: Aorta/cava

value: Aorta/cava


title: NB_Xenograft-SJNBL030721_X2-frozen

value: Retroperitoneum


title: NB_Xenograft-SJNBL124_X-frozen


title: NB_Patient tumor-SJNBL047443_R2-FFPE_rep1


title: NB_Patient tumor-SJNBL006124_D2-FFPE


title: NB_Xenograft-SJNBL063820_X1-frozen


title: NB_Xenograft-SJNBL030513_X1-frozen


title: NB_Xenograft-SJNBL046148_X1-frozen

value: N


title: NB_Xenograft-SJNBL047443_X1-frozen


title: NB_Xenograft-SJNBL046145_X1-frozen

source_name: Paraspinal

value: Paraspinal


title: NB_Xenograft-SJNBL013762_X1-frozen


title: MRT_Xenograft-SJMRT031758_X1-frozen_rep2

source_name: Kidney

value: F

value: MRT

value: Kidney


title: MRT_Patient tumor-SJMRT031055_D2-FFPE

source_name: Liver

value: Liver


title: NB_Patient tumor-SJNBL063821_D3-FFPE

value: Mediastinum


title: NB_Patient tumor-SJNBL030824_R3-FFPE

value: Y

value: Patient tumor


title: MRT_Xenograft-SJMRT031055_X1-frozen


title: MRT_Xenograft-SJMRT015723_X1-frozen

source_name: Lung


title: MRT_Xenograft-SJMRT030873_X1-frozen_rep2


title: NB_Patient tumor-SJNBL012407_D1-FFPE

value: NB


title: MRT_Xenograft-SJMRT030873_X1-frozen_rep1

value: Xenograft


title: MRT_Patient tumor-SJMRT030873_D2-frozen


title: MRT_Patient tumor-SJMRT031758_D1-FFPE


title: MRT_Patient tumor-SJMRT015723_D1-frozen


title: MISC_Patient tumor-SJCCS030604_R2-FFPE

source_name: Thumb

value: CCS

value: Thumb

value: MISC


title: MISC_Xenograft-SJSTS030383_X2-frozen

source_name: Neck

value: M

value: CIC-rearranged sarcoma

value: Neck


title: MISC_Patient tumor-SJST030383_D4-FFPE


title: MISC_Patient tumor-SJCCS030604_R1-FFPE


title: MISC_Patient tumor-SJHGS030383_D1-FFPE

value: Lung


title: MISC_Patient tumor-SJHGS015726_R1-FFPE

source_name: Leg

value: Leg


title: MISC_Xenograft-SJCCS030604_X1-frozen

value: F


title: MISC_Xenograft-SJSTS030383_X3-frozen


title: MISC_Xenograft-SJSTS030383_X4-frozen


title: MISC_Xenograft-SJSTS030383_X1-frozen

source_name: Lymph Node

value: Lymph Node


title: MEL_Patient tumor-SJMEL030083_R5-FFPE

value: MEL


title: NB_Patient tumor-SJNBL015724_D2-FFPE

source_name: Adrenal

value: Adrenal

value: N


title: MEL_Patient tumor-SJMEL030083_R4-FFPE

value: Y


title: MISC_Patient tumor-SJHGS015726_D2-frozen

value: Patient tumor


title: MISC_Patient tumor-SJHGS012411_D1-frozen


title: MEL_Patient tumor-SJMEL031086_R1-FFPE

source_name: Scalp

value: Scalp


title: MEL_Xenograft-SJMEL031086_X3-frozen

value: Xenograft


title: MEL_Patient tumor-SJMEL031086_D3-frozen


title: MEL_Xenograft-SJMEL030083_X2-frozen


title: MEL_Xenograft-SJMEL063827_X1-frozen

source_name: Brain

value: Brain


title: MEL_Patient tumor-SJMEL063827_D1-frozen


title: MEL_Xenograft-SJMEL030083_X1-frozen


title: LIVER_Patient tumor-SJHB031109_R1-FFPE

value: HB

value: LIVER


title: MRT_Xenograft-SJMRT031758_X1-frozen_rep1

value: MRT

value: Kidney


title: LIVER_Patient tumor-SJHB031109_D1-FFPE


title: MEL_Xenograft-SJMEL031086_X4-frozen


title: LIVER_Xenograft-SJHB030622_X1-frozen


title: LIVER_Patient tumor-SJST031109_D1-frozen

value: Liver


title: LIVER_Xenograft-SJHB031109_X1-frozen


title: LIVER_Xenograft-SJUESL030381_X1-frozen

value: Embryonal sarcoma


title: MISC_Patient tumor-SJST030383_R2-FFPE

value: M

value: CIC-rearranged sarcoma

value: Lung

value: MISC


title: LIVER_Patient tumor-SJHB030622_D1-FFPE

value: F


title: LIVER_Patient tumor-SJUESL030381_D1-frozen

value: N


title: EWS_Patient tumor-SJEWS046144_D2-FFPE

source_name: Chest

value: EWS

value: Chest


title: EWS_Patient tumor-SJEWS001321_D2-frozen

source_name: Tibia

value: Tibia

value: Y

value: Patient tumor


title: EWS_Patient tumor-SJEWS049193_D2-frozen


title: EWS_Patient tumor-SJEWS049193_D1-frozen


title: EWS_Patient tumor-SJEWS063826_D1-frozen

source_name: Axilla

value: Axilla


title: EWS_Patient tumor-SJEWS063834_A1-frozen


title: EWS_Xenograft-SJEWS063829_X1-frozen

source_name: Femur

value: Femur

value: Xenograft


title: EWS_Patient tumor-SJEWS071785_R1-FFPE

source_name: Spine

value: Spine


title: EWS_Xenograft-SJEWS063834_X2-frozen


title: EWS_Patient tumor-SJEWS063829_D1-frozen


title: EWS_Patient tumor-SJEWS071783_R1-FFPE


title: EWS_Xenograft-SJEWS001321_X1-frozen


title: EWS_Patient tumor-SJEWS030565_D1-frozen


title: EWS_Xenograft-SJEWS049193_X2-frozen


title: EWS_Xenograft-SJEWS049193_X1-frozen


title: LIVER_Xenograft-SJHB030622_X2-frozen

value: HB

value: LIVER


title: EWS_Patient tumor-SJEWS030393_A1-FFPE


title: EWS_Patient tumor-SJEWS071783_A3-FFPE

value: M

value: Liver


title: EWS_Xenograft-SJEWS030565_X1-frozen

value: Lung


title: EWS_Patient tumor-SJEWS071785_A2-FFPE

source_name: Periorbital

value: Periorbital


title: EWS_Patient tumor-SJEWS071785_A1-FFPE

value: F


title: LIVER_Patient tumor-SJHB031109_D2-FFPE


title: EWS_Patient tumor-SJEWS071783_A1-FFPE


title: EWS_Patient tumor-SJEWS056156_A2-FFPE

source_name: Rib

value: Rib


title: EWS_Patient tumor-SJEWS056156_A1-FFPE

value: EWS


title: EWS_Xenograft-SJEWS063834_X1-frozen

value: Chest

value: N


title: EWS_Patient tumor-SJEWS071780_D1-FFPE

value: Y


title: EWS_Xenograft-SJEWS071785_X2-frozen


title: EWS_Xenograft-SJEWS071785_X1-frozen


title: EWS_Xenograft-SJEWS071783_X3-frozen


title: EWS_Xenograft-SJEWS071783_X4-frozen

source_name: Spleen

value: Spleen


title: EWS_Xenograft-SJEWS071780_X1-frozen


title: EWS_Xenograft-SJEWS046144_X1-frozen


title: EWS_Xenograft-SJEWS071783_X5-frozen

source_name: Liver


title: EWS_Xenograft-SJEWS071783_X1-frozen


title: DSRCT_Patient tumor-SJDSRCT030041_D7-FFPE

source_name: Abdomen

value: DSRCT

value: Abdomen

value: Patient tumor


title: EWS_Xenograft-SJEWS071783_X2-frozen

source_name: Lung

value: Xenograft


title: EWS_Xenograft-SJEWS056156_X2-frozen


title: DSRCT_Xenograft-SJDSRCT046155_X1-frozen


title: DSRCT_Xenograft-SJDSRCT046151_X1-frozen


title: EWS_Xenograft-SJEWS056156_X1-frozen


title: DSRCT_Xenograft-SJDSRCT049192_X1-frozen

source_name: Pelvis

value: Pelvis


title: DSRCT_Xenograft-SJDSRCT049192_X3-frozen


title: EWS_Patient tumor-SJEWS071783_A2-FFPE


title: DSRCT_Patient tumor-SJDSRCT030722_D3-FFPE

source_name: Thigh

value: Thigh


title: DSRCT_Patient tumor-SJDSRCT049192_D3-frozen

value: M


title: DSRCT_Patient tumor-SJDSRCT049192_R1-frozen

value: Liver


title: EWS_Xenograft-SJEWS063826_X1-frozen

value: Axilla


title: DSRCT_Xenograft-SJDSRCT030490_X1-frozen


title: ACT/ACC_Patient tumor-SJACT030812_D2-FFPE

source_name: Pancreas

value: ACC

value: Pancreas

value: ACT/ACC


title: ACT/ACC_Xenograft-SJACT030812_X2-frozen


title: D_GBM_020_control_s15

city: Frankfurt am Main

first: Katharina

last: Imkeller

address: Heinrich-Hoffmann-Str. 7

country: Germany

institute: University Hospital Frankfurt

data_processing:
Reads generated were filtered and normalised on GeoMx DSP Analysis Suite using the default settings. The reads were then scaled to nuclei prior to downstream analysis in R.
Assembly: GRCh38/hg38
Supplementary files format and content: counts.csv: Comma-delimited csv file includes the raw counts from each roi form a sample. Each column is a ROI and each row is a gene.
Supplementary files format and content: metadata.csv: Comma-delimited csv metadata file containing additional information about the each roi  in the count matrix file.
Library strategy: Spatial Transcriptomics

source_name: Glioma

extract_protocol:
FFPE tissue cuts (5 μm) were placed onto microscope slides and the GeoMx ® Human Whole Transcriptome Atlas Assay (NanoString Technologies, United States) was conducted following the manufacturer’s protocol.
The library was constructed according to Nanostring GeoMx DSP manufacturer’s protocol.

value: Glioma

value: control

tag: patient


title: ACT/ACC_Xenograft-SJACT030812_X1-frozen

source_name: Adrenal

value: Adrenal

value: N


title: EWS_Xenograft-SJEWS030393_X1-frozen

value: F

value: EWS

value: Lung

value: Y


title: ACT/ACC_Patient tumor-SJACT030812_D3-FFPE

value: Patient tumor


title: D_GBM_019_TLS_s15

value: TLS


title: D_GBM_017_TLS_s15


title: DSRCT_Patient tumor-SJDSRCT030490_R3-FFPE

value: DSRCT

value: Pelvis


title: D_GBM_015_TLS_s15


title: DSRCT_Xenograft-SJDSCRT030722_X1-frozen

value: M

value: Thigh

value: Xenograft


title: WT_Patient tumor-SJWLM031124_D1-frozen

source_name: Kidney

value: WT

value: Kidney


title: D_GBM_011_control_s15

value: Glioma


title: WT_Patient tumor-SJWLM030924_D2-frozen


title: D_GBM_014_TLS_s15


title: DSRCT_Patient tumor-SJDSRCT046155_D1-FFPE

value: Abdomen


title: WT_Patient tumor-SJWLM030792_D2-frozen


title: D_GBM_013_TLS_s15


title: D_GBM_012_TLS_s15


title: WT_Patient tumor-SJWLM031333_D1-frozen


title: WT_Patient tumor-SJST031558_D1-frozen

value: Adrenal


title: WT_Patient tumor-SJWLM030951_D1-frozen


title: D_GBM_008_TLS_s15


title: D_GBM_010_TLS_s15


title: D_GBM_007_control_s15

value: control


title: WT_Patient tumor-SJWLM031224_D1-frozen

value: F


title: WT_Patient tumor-SJWLM049191_D2-frozen

value: N


title: D_GBM_018_control_s15


title: D_GBM_006_TLS_s15


title: D_GBM_016_control_s15


title: D_GBM_005_TLS_s15


title: WT_Patient tumor-SJWLM031811_D1-frozen


title: WT_Patient tumor-SJWLM030902_D1-frozen

source_name: Retroperitoneum

value: Retroperitoneum


title: D_GBM_004_TLS_s15


title: WT_Patient tumor-SJWLM030467_D1-frozen


title: D_GBM_003_TLS_s15


title: D_GBM_009_TLS_s15


title: D_GBM_023_control_s9


title: D_GBM_001_TLS_s15


title: WT_Patient tumor-SJWLM030739_D1-frozen


title: WT_Patient tumor-SJWLM031677_D6-frozen

source_name: Lymph node

value: Lymph node

value: Y


title: WT_Patient tumor-SJWLM031308_D1-frozen

value: Patient tumor


title: WT_Patient tumor-SJWLM046158_D2-FFPE


title: D_GBM_020_TLS_s9

value: TLS


title: D_GBM_021_TLS_s9


title: WT_Xenograft-SJWLM030467_X1-frozen


title: WT_Xenograft-SJWLM046158_X1-frozen


title: D_GBM_022_TLS_s9


title: D_GBM_019_TLS_s9


title: WT_Xenograft-SJWLM030548_X1-frozen


title: WT_Xenograft-SJWLM046157_X1-frozen


title: WT_Xenograft-SJWLM071774_X1-frozen


title: D_GBM_002_TLS_s15


title: D_GBM_018_control_s9


title: D_GBM_017_TLS_s9


title: D_GBM_015_TLS_s9


title: D_GBM_013_TLS_s9


title: WT_Patient tumor-SJWLM071774_D1-FFPE


title: WT_Patient tumor-SJWLM030704_D4-frozen


title: D_GBM_016_TLS_s9


title: D_GBM_014_control_s9


title: WT_Patient tumor-SJWLM031558_R1-FFPE


title: WT_Patient tumor-SJWLM030043_D3-FFPE


title: D_GBM_012_TLS_s9


title: D_GBM_011_control_s9


title: D_GBM_010_TLS_s9


title: WT_Patient tumor-SJWLM059681_D5-FFPE


title: WT_Patient tumor-SJWLM030180_D5-FFPE


title: D_GBM_009_TLS_s9


title: genomic DNA from KATO-III

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

description: gastric cancer cell line with p53 mutation (null)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: KATO-III

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from cell lines or clinical samples using QIAquick DNA mini kit according to standard instructions

tag: gender

value: Male

value: cell line

value: gastric cancer


title: genomic DNA from IM95

description: gastric cancer cell line with MSI+ and p53 wild-type


title: WT_Patient tumor-SJWLM030467_D3-FFPE

value: M


title: genomic DNA from TMK1

description: gastric cancer cell line with p53 mutation


title: WT_Patient tumor-SJWLM059681_D3-FFPE

value: WT


title: D_GBM_008_TLS_s9


title: genomic DNA from MKN45

description: gastric cancer cell line with p53 wild-type

value: Female


title: D_GBM_007_TLS_s9

value: Glioma


title: D_GBM_005_TLS_s9


title: D_GBM_004_control_s9


title: D_GBM_006_TLS_s9


title: WT_Patient tumor-SJWLM031677_D3-FFPE

source_name: Lymph Node

value: Lymph Node


title: C_GBM_015_control


title: D_GBM_001_TLS_s9


title: WT_Patient tumor-SJWLM030704_D3-FFPE

value: Kidney


title: D_GBM_003_TLS_s9


title: WT_Patient tumor-SJWLM071786_D1-FFPE


title: WT_Patient tumor-SJWLM031124_D4-FFPE


title: WT_Patient tumor-SJWLM031677_D2-FFPE


title: D_GBM_002_TLS_s9


title: C_GBM_013_TLS


title: WT_Patient tumor-SJWLM071784_D1-FFPE


title: WT_Patient tumor-SJWLM071778_D1-FFPE


title: genomic DNA from SNU-1


title: WT_Patient tumor-SJWLM031558_D3-FFPE


title: C_GBM_014_TLS


title: WT_Patient tumor-SJWLM030548_D4-FFPE


title: C_GBM_011_control

value: control


title: WT_Patient tumor-SJWLM030043_D2-FFPE

value: F


title: C_GBM_010_TLS


title: WT_Patient tumor-SJWLM030897_D3-FFPE

value: N


title: C_GBM_009_TLS


title: genomic DNA from YCCEL1

description: gastric cancer cell line with EBV+ and p53 wild-type


title: C_GBM_012_TLS


title: WT_Patient tumor-SJWLM071563_D2-FFPE


title: WT_Patient tumor-SJWLM030739_D3-FFPE


title: WT_Patient tumor-SJWLM059681_D4-FFPE


title: WT_Xenograft-SJWLM049191_X1-frozen

value: Xenograft


title: C_GBM_006_TLS


title: WT_Xenograft-SJWLM031333_X1-frozen


title: WT_Xenograft-SJWLM030704_X2-frozen


title: WT_Xenograft-SJWLM071563_X1-frozen


title: C_GBM_004_control


title: C_GBM_005_TLS


title: WT_Xenograft-SJWLM030897_X1-frozen


title: WT_Xenograft-SJWLM030897_X2-frozen


title: C_GBM_002_TLS


title: WT_Xenograft-SJWLM030951_X1-frozen


title: B_GBM_016_control


title: WT_Xenograft-SJWLM030924_X1-frozen


title: WT_Xenograft-SJWLM030739_X1-frozen


title: C_GBM_003_TLS


title: B_GBM_015_TLS


title: B_GBM_014_TLS


title: WT_Xenograft-SJWLM030902_X2-frozen

value: Retroperitoneum


title: WT_Xenograft-SJWLM071786_X2-frozen


title: WT_Xenograft-SJWLM046152_X1-frozen


title: C_GBM_007_control


title: B_GBM_013_TLS


title: B_GBM_012_TLS


title: WT_Xenograft-SJWLM071786_X1-frozen


title: B_GBM_011_control


title: WT_Xenograft-SJWLM071784_X1-frozen

value: Y


title: B_GBM_010_TLS


title: WT_Xenograft-SJWLM031677_X1-frozen


title: B_GBM_008_control


title: WT_Xenograft-SJWLM030792_X1-frozen


title: B_GBM_009_TLS


title: C_GBM_001_TLS


title: B_GBM_007_TLS


title: WT_Xenograft-SJWLM031224_X1-frozen


title: WT_Xenograft-SJWLM031811_X1-frozen


title: B_GBM_006_TLS


title: WT_Xenograft-SJWLM030043_X1-frozen


title: B_GBM_005_TLS


title: WT_Xenograft-SJWLM059681_X2-frozen


title: WT_Xenograft-SJWLM031308_X1-frozen


title: B_GBM_004_control


title: B_GBM_003_TLS


title: B_GBM_001_TLS


title: WT_Xenograft-SJWLM031677_X2-frozen


title: WT_Xenograft-SJWLM031124_X2-frozen


title: WT_Xenograft-SJWLM031558_X2-frozen

value: Adrenal


title: WT_Xenograft-SJWLM031124_X1-frozen


title: A_GBM_014_TLS

value: TLS


title: WT_Xenograft-SJWLM030704_X1-frozen


title: SS_Patient tumor-SJSS063828_D1-frozen

source_name: Femur

value: SS

value: Femur

value: Patient tumor


title: A_GBM_006_TLS


title: WT_Patient tumor-SJWLM031811_D2-FFPE

value: M


title: A_GBM_004_TLS


title: SS_Patient tumor-SJSS049190_R1-frozen

value: Lung


title: SS_Xenograft-SJSS063828_X1-frozen


title: A_GBM_003_control


title: SS_Patient tumor-SJSS063828_D2-FFPE


title: A_GBM_007_control


title: PAT-548_P

data_processing:
DRAGEN RNA pipeline (v 4.0.4, Illumina)
Assembly: GRCh38/hg38
Supplementary files format and content: raw_counts.csv: Comma-delimited csv file includes the raw counts from the samples. Each column is a sample and each row is a gene.
Supplementary files format and content: tpm_counts.csv: Comma-delimited csv file includes the TPM counts from the samples. Each column is a sample and each row is a gene.
Supplementary files format and content: Metadata.csv: Comma-delimited csv metadata file containing additional information about the samples in the count matrix file.

extract_protocol:
RNA was extractioned from FFPE sections using Maxwell RSC FFPE RNA kit in accordance with the manufacturer’s manual (Promega, United States)
RNA libraries were generated from 200 ng RNA using the Illumina total RNA Prep Ligation with Ribo-Zero Plus kit (Illumina, United States)

value: B cells aggregation


title: RMS_Patient tumor-SJRHB030765_R1-frozen

source_name: Orbit

value: RMS

value: Orbit


title: B_GBM_002_TLS

value: Glioma


title: PAT-645_P


title: RMS_Xenograft-SJRHB015721_X1-frozen


title: C_GBM_008_TLS


title: PAT-553_P


title: RMS_Xenograft-SJRHB015720_X1-frozen

source_name: Oropharyngeal

value: Oropharyngeal


title: PAT-568_P


title: RMS_Patient tumor-SJRHB046156_A3-FFPE

source_name: Chest

value: F

value: Chest


title: RMS_Patient tumor-SJRHB013758_D4-FFPE

value: Abdomen


title: WT_Xenograft-SJWLM071778_X1-frozen

value: WT

value: Kidney

value: Xenograft


title: PAT-251_R


title: RMS_Patient tumor-SJRHB012_R-frozen

source_name: Prostate

value: Prostate

value: N


title: PAT-507_P


title: PAT-567_R


title: RMS_Patient tumor-SJRHB031320_D2-frozen

source_name: Abdomen

value: Y


title: PAT-569_P


title: PAT-566_P


title: RMS_Patient tumor-SJRHB013759_D1-frozen

source_name: Groin

value: Groin

value: Patient tumor


title: A_GBM_002_TLS

value: TLS


title: SS_Xenograft-SJSS049190_X1-frozen

source_name: Lung

value: M

value: SS

value: Lung


title: RMS_Patient tumor-SJRHB013758_D3-FFPE

source_name: Pelvis

value: RMS

value: Pelvis


title: PAT-394_P

value: Glioma

value: B cells aggregation


title: PAT-408_P


title: RMS_Patient tumor-SJRHB030730_D1-FFPE

value: Lymph Node


title: PAT-185_P


title: PAT-27_R


title: RMS_Patient tumor-SJRHB000026_R1-FFPE

source_name: Stomach

value: F

value: Stomach


title: RMS_Patient tumor-SJRHB015721_R2-FFPE

value: Retroperitoneum


title: PAT-560_P

source_name: Glioma


title: RMS_Patient tumor-SJRHB063831_R2-frozen

value: Abdomen

value: unknown


title: RMS_Patient tumor-SJRHB031412_D3-FFPE

source_name: Testicle

value: Testicle

value: N


title: PAT-139_P


title: RMS_Xenograft-SJRHB013757_X2-frozen

source_name: Calf

value: Calf

value: Y

value: Xenograft


title: RMS_Xenograft-SJRHB012_Y-frozen

value: M

value: Prostate


title: PAT-94_P


title: RMS_Xenograft-SJRHB030787_X1-frozen

source_name: Pancreas

value: RMS

value: Pancreas


title: PAT-555_P

value: Glioma


title: PAT-328_P

value: B cells aggregation


title: PAT-162_P


title: RMS_Xenograft-SJRHB046156_X1-frozen

value: Chest


title: RMS_Xenograft-SJRHB063830_X1-frozen

value: Lymph Node


title: RMS_Xenograft-SJRHB046156_X2-frozen

source_name: Breast

value: F

value: Breast


title: PAT-401_P


title: PAT-418_P


title: PAT-446_P


title: RMS_Patient tumor-SJRHB015720_R3-FFPE

value: Oropharyngeal

value: Patient tumor


title: RMS_Xenograft-SJRHB013759_X15-frozen

source_name: Omentum

value: Omentum


title: PAT-644_P


title: RMS_Xenograft-SJRHB013758_X1-frozen

value: Pelvis

value: N


title: RMS_Xenograft-SJRHB013758_X2-frozen

value: Abdomen

value: Y


title: RMS_Xenograft-SJRHB013759_X14-frozen

value: M

value: Xenograft


title: PAT-480_P


title: RMS_Xenograft-SJRHB013759_X1-frozen

value: RMS

value: Groin


title: PAT-314_P

value: Glioma


title: PAT-429_R

value: B cells aggregation


title: PAT-322_R


title: RMS_Xenograft-SJRHB012405_X1-frozen

source_name: Bladder

value: Bladder


title: PAT-330_P


title: PAT-402_P


title: PAT-465_P


title: RMS_Xenograft-SJRHB010927_X1-frozen

source_name: Parapharyngeal

value: Parapharyngeal


title: PAT-511_R


title: RMS_Xenograft-SJRHB010928_X1-frozen

source_name: Bladder/Prostate

value: Bladder/Prostate


title: RMS_Xenograft-SJRHB010463_X16-frozen

value: Lung


title: RMS_Xenograft-SJRHB012_X-FFPE

value: Prostate


title: PAT-493_P2

value: no B cell aggregation


title: PAT-496_P


title: RMS_Xenograft-SJRHB063825_X1-FFPE


title: RMS_Patient tumor-SJRHB030787_D3-FFPE

value: F

value: Pancreas

value: Patient tumor


title: RMS_Patient tumor-SJRHB011_E-frozen

source_name: Neck

value: Neck

value: N


title: PAT-493_P


title: PAT-497_P


title: RMS_Xenograft-SJRHB011_Y-frozen

value: M


title: A_GBM_005_TLS

value: TLS


title: RMS_Xenograft-SJRHB030730_X1-frozen

source_name: Lymph Node

value: RMS

value: Lymph Node

value: Xenograft


title: RMS_Xenograft-SJRHB030765_X1-frozen

source_name: Orbit

value: Orbit


title: PAT-483_P

value: Glioma


title: PAT-482_P


title: PAT-484_P

value: B cells aggregation


title: PAT-554_P


title: RMS_Xenograft-SJRHB063831_X1-frozen

source_name: Abdomen

value: Abdomen

value: unknown


title: RMS_Xenograft-SJRHB030705_X1-frozen

source_name: Peritracheal

value: Peritracheal


title: RMS_Xenograft-SJRHB049189_X1-frozen

source_name: Prostate

value: Prostate

value: Y


title: PAT-495_P

value: no B cell aggregation


title: RMS_Xenograft-SJRHB049188_X1-frozen

source_name: Retroperitoneum

value: Retroperitoneum


title: PAT-462_P


title: PAT-499_P


title: PAT-457_P


title: RMS_Xenograft-SJRHB030680_X1-frozen

source_name: Lung

value: Lung


title: RMS_Xenograft-SJRHB071775_X1-frozen

source_name: Paranasal

value: Paranasal


title: RMS_Xenograft-SJRHB030451_X1-frozen

value: F

value: N


title: RMS_Xenograft-SJRHB031117_X1-frozen

source_name: Testicle

value: M

value: RMS

value: Testicle


title: RMS_Xenograft-SJRHB030476_X1-frozen

value: Xenograft


title: PAT-409_P

source_name: Glioma

value: Glioma


title: RMS_Xenograft-SJRHB030549_X1-frozen


title: PAT-410_P


title: PAT-406_R


title: RMS_Xenograft-SJRHB071779_X1-frozen


title: RMS_Xenograft-SJRHB030550_X1-frozen

value: Breast


title: PAT-407_P

value: B cells aggregation


title: RMS_Patient tumor-SJRHB013759_A3-FFPE

value: Omentum

value: Patient tumor


title: RMS_Xenograft-SJRHB031691_X2-frozen

source_name: Pelvis

value: Pelvis


title: RMS_Xenograft-SJRHB031691_X3-frozen

value: Y


title: PAT-357_P


title: PAT-421_P

value: no B cell aggregation


title: PAT-470_R


title: PAT-351_P


title: PAT-565_P


title: PAT-417_P


title: RMS_Xenograft-SJRHB071779_X2-frozen

value: Retroperitoneum


title: RMS_Xenograft-SJRHB031691_X1-frozen


title: PAT-332_R


title: PAT-597_P


title: RMS_Patient tumor-SJRHB030550_R1-FFPE

source_name: Breast


title: PAT-374_R


title: RMS_Xenograft-SJRHB031320_X1-frozen

value: Abdomen


title: PAT-307_P


title: RMS_Patient tumor-SJRHB031691_D3-FFPE


title: RMS_Xenograft-SJRHB031412_X1-frozen


title: PAT-377_P


title: RMS_Patient tumor-SJRHB030680_R1-FFPE

value: Lung


title: RMS_Patient tumor-SJRHB031691_D4-FFPE

value: F


title: PAT-393_P


title: RMS_Patient tumor-SJRHB071775_D1-FFPE

value: Paranasal


title: PAT-63_R


title: RMS_Xenograft-SJRHB000026_X2-frozen

source_name: Stomach

value: Stomach


title: PAT-181_R2


title: DisrR_NRPMI_R2

city: STRASBOURG

last: Lalaouna

address: 2, Allée Konrad Roentgen

department: Institut de Biologie Moléculaire et Cellulaire

institute: CNRS

description: Library name: Sample_8

data_processing:
Basecalling pipeline: 1. HiSeq Control Software 2.2.38; 2. RTA 1.18.61.0; 3. CASAVA-1.8.2
Adapter sequences and poor quality reads removed with Trimmomatic
Reads alignement on the HG001 genome (GenBank assembly accession: GCA_001900185.1) using BOWTIE2 (very sensitive end-to-end protocol with maximum 4 mismatches allowed).
Reads per feature counted with Htseq-count. The protocol chosen is interception non-empty, with reverse strand interpretation.
Differential analysis with DEseq2 (n=2)
Assembly: GCA_001900185.1
Supplementary files format and content: tab-delimited text file including Fold changes and P-values.

molecule: cytoplasmic RNA

organism: Staphylococcus aureus

source_name: HG001 WT

growth_protocol: Bacteria were grown in (i) BHI medium and exposed to 250 µM 2,2′-dipyridyl (DIP) for 15 min or (ii) NRPMI medium supplemented with 1 mM MgCl2 and 100 µM CaCl2. Cells were collected at an OD600nm of 1

extract_protocol:
Bacterial cells were resuspended in lysis Buffer (20 mM Tris-HCl pH 8, 150 mM KCl, 1 mM MgCl2, 1 mM DTT) and broken using the FastPrep apparatus (MP Biomedicals). Crude extract were loaded on a MS2-MBP coated column and purified by affinity chromatography. Eluted RNA were extracted with phenol:chloroform:isoamylalcohol prior to RNAseq analysis.
DNase I (0.1 U/ml) treatment was performed 30 min at 37°C. The reactions mixtures were then purified by phenol/chloroform/isoamylalcohol and subsequent ethanol precipitation. RNA pellets were re-suspended in sterile milliQ water. RNA quality and quantity assessments were performed on Agilent Nano Chip on the Bioanalyzer 2100. Ribosomal RNA was depleted from RNA samples using the QIAseq FastSelect rRNA removal kit (QIAGEN), and cDNA libraries were prepared with the NEBNext Ultra II directional RNA library prep kit for Illumina (NEB). Sequencing of cDNA libraries was performed on the NextSeq 2000 system (Illumina).

value: HG001 delta-isrR

value: NRPMI medium


title: RMS_Patient tumor-SJRHB030705_D1-FFPE

source_name: Peritrachea

value: RMS

value: Peritrachea

value: N


title: DisrR_NRPMI_R1

description: Library name: Sample_7


title: RMS_Patient tumor-SJRHB071779_D2-FFPE


title: MS2-IsrR_NRPMI_R1

description: Library name: Sample_5

source_name: HG001 MS2-isrR

value: HG001 MS2-isrR


title: PAT-210_P

value: Glioma

value: B cells aggregation


title: RMS_Patient tumor-SJRHB013759_A4-FFPE

source_name: Chest

value: M

value: Chest

value: Patient tumor


title: PAT-174_P


title: RMS_Patient tumor-SJRHB010463_R1-FFPE


title: DisrR_BHI_R2

description: Library name: Sample_4

value: BHI medium + 250 µM DIP


title: DisrR_BHI_R1

description: Library name: Sample_3


title: RMS_Patient tumor-SJRHB031691_D2-frozen

value: Pelvis

value: Y


title: MS2-IsrR_BHI_R1

description: Library name: Sample_1


title: RMS_Patient tumor-SJRHB010928_R1-frozen

source_name: Bladder/Prostate

value: Bladder/Prostate


title: RMS_Patient tumor-SJRHB030451_R1-FFPE

source_name: Lymph Node

value: F

value: Lymph Node


title: PAT-181_R

value: no B cell aggregation


title: RMS_Patient tumor-SJRHB010927_D1-frozen

source_name: Parapharyngeal

value: Parapharyngeal


title: S3 array, acidic patch mutant octamer chromatin, 100uM ATP

city: San Francisco

first: Vijay

last: Ramani

state: CA

address: 1700 Owen Street

institute: Gladstone Institues

description: Library name: Sample 36

library_source: other

data_processing:
Raw subreads were processed by the ccs package (v 6.9.99) to generate a circular concensus sequence (CCS) for each ZMW. These ccs reads also have kinetic information for each base in the read. Reads are stored in a BAM file.
CCS reads in the CCS BAM were demultiplexed into individual sample BAMs using lima (v2.6.0) with parameters --same --split-bam-named. This generates two files, the BAM and the .pbi index.
Assembly: Reads were aligned to the S3 amplicon sequence using pbmm2 (v1.17.0) with parameters --preset CCS --sort --median-filter --bam-index BAI.
Supplementary files format and content: Processed files are in the format of aligned CCS BAM files that contain our processed accessibility tracks as a tag 'sa' for each CCS read in the BAM file.

molecule: other

organism: Mus musculus

source_name: in vitro

extract_protocol:
A 3.2kb fragment of Cyp3a11 was amplified from the Mus musculus genome and cloned into puc18. The 'S3' array sequence used in the paper was then excised from the plasmid via restriction enzyme digestion and this sequence was assembled into chromatin via salt gradient dialaysis. Chromatin was remodeled with ATP-dependent chromatin remodelers, then footprinted via SAMOSA-ChAAT. After footprinting, reactions were incubated with Proteinase K. DNA was purified from reactions via SMRTBell Beads.
Samples were prepared for sequencing using Pacbio Template Express kits (v2.0 and 3.0) and PacBio adapters (with overhang).

value: in vitro


title: RMS_Patient tumor-SJRHB000026_R7-FFPE

value: RMS


title: RMS_Patient tumor-SJRHB071779_D1-FFPE

value: Retroperitoneum


title: RMS_Xenograft-SJRHB000026_X1-frozen

value: N

value: Xenograft


title: S3 array, acidic patch mutant octamer chromatin +800nM RSC spike in, 100uM ATP

description: Library name: Sample 35


title: Second heart field cells, E9.5, WT

city: Houston

first: Ke

last: Zhang

state: TX

address: 2121 W Holcombe Blvd

department: Center for Epigenetics & Disease Prevention

institute: Texas A&M IBT

description:
Library name: Sample 1
Osr1+ cells, sample barcode suffix (1-3) represents cells from various anatomical locations: 1-anterior, 2-middle, 3-posterior

library_source: transcriptomic single cell

data_processing:
scRNA-seq reads were demultiplexed by Cell Ranger 3.0. The raw data were then normalized by a SCTransform and were initially processed with Seurat for individual time stages.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values and matrix table

source_name: Second heart field

extract_protocol:
Second heart field were harvested from WT mice at E9.5 and E10.5. After dissection, hearts were minced and subjected to cell dissociation using trypsin. After digestion, the samples were centrifuged at 500 x g for 10 minutes. After removing the supernatant, the cells were resuspended and washed in PBS containing RNase inhibitor, and the cell number was measured. Subsequently, cells were processed using the 10x Genomics Chromium Controller to encapsulate them with gel beads in emulsion.
Library preparation followed the protocol provided by 10x Genomics. Sequencing was performed using NextSeq (Illumina). All sequence reads were aligned to the mm10 mouse reference genome.

value: Second heart field

value: Osr1+ cells

tag: age


title: RMS_Patient tumor-SJRHB013757_D3-frozen

source_name: Calf

value: Calf


title: S3 array, acidic patch mutant octamer chromatin +350nM RSC spike in, 100uM ATP

description: Library name: Sample 34


title: RMS_Patient tumor-SJRHB011_D-frozen

source_name: Skull

value: M

value: Skull

value: Patient tumor


title: S3 array, 100nM RSC +100uM ADP, 2x beads incubation

description: Library name: Sample 33


title: RMS_Xenograft-SJRHB010468_X1-frozen

source_name: Thigh

value: Thigh

value: Y


title: MS2-IsrR_NRPMI_R2

description: Library name: Sample_6

value: HG001 MS2-isrR

value: NRPMI medium


title: RMS_Patient tumor-SJRHB012_D-frozen

source_name: Prostate

value: Prostate


title: S3 array, 100uM ATP, 2x beads incubation, RSC removal exp

description: Library name: Sample 31


title: A_biol rep2

city: Hospitalet de Llobregat

first: Loris

last: Mularoni

state: Barcelona

address: Gran Via de l'Hospitalet, 199

department: P-CMR[C]

country: Spain

institute: IDIBELL

description: Library name: A_2

data_processing:
Analysis of data was conducted using the nf-core/atacseq (10.5281/zenodo.2634132) pipeline implemented in Nextflow (34556866). This pipeline integrates various software tools for quality control, read alignment, peak calling, and differential accessibility analysis. Raw sequencing reads were pre-processed by adapter trimming using Trim Galore!(https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adapter sequences and low-quality bases. Subsequently, read mapping to the hg38 reference genome was performed with BWA (19451168). SAMtools (19505943) was employed for sorting, indexing, and filtering of aligned reads. Normalized coverage tracks were generated using BEDTools (20110278) and bedGraphToBigWig (20639541). Peak calling was performed using MACS2 (18798982), and annotation relative to gene features was conducted with HOMER (20513432). Consensus peak sets were created using BEDTools. Quantification of reads was achieved using featureCounts (24227677), and quality control assessment was performed using MultiQC (27312411) and FastQC (27312411). Differential accessibility analysis was conducted with DESeq2 (25516281) within the R programming environment. Tornado plots were generated using Deeptools (27079975) computeMatrix and plotHeatmaps tools. An adjusted P value ≤0.05 was used as the significance threshold for the identification of differentially accessible regions.
Assembly: hg38
Supplementary files format and content: bigWig files containing peak calling results

source_name: hiPSCs

extract_protocol:
We spun 50,000 cells at 500 × g for 5 minutes, followed by a wash using 50 μL of cold 1x PBS and centrifugation at 500 × g for 5 minutes. Cells were lysed using cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500 × g for 10 minutes using a refrigerated centrifuge. To avoid losing cells during the nuclei prep, we used a fixed angle centrifuge and carefully pipetted away from the pellet after centrifugations. Transpose and purify: Immediately following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 μL 2x TD buffer, 2.5 μL Transposase (Illumina) and 22.5 μL of nuclease free water). The transposition reaction was carried out for 30 minutes at 37 °C. Directly following transposition the sample was purified using a Qiagen Minelute kit
Following purification, we amplified library fragments using 1x NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2 (see table below), using the following PCR conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermocycling at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. To reduce GC and size bias in our PCR we monitored the PCR reaction using qPCR in order to stop amplification prior to saturation. To do this, we amplified the full libraries for 5 cycles, after 5 cycles we took an aliquot of the PCR reaction and added 10 μl of the PCR cocktail with Sybr Green at a final concentration of 0.6x. We ran this reaction for 20 cycles, to determine the additional number of cycles needed for the remaining 45 μL reaction. The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ~30 nM in 20 μL. Libraries were amplified for a total of 10–12 cycles

value: hiPSCs

value: CD34+CD43+CD33+ iPSC-derived cells


title: GA_biol rep1

description: Library name: GA_1

value: GATA2+/- ASXL1mut


title: GA_biol rep2

description: Library name: GA_2


title: RMS_Patient tumor-SJRHB010468_D2-FFPE

value: RMS


title: S_biol rep2

description: Library name: S_2

value: GATA2+/- SETBP1 mutation


title: A_biol rep1

description: Library name: A_1


title: RMS_Patient tumor-SJRHB012_S-frozen

value: Bladder/Prostate


title: GSA_biol rep1

extract_protocol:
we spun 50,000 cells at 500 × g for 5 minutes, followed by a wash using 50 μL of cold 1x PBS and centrifugation at 500 × g for 5 minutes. Cells were lysed using cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500 × g for 10 minutes using a refrigerated centrifuge. To avoid losing cells during the nuclei prep, we used a fixed angle centrifuge and carefully pipetted away from the pellet after centrifugations. Transpose and purify: Immediately following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 μL 2x TD buffer, 2.5 μL Transposase (Illumina) and 22.5 μL of nuclease free water). The transposition reaction was carried out for 30 minutes at 37 °C. Directly following transposition the sample was purified using a Qiagen Minelute kit
Following purification, we amplified library fragments using 1x NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2 (see table below), using the following PCR conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermocycling at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. To reduce GC and size bias in our PCR we monitored the PCR reaction using qPCR in order to stop amplification prior to saturation. To do this, we amplified the full libraries for 5 cycles, after 5 cycles we took an aliquot of the PCR reaction and added 10 μl of the PCR cocktail with Sybr Green at a final concentration of 0.6x. We ran this reaction for 20 cycles, to determine the additional number of cycles needed for the remaining 45 μL reaction. The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ~30 nM in 20 μL. Libraries were amplified for a total of 10–12 cycles

value: GATA2+/- SETBP1mut ASXL1mut G646X


title: GSA_biol rep2


title: S3 array, 100nM RSC + 100uM ATP, no beads

description: Library name: Sample 29

value: in vitro


title: S3 array, 100nM RSC +100uM ATP, 2x beads incubation

description: Library name: Sample 32


title: MS2-IsrR_BHI_R2

description: Library name: Sample_2

value: BHI medium + 250 µM DIP


title: RMS_Patient tumor-SJRHB031117_D1-frozen

source_name: Testicle

value: M

value: Testicle


title: S_biol rep1

description: Library name: S_1


title: RMS_Xenograft-SJRHB012_Z-frozen

value: Xenograft


title: Second heart field cells, E10.5, WT

description:
Library name: Sample 2
Osr1+ cells, sample barcode suffix (1-4) represents cells from various anatomical locations: 1-outflow tract, 2-anterior, 3-middle, 4-posterior

value: Second heart field

value: Osr1+ cells


title: G_biol rep2

value: GATA2+/- R396Q mutation


title: S3 array, 260nM ACF + 100uM ATP, no beads

description: Library name: Sample 28


title: G_biol rep1


title: S3 array, 260nM ACF + 100uM ADP, 2x beads incubation

description: Library name: Sample 27


title: RMS_Patient tumor-SJRHB030476_D2-frozen

source_name: Abdomen

value: Abdomen

value: N

value: Patient tumor


title: CTRL_biol rep2

value: hiPSCs

value: WT

value: CD34+CD43+CD33+ iPSC-derived cells


title: CTRL_biol rep1


title: S3 array, 260nM ACF + 100uM ATP, 2x beads incubation

description: Library name: Sample 26


title: CP97

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

description: Library name: 10579-CP-97

data_processing:
Illumina Casava1.7 software used for basecalling.
The reads were trimmed using Cutadapt v2.3 (Martin, 2011). The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data. Reads were mapped to the reference genome GRCm38 (ENSEMBL 102), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq (Dobin). QC metrics from several different steps in the pipeline were aggregated by multiQC v1.7 (Ewels et al., 2016).
Normalized by DESeq2 with rlogTransformed
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include rlogTransformed values for each sample

source_name: Hippocampus

growth_protocol: The 11-week-old male C57BL/6J mice were purchased from Jackson Laboratory (cat# 000664; RRID:IMSR_JAX:000664; Bar Harbor, ME). For the study, all mice were singly housed, given access to food and water ad libitum, and maintained on a 12:12 h light/dark cycle.

extract_protocol:
Total RNA was extracted from mouse hippocampus tissues using TRIzol reagent (Invitrogen, Carlsbad, CA) and purified by an RNA clean-up and concentration kit (Norgen Biotek, Thorold, ON, Canada). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina, per manufacturer instructions (New England Biolabs, Ipswich, MA). This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeqXPlus). BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files.

value: Hippocampus

value: EX


title: RMS_Patient tumor-SJRHB063830_D1-frozen

value: RMS

value: Lymph Node


title: S3 array, 100uM ATP, 2x beads incubation, ACF removal exp

description: Library name: Sample 25

value: in vitro


title: CP88

description: Library name: 10579-CP-88


title: GS_biol rep2

value: GATA2+/- SETBP1mut D898N


title: CP91

description: Library name: 10579-CP-91

value: HFD


title: CP85

description: Library name: 10579-CP-85

value: SD


title: CP89

description: Library name: 10579-CP-89

value: KD


title: CP84

description: Library name: 10579-CP-84


title: RMS_Patient tumor-SJRHB049189_D1-frozen

value: M

value: Prostate

value: Y


title: RMS_Patient tumor-SJRHB063825_R1-frozen

value: Bladder/Prostate


title: S3 array, 70nM ACF spike in, 488-labeled ACF, 100uM ATP

description: Library name: Sample 24


title: GS_biol rep1


title: S3 array, 140nM ACF premix, 100uM ATP, Fig2

description: Library name: Sample 22


title: CP81

description: Library name: 10579-CP-81

value: DR


title: S3 array, 350nM ACF spike in, 488-labeled ACF, 100uM ATP

description: Library name: Sample 23


title: RMS_Patient tumor-SJRHB049188_D1-frozen

source_name: Retroperitoneum

value: Retroperitoneum

value: Patient tumor


title: S3 array, 70nM ACF premix, 100uM ATP, Fig2

description: Library name: Sample 21


title: CP79

description: Library name: 10579-CP-79


title: RMS_Patient tumor-SJRHB030549_D2-frozen

source_name: Lung

value: Lung


title: CP75

description: Library name: 10579-CP-75

value: Hippocampus


title: CP78

description: Library name: 10579-CP-78


title: CP73

description: Library name: 10579-CP-73


title: CP72

description: Library name: 10579-CP-72


title: CP71

description: Library name: 10579-CP-71


title: RMS_Patient tumor-SJRHB000912_R3-FFPE


title: S3 array, 35nM ACF premix, 100uM ATP, Fig2

description: Library name: Sample 20


title: CP69

description: Library name: 10579-CP-69


title: RMS_Patient tumor-SJRHB031412_D2-frozen

value: Testicle

value: N


title: RMS_Xenograft-SJRHB011_X-frozen

value: RMS

value: Skull

value: Xenograft


title: CP66

description: Library name: 10579-CP-66


title: S3 array, 100uM ATP, ACF premix exp Fig2

description: Library name: Sample 18

value: in vitro


title: CP61

description: Library name: 10579-CP-61

value: EX


title: S3 array, 100nM RSC premix, 100uM ATP

description: Library name: Sample 17


title: CP59

description: Library name: 10579-CP-59

value: SD


title: S3 array, 17nM ACF premix, 100uM ATP, Fig2

description: Library name: Sample 19


title: S3 array, 100nM RSC premix, 100uM AMPPNP

description: Library name: Sample 16


title: CP65

description: Library name: 10579-CP-65


title: RB_Patient tumor-SJRB030188_D5-frozen

source_name: Eye

value: M

value: RB

value: Eye


title: S3 array, 100nM RSC premix, 100uM ADP

description: Library name: Sample 15


title: RB_Patient tumor-SJRB030199_D4-frozen


title: RB_Patient tumor-SJRB049187_D3-frozen

value: F


title: CP58

description: Library name: 10579-CP-58

value: KDI


title: S3 array, 100nM RSC + 100uM ADP, no beads

description: Library name: Sample 30


title: CP55

description: Library name: 10579-CP-55


title: CP50

description: Library name: 10579-CP-50


title: CP48

description: Library name: 10579-CP-48


title: RB_Patient tumor-SJRB030289_D4-frozen


title: S3 array, 280nM ACF, 100uM ADP

description: Library name: Sample 13


title: CP38

description: Library name: 10579-CP-38


title: S3 array, 100uM ATP, RSC premix exp

description: Library name: Sample 14


title: RB_Patient tumor-SJRB030197_D4-frozen


title: CP44

description: Library name: 10579-CP-44


title: CP60

description: Library name: 10579-CP-60

value: KD


title: CP34

description: Library name: 10579-CP-34


title: S3 array, 140nM ACF, 100uM ADP

description: Library name: Sample 12


title: RB_Patient tumor-SJRB030240_D4-frozen

value: Patient tumor


title: RB_Patient tumor-SJRB030149_D4-frozen


title: CP31

description: Library name: 10579-CP-31


title: S3 array, 350nM ACF premix, 100uM ATP

description: Library name: Sample 11


title: CP32

description: Library name: 10579-CP-32


title: CP28

description: Library name: 10579-CP-28


title: CP53

description: Library name: 10579-CP-53


title: CP30

description: Library name: 10579-CP-30


title: S3 array, 140nM ACF premix, 100uM ATP

description: Library name: Sample 10


title: RB_Patient tumor-SJRB030485_D1-frozen


title: CP27

description: Library name: 10579-CP-27

value: HFD


title: CP49

description: Library name: 10579-CP-49

value: Hippocampus

value: DR


title: RB_Patient tumor-SJRB030317_D1-frozen

value: N


title: CP24

description: Library name: 10579-CP-24


title: S3 array, 70nM ACF premix, 100uM ATP

description: Library name: Sample 9


title: CP25

description: Library name: 10579-CP-25


title: CP26

description: Library name: 10579-CP-26


title: RB_Patient tumor-SJRB030252_D1-fresh


title: CP23

description: Library name: 10579-CP-23


title: S3 array, 100uM ADP, ACF premix exp

description: Library name: Sample 8


title: CP18

description: Library name: 10579-CP-18


title: S3 array, 800nM ACF premix, 2mM ATP-Mg

description: Library name: Sample 7


title: RB_Patient tumor-SJRB030149_D1-frozen


title: CP16

description: Library name: 10579-CP-16


title: CP14

description: Library name: 10579-CP-14


title: S3 chromatin no spike in, 3.75mM ATP-Mg

description: Library name: Sample 6


title: RB_Patient tumor-SJRB071801_D1-FFPE


title: CP13

description: Library name: 10579-CP-13


title: Hashtags, lane B

city: Melbourne

first: Lachlan

last: Dryburgh

state: Victoria

address: 792 Elizabeth Street

department: The Department of Microbiology and Immunology,  The University of Melbourne

country: Australia

institute: The Peter Doherty Institute for Infection and Immunity

description: Library name: HASH-B

data_processing:
cellranger-6.1.2 multi pipeline
Assembly: refdata-gex-mm10-2020-A-GFP
Supplementary files format and content: Cell ranger output feature count matrix
Library strategy: CITE-seq

molecule: polyA RNA

source_name: B16-gB tumours, female mice

extract_protocol:
B16-gB melanoma tumours were excised, minced, and digested in Liberase TL research grade solution at 0.25 mg per ml for 60 min at 37 °C. Cell suspensions were triturated, passed through 70 µm strainers, and erythrocytes were removed with eBioscience red cell lysis buffer. Cells were Cells were cryopreserved in 10% DMSO: 90% FCS and stored in liquid nitrogen. Viable DAPI negative transgenic CD8 T cells (OT I or gBT I) were stained and sorted via fluorescence activated cell sorting, then stained with hashtag antibodies (Biolegend) according to manufacturer’s protocol.
Libraries were made according to the 10x Genomics protocol (Chromium Single Cell 5' v2)

value: Pooled samples (tumour, skin, spleen)

value: T cells (OT-I or gBT-I transgenic)


title: CP12

description: Library name: 10579-CP-12


title: Gene expression, lane B

description: Library name: GEX-B

data_processing:
cellranger-6.1.2 multi pipeline
Assembly: refdata-gex-mm10-2020-A-GFP
Supplementary files format and content: Cell ranger output feature count matrix


title: RB_Patient tumor-SJRB063840_D2-FFPE


title: RB_Patient tumor-SJRB049186_D2-frozen

value: Y


title: RB_Patient tumor-SJRB063837_D3-FFPE


title: CP10

description: Library name: 10579-CP-10


title: Hashtags, lane A

description: Library name: HASH-A


title: RB_Patient tumor-SJRB030304_D2-FFPE


title: CP9

description: Library name: 10579-CP-9


title: S3 array, 800nM acf spike in, 2mM ATP-Mg

description: Library name: Sample 4

value: in vitro


title: S3 array, 16:1 nucleosomes:DNA

description: Library name: Sample 3


title: Gene expression, lane A

description: Library name: GEX-A


title: RB_Patient tumor-SJRB046161_D2-FFPE


title: S3 array, 3:1 nucleosomes:DNA

description: Library name: Sample 2


title: CP7

description: Library name: 10579-CP-7


title: RB_Xenograft-SJRB071789_X1-frozen

value: Xenograft


title: CP6

description: Library name: 10579-CP-6

value: EX


title: LMO cell hashing library: Pooled draining lymph node samples (n=6 control aCTLA-4-treated and n=6 FLT3L aCTLA-4-treated)

city: Perth

first: Jesse

middle: David

last: Armitage

state: WA

address: 35 Stirling Hwy, Crawley

department: School of Biomedical Sciences

institute: University of Western Australia

description: Library name: LN4_MULTIseq

data_processing:
Raw FASTQ files for TCR and GEX libraries were processed using CellRanger (Version 8.0.1, 10x Genomics) and aligned to the mm10 genome assembly. Demixing of MULTIseq FASTQ files was performed using MULTI-seq (v1.0.2). Both pipelines were run using default parameters. GEX, TCR and LMO information was combined in Seurat v5.
Barcode-level LMO count data (MULTIseq libraries) are provided in .txt format.
Assembly: mm10
Supplementary files format and content: Barcode-level count data (GEX libraries) are provided in .h5 format.
Supplementary files format and content: Barcode-level LMO count data (MULTIseq libraries) are provided in .txt format.
Supplementary files format and content: Barcode-level contig annotations (TCR libraries) are provided in .csv format

source_name: Draining lymph node

extract_protocol:
Mice were euthanised for tumor, dLN, BM and spleen collection. Tumors were finely sliced and enzymatically digested in DMEM containing 0.02 mg ml−1 DNase (Sigma Aldrich) and 1 mg ml−1 type IV collagenase (Sigma Aldrich). Digestion was performed in a rocking incubator at 120 r.p.m. for 30 min at 37 °C. Following digestion, cells were filtered through a 70μm filter twice and resuspended in Fc receptor block before being stained with fluorochrome-conjugated antibodies. For tumor-dLNs, samples were processed into single cells through 70-μm filter mesh in FACS buffer containing Fc receptor block.
Single cell suspensions from digested tumors and draining lymph nodes were processed with V3 chemistry using the Chromium GEM-X Gel Bead kits and Chromium GEM-X Single Cell Library Prep Kit (10X Genomics) according to manufacturers' instructions. Samples were sequenced on a NextSeq2000 (Illumina) using a P1 600 cycle flow cell (PN: 20100981) on a paired-end 300 cycle format, according to manufacturer’s protocol.

value: Draining lymph node

tag: library type

value: MULTIseq


title: CP3

description: Library name: 10579-CP-3


title: RB_Patient tumor-SJRB071804_D2-frozen

value: M

value: RB

value: Eye


title: D14_WT_CD8T_21-11-00081

city: Guangzhou

first: Jing

last: Liao

state: Guangdong

address: No.1 Xinzao Road, Xinzao, Panyu District

department: GMU-GIBH Joint School of Life Sciences

institute: Guangzhou Medical University

description: Library name: Sample 20

data_processing:
This data processing pipeline adheres to a standard RNA sequencing analysis workflow: first, Quality Control was performed using fastqc for initial assessment, followed by read cleaning via trimmomatic to remove adapters, trim low-quality bases, and filter by minimum length. Next, the high-quality reads were Aligned to the reference genome, after index construction, using the STAR aligner. Finally, Gene Expression Quantification was completed by employing featureCounts to tally the number of reads mapped to each gene locus, generating the necessary raw count data for downstream differential expression analysis.
This data processing pipeline adheres to a standard TCR repertoire analysis workflow: first, Unique Molecular Barcodes (UMBs) were applied to correct PCR and sequencing errors and to eliminate PCR duplicates, thereby maximizing sequencing accuracy and quantification. This was followed by mapping the sequences against the IMGT® database to define V, D, J, and C segments. Next, the CDR3 regions were extracted and clonotypes were assembled, undergoing a critical quality control step that eliminated sequences with out-of-frame or stop codons. Finally, the abundance of each TRB clonotype was accurately determined by summing the number of individual clones sharing the identical CDR3 nucleotide sequence.
Assembly: mm10
Supplementary files format and content: The tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: The tab-delimited text file comprehensively contains all sequencing information for both the TCR alpha (α) chain and the TCR beta (β) chain of the corresponding sample. Specifically, the file details VDJC segment usage, precise CDR3 sequences, and the abundance counts for each unique clonotype after error correction and deduplication.
Library strategy: TCR-Seq

source_name: Splenic CD8+ T

growth_protocol: MC38 murine colon cancer cell line were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, and 1% L-glutamine under a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from tumor tissue with TRIzol reagent (Sigma-Aldrich) according to the manufacturer’s instructions.
Library construction began with the enrichment of mRNA using Oligo(dT) beads (by binding to the poly-A tail). The enriched mRNA was fragmented and reverse transcribed into cDNA. The resulting cDNA fragments were then processed using the NEBNext Ultra RNA Library Prep Kit for Illumina, which involved end repair, A-tailing, and ligation of Illumina sequencing adapters to finalize the cDNA library.
Library construction utilized the ImmuHub® TCR profiling system, employing a 5' RACE unbiased amplification protocol. Unique molecular barcodes (UMBs) were introduced during first-strand cDNA synthesis, along with a common adaptor and a reverse primer corresponding to the constant (C) regions of the TRB. This method facilitates the high-throughput sequencing of TRB (TCR β) sequences by using UMBs to control bottlenecks and eliminate PCR and sequencing errors.

treatment_protocol:
Six- to eight-week-old immunocompetent wild-type C57BL/6 mice received a single intraperitoneal injection of azoxymethane at 8 mg/kg on day 0. Mice were subsequently given 2.5% dextran sodium sulfate in their drinking water during weeks 1, 4, 7, and 10, with regular water provided at other times. Colorectal tumors were harvested on day 70 for RNA sequencing analysis.
Wild-type C57BL/6J mice were subcutaneously injected with 1 × 10⁶ Ctrl or Galnt7-/- MC38 cells. Tumors were harvested on day 8 for RNA sequencing analysis.
Wild-type C57BL/6J mice were subcutaneously inoculated with 2 × 10⁶ Ctrl or Galnt7-/- MC38 cells. On day 14, CD8⁺ T cells were isolated from the spleens of tumor-bearing mice using magnetic beads for RNA sequencing and T cell receptor sequencing.

value: Splenic CD8+ T

value: CD8⁺ T cells isolated on day 14 from the spleens of C57BL/6J mice inoculated with MC38-Ctrl cells


title: RB_Patient tumor-SJRB030260_D1-frozen

value: F

value: Patient tumor


title: Gene expression library: Pooled draining lymph node samples (n=6 control aCTLA-4-treated and n=6 FLT3L aCTLA-4-treated)

description: Library name: LN4-GEX

value: mRNA


title: TCR library: Pooled draining lymph node samples (n=6 control non-treated and n=6 FLT3L non-treated)

description: Library name: LN3-TCR

value: TCR


title: CP1

description: Library name: 10579-CP-1

value: Hippocampus

value: KD


title: S3 array, no spike in, 2mM ATP-Mg

description: Library name: Sample 5


title: Gcm1OE_5_RNAseq

city: Okazaki

first: SHOJI

last: TATSUMOTO

address: Myodaiji

institute: The National Institutes of Natural Sciences NINS

description: library 10

data_processing:
The RNA-seq libraries were each sequenced (101 cycles) using the HiSeq 4000 platforms.
Raw sequence reads were aligned to the reference mouse genomes (GRCm38) by TOPHAT2.
Genome-wide expression levels were measured as a unit of FPKM (fragments per kilobase of exon model per million reads mapped) using Cufflinks and the numbers of reads were counted per gene per sample using htseq-count within HTSeq.
Differentially expressed genes (DEGs) were identified by DESeq2.
Assembly: GRCm38.p4
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: embryonic brain (E16.5)

extract_protocol:
Total RNA was extracted from GFP positive portions of brains of 5 control and 5 Gcm1 overexpressed mice at E16.5 using RNeasy Plus Universal Kit (Qiagen). Quality and quantity measurements of extracted RNA were performed using NanoDrop (Thermo Fisher Scientific) and Qubit Fluorometer (Thermo Fisher Scientific), respectively.
Sequencing libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for directional libraries (New England BioLabs) and the KAPA HTP Library Preparation Kits (KAPA Biosystems) according to the manufacturer’s instructions. The RNA-seq libraries were each sequenced (101 cycles) using the Illumina HiSeq platforms.

value: embryonic brain (E16.5)

value: Gcm1 overexpression


title: RB_Patient tumor-SJRB030518_R1-frozen

value: Y


title: LMO cell hashing library: Pooled draining lymph node samples (n=6 control non-treated and n=6 FLT3L non-treated)

description: Library name: LN3_MULTIseq


title: D8_KO_C906

description: Library name: Sample 12

data_processing:
This data processing pipeline adheres to a standard RNA sequencing analysis workflow: first, Quality Control was performed using fastqc for initial assessment, followed by read cleaning via trimmomatic to remove adapters, trim low-quality bases, and filter by minimum length. Next, the high-quality reads were Aligned to the reference genome, after index construction, using the STAR aligner. Finally, Gene Expression Quantification was completed by employing featureCounts to tally the number of reads mapped to each gene locus, generating the necessary raw count data for downstream differential expression analysis.
This data processing pipeline adheres to a standard TCR repertoire analysis workflow: first, Unique Molecular Barcodes (UMBs) were applied to correct PCR and sequencing errors and to eliminate PCR duplicates, thereby maximizing sequencing accuracy and quantification. This was followed by mapping the sequences against the IMGT® database to define V, D, J, and C segments. Next, the CDR3 regions were extracted and clonotypes were assembled, undergoing a critical quality control step that eliminated sequences with out-of-frame or stop codons. Finally, the abundance of each TRB clonotype was accurately determined by summing the number of individual clones sharing the identical CDR3 nucleotide sequence.
Assembly: mm10
Supplementary files format and content: The tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: The tab-delimited text file comprehensively contains all sequencing information for both the TCR alpha (α) chain and the TCR beta (β) chain of the corresponding sample. Specifically, the file details VDJC segment usage, precise CDR3 sequences, and the abundance counts for each unique clonotype after error correction and deduplication.

source_name: Tumor

value: Tumor

value: Tumor tissues collected on day 8 from wild-type C57BL/6J mice subcutaneously injected with MC38-Galnt7⁻/⁻ cells


title: D8_KO_C907

description: Library name: Sample 13


title: D8_KO_C905

description: Library name: Sample 11


title: Gcm1OE_4_RNAseq

description: library 9


title: RB_Patient tumor-SJRB030241_D1-frozen

value: N


title: TCR library: Pooled tumor samples (n=6 control aCTLA-4-treated and n=6 FLT3L aCTLA-4-treated)

description: Library name: T2-TCR

source_name: Whole tumor

value: Whole tumor


title: Gene expression library: Pooled draining lymph node samples (n=6 control non-treated and n=6 FLT3L non-treated)

description: Library name: LN3-GEX

value: Draining lymph node


title: RB_Patient tumor-SJRB030178_D5-FFPE

value: RB

value: Eye


title: TCR library: Pooled draining lymph node samples (n=6 control aCTLA-4-treated and n=6 FLT3L aCTLA-4-treated)

description: Library name: LN4-TCR


title: Gcm1OE_3_RNAseq

description: library 8


title: RB_Patient tumor-SJRB030046_D5-FFPE


title: S3 array, 10:1 nucleosomes:DNA

description: Library name: Sample 1

source_name: in vitro

value: in vitro


title: LMO cell hashing library: Pooled tumor samples (n=6 control aCTLA-4-treated and n=6 FLT3L aCTLA-4-treated)

description: Library name: T2_MULTIseq

value: MULTIseq


title: Gcm1OE_1_RNAseq

description: library 6


title: D14_KO_CD8T_21-11-00082

description: Library name: Sample 21

value: Splenic CD8+ T

value: CD8⁺ T cells isolated on day 14 from the spleens of C57BL/6J mice inoculated with MC38-Ctrl or MC38-Galnt7⁻/⁻ cells


title: D8_Ctrl_C902

description: Library name: Sample 9

value: Tumor tissues collected on day 8 from wild-type C57BL/6J mice subcutaneously injected with MC38-Ctrl cells


title: Gcm1OE_2_RNAseq

description: library 7


title: D8_Ctrl_C901

description: Library name: Sample 8


title: RB_Xenograft-SJRB071807_X1-frozen

value: F

value: Xenograft


title: Control_4_RNASeq

description: library 4

value: embryonic brain (E16.5)

value: control


title: TCR library: Pooled tumor samples (n=6 control non-treated and n=6 FLT3L non-treated)

description: Library name: T1-TCR

value: TCR


title: WT_MC38_3

description: Library name: Sample 7

tag: cell line

value: Wild-type MC38 cells


title: Control_3_RNASeq

description: library 3


title: WT_MC38_2

description: Library name: Sample 6


title: RB_Xenograft-SJRB071806_X1-frozen

value: M


title: RB_Xenograft-SJRB071804_X1-frozen_rep2

value: N


title: LMO cell hashing library: Pooled tumor samples (n=6 control non-treated and n=6 FLT3L non-treated)

description: Library name: T1_MULTIseq

value: Whole tumor


title: Control_2_RNASeq

description: library 2


title: Mixed sample, replicate III, HTO, B6

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

institute: Leibniz Institute for Immunotherapy

description:
Sequenced on NextSeq, two libraries per biological replicate
p123_B6_library_run_1_2_matrix.mtx.gz
p123_B6_library_run_1_2_features.tsv.gz
p123_B6_library_run_1_2_barcodes.tsv.gz
SeuratObj_raw_merged_2023-05-04.rds

data_processing:
Sequencing of libraries on NovaSeq 6000 and NextSeq 2000, producing bcl files
Demultiplexing of bcl files with Illumina Dragon bclconvert (v 3.8.4,NextSeq 2000)  and DragonServer (v 2.1 NextSeq 6000)
Mapping to mouse genome with cellranger v.7.0.0 using default parameters
Demultiplexing of treatments using HTOs with Seurat (version 4.0.5), identification of doublets via Cell Hashing and scDblFinder (version 1.8.0)
Normalization, scaling, finding variable features and PCA with Seurat, integration of batches with Harmony (version 0.1.0)
Clustering with Seurat
Annotation with SingleR (version 1.8.1)
Assembly: refdata-gex-mm10-2020-A:ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz, ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M23/gencode.vM23.primary_assembly.annotation.gtf.gz
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz for each library, mRNA and HTO combined
Supplementary files format and content: Seurat objects, raw/unfiltered and filtered/processed (dimensionality reduction, clustering, annotation…)

molecule: protein

source_name: small intestine

growth_protocol: Crypts were suspended in liquefied growth factor reduced Matrigel (Corning) (33% ENR-medium or PBS; 66% growth factor-reduced Matrigel) at 4°C, and were plated in delta-surface Nunc 24-well plates in 30 μL drops, each containing approximately 200 crypts. After the Matrigel drops polymerized, 500 µl complete crypt culture medium was added to small intestine crypt cultures. ENR-medium was prepared as follows: advanced DMEM/F12 (Life technologies), 2 mM L glutamine (Sigma), 10 mM HEPES (Life technologies), 100 U/ml penicillin, 100 μg/ml streptomycin (Life technologies), 1.25 mM N-acetyl cysteine (Sigma), 1x B27 supplement (Life technologies), 1x N2 supplement (Life technologies), 50 ng/ml mEGF (Peprotech), 100 ng/ml rec. mNoggin (Peprotech), 10% human R-spondin-1-conditioned medium of hR spondin-1 transfected HEK 293T cells. All plates were incubated at 37 °C / 5% CO2 and medium was replaced every 2-3 days. After 7 days organoids were passaged by mechanical disruption with a 5 ml syringe and a 18 G needle.

extract_protocol:
Intestinal organoids were washed with PBS, resuspended in TrypLE Express Enzyme and digested for 10 minutes at 37°C. Afterwards the reaction was stopped by adding PBS + 0,5% FBS and passed through a 100µm strainer. The single cells were stained with EpCAM-BUV395 and respective Hashing antibodies (TotalSeq B). Live/dead staining was performed with Propidiumiodid. Single cells were sorted by FACS as live/dead- EpCAM+ single cells and directly processed for scRNA-seq
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 and 3’ Feature Barcode Kit (Dual Index)
Oligo-dT priming of full length poly adenylated mRNA, Capture Sequence 1 and 2 for Feature Barcoding library, followed by enzymatic fragmentation, P5,P7 i5,i7 are added via EndRepair, A-tailing and Adaptor Ligation

treatment_protocol: For coculture, allogeneic T cells were added to passaged Balb/c small intestinal organoids with murine IL-2 (30 U/ml, Peprotec) and Dynabeads murine T-activator CD3/CD28 (ThermoFisher, 2 µl per well) respectively. To prevent direct contact between organoids and T cells, plates were kept slightly tilted with the organoid drop above the T cells. T cells were added in concentrations of 100000 cells/well. Blocking antibodies (InVivoMAb anti-mouse IL-10R (CD210), InVivoMAb anti-mouse IFNγ, all Bioxcell) were added in a concentration of 10µg/ml at onset of the coculture. Recombinant IFNγ (Recombinant Murine IFN-γ, Peprotec) was added in a concentration of 0.25ng/ml and rIL-10 (recombinant murine IL-10, Peprotec) in a concentration of 10ng/ml. After 4 days, T cells were removed.

value: small intestine

value: intestinal organoids

tag: cell type

value: intestinal epithelial cells

value: WT

value: mixed sample (all treatments)

value: HTO


title: Control_1_RNASeq

description: library 1

tag: genotype


title: RB_Xenograft-SJRB071797_X1-frozen

value: RB

value: Eye

tag: treatment


title: D70_AOM_DSS_WT_J49

description: Library name: Sample 4

source_name: Colorectal tumors

value: Colorectal tumors

value: Colorectal tumor tissues from the AOM/DSS-induced tumorigenesis model at day 70


title: WT_MC38_1

description: Library name: Sample 5


title: RB_Xenograft-SJRB071800_X1-frozen

value: Xenograft


title: Mixed sample, replicate III, HTO, B5

description:
Sequenced on both NovaSeq and NextSeq, two libraries per biological replicate
p123_B5_library_run_1_2_matrix.mtx.gz
p123_B5_library_run_1_2_features.tsv.gz
p123_B5_library_run_1_2_barcodes.tsv.gz
SeuratObj_raw_merged_2023-05-04.rds
SeuratObj_clustered_2023-05-04.rds