title: iPSC, ASD, donor 6, rep 2

description: D8_ASD_434_filtered_feature_bc_matrix.h5

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were done using the Cell Ranger software (version: 6.0.1, chemistry: SC3Pv3).
Assembly: hg38
Supplementary files format and content: h5 matrix of gene count values

extract_protocol:
DIV8 NSCs were dissociated using Accutase for 5 min at 37oC, collected and washed in NB medium, then filtered through 40 mm cell strainers. Cells were diluted in NB and processed for single cell RNA-seq within 20 min at Yale Center for Genome Analysis (YCGA) core facility.
10X genomic Single Cell 3’ RNA-Seq libraries

treatment_protocol: iPSC were seeded in mTesR medium + ROCK inhibitor then switched to N2-B27 medium supplemented with 2 mM XAV939, LDN193189 (100 nM) and SB431542 (10 mM) (XLSB) for 8 days. NSCs were dissociated on day 8 for scRNA-seq.

value: male

tag: time

value: 8 days in vitro

value: N2-B27 + XLSB-induced neuronal differentiation of the iPSCs.


title: 2341, BRAFi+MEKI, 72hrs, biol rep 2

status: Public on Apr 25 2025

type: SRA

city: Palo Alto

first: Claudia K

last: Petritsch

state: CA

address: 265 Campus Drive

country: USA

institute: Stanford University

description:
Library name: Sample 4
DT3A_1

library_source: transcriptomic

data_processing:
Data processing was performed using Workflow of Novogene Bioinformatics Analysis
Assembly: hg19 or mm10
Supplementary files format and content: csv files including raw counts for each sample

molecule: total RNA

organism: Mus musculus

growth_protocol: In vitro cell lines were maintained in high-glucose glioma medium (Neurobasal-A medium without L-Glutamine, D-MEM/F12 Medium, MEM Non-Essential Amino Acids Solution, MEM Sodium Pyruvate solution, GlutaMAX-I Supplement, HEPES Buffer solution, B27 Supplement without vitamin A and N2 Supplement). This base medium mixture was changed twice a week. In paralell, we added growth factors (FGF, EGF, PDGFAA, PDGFBB and Heparin).

extract_protocol:
2341, aGBM5, STN49 cell lines: Total RNA was extracted using the RNeasy Plus kit (QIAGEN). 0.4µg of total RNA was submitted to Novogene (Novogene Corporation Inc) for RNA sample QC, library preparation and sequencing.
RNA libraries for RNA-seq were prepared using Workflow of Novogene mRNA-seq services

treatment_protocol: 2341, aGBM5, STN49 cell lines: stock solutions of dabrafenib and trametinib were dissolved at 10 mM concentration in DMSO (3176-100 ml; ThermoFisher Scientific,), aliquoted and stored at -80 oC.  For measuring viability and constructing dose-response curves, cells were dissociated with Accutase (NC9389010; ThermoFisher Scientific,) and 104 cells were plated per well in a 96-well half-white plates (3688; ThermoFisher Scientific,) using the corresponding vessel. After 24 hours, a serial dilution of 10 μM dabrafenib or trametinib were added in triplicate to the seeded cells.

tag: tissue

tag: cell line

value: Murine glioma cell line

tag: cell type

value: Glioma cell line

tag: genotype

value: BRAF V600E mutation

tag: treatment

value: BRAFi+MEKi


title: iPSC, ASD, donor 5, rep 2

city: Barcelona

first: Xoel

last: Mato Blanco

state: Barcelona

address: Doctor Aiguader, 88

department: Neurogenomics

country: Spain

institute: Institut Hospital del Mar d'Investigacions Mèdiques

description: D8_ASD_384_filtered_feature_bc_matrix.h5

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Homo sapiens

source_name: fibroblast

growth_protocol: iPSC lines were maintained in feeder-free condition, then dissociated in single cells with Accutase, plated in a Matrigel-coated 6 well plates with mTeSR1 + 5 mM Y27632, ROCK inhibitor at 37 oC, 5% CO2. ROCK inhibitor was removed after 24 hours and cells were cultured for 4 days before the next passage.

value: fibroblast

value: iPSC

value: Neural Stem Cells

tag: line

tag: Sex

tag: disease

value: Idiophatic  ASD


title: RNAseq_MYCNER_shTCEAL1_Ctrl_rep2

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

description: polyA-RNAseq

data_processing:
Fastq files were generated on Illumina’s BaseSpace platform, using Illumina_DRAGEN_FASTQ_Generation_v3.7.4. Overall sequencing quality was determined by analyzing the FASTQ files with the FastQC script.
For ChIP, ChIP-Rx and RNA sequencing, reads were aligned to hg19 using Bowtie2 or STAR with default parameters. For ChIP-Rx, the reads from the spiked mouse genome were aligned to mm10 using Bowtie or STAR with default parameters. The corresponding datasets were normalized based on mm10 reads.
Following normalization, alignment files were converted to bedgraph files to be viewed in a genome browser. For RNA-sequencing, featureCounts was used to count reads per gene.
Assembly: hg19
Supplementary files format and content: For ChIP and ChIP-Rx sequencing experimets, processed files are in bedgraph format. For RNA sequencing, the processed file is a featureCounts generated tab-delimited text file.

source_name: SHEP

growth_protocol: All used human neuroblastoma SHEP cells were grown in RPMI-1640 medium supplemented with with 10% bovine serum and 1% penicillin/ streptomycin. Mouse NIH-3T3 spike-in cells were grown in DMEM medium supplemented with 10% bovine serum and 1% penicillin/ streptomycin. Cells were cultured at 37°C at 5% CO2.

extract_protocol:
For ChIP and ChIP-Rx sequencing, cells were fixed with formaldehyde and spiked with murine NIH-3T3 cells at a 1:10 cell ratio. The crosslinked chromatin was extracted and fragmented using a Covaris Ultrasonicator. Chromatin was then added to a pre-incubated bead/antibody mix. Following incubation and stringent washing, chromatin was eluted, protein and RNA were digested with proteinase K and RNase A and DNA was isolated by phenol-chloroform.
For RNA sequencing, cells were harvested and total RNA was extracted with RNeasy MiniKit (Qiagen) according to manufacturer's instructions. On-column Dnase I digestion was performed followed by mRNA isolation with the NEBNext Poly(A) mRNA Magnetic Isolation Kit (NEB).
ChIP and ChIP-Rx libraries were prepared with the NEBNext Ultra II DNA Library Prep kit. RNAseq libraries were generated with the NEBNext Ultra II Directional RNA Library Prep kit. All libraries were PCR-amplified using a set of Illumina compatible index primers.
For all described libraries, a qPCR was performed prior to the indexing-PCR, to determine optimal PCR cycle numbers. Following the indexing-PCR, libraries were purified using SPRI-beads (Backman Coulter). Library quality and fragment size distribution was analyzed on a Fragment Analyzer (Advanced Analytical). Sequencing was performed in single-read or paired-end mode on a NextSeq2000 platform (Illumina).

treatment_protocol: The induction of NMYC in the SHEP MYCN-ER cells was achieved by adding 4-OHT (200 nM). The expression of an shRNA targeting TCEAL1 in the SHEP cells was induced with 1 µg/ml doxycycline (=Dox). Where indicated, SHEP cells were treated with the CDK7 inhibitor THZ1 (800 nM) or the CDK9 inhibitor NVP-2 (1 µM).

value: SHEP

value: Neuroblastoma

tag: oht treatment_(mycn_active)

value: No

tag: dox treatment_(shtceal1_active)

tag: antibody


title: 2341, BRAFi+MEKI, 72hrs, biol rep 1

description:
Library name: Sample 3
DT2A_1


title: Psoriasis skin 5

city: Seoul

first: Hye Li

last: Kim

address: 50-1, Yonsei-ro

country: South Korea

institute: Yonsei university

description: Library name: PSO5

data_processing:
Raw sequencing reads were processed using the Galaxy platform (https://usegalaxy.org). Adapter sequences and low-quality bases were trimmed using Cutadap. Reads were aligned to the human reference genome (GRCh38) using HISAT2.
Assembly: GRCh38
Supplementary files format and content: csv file include raw counts for each sample

source_name: skin

extract_protocol:
Total RNA was extracted from skin using the Rneasy Plus Mini Kit (Qiagen), according to the manufacturer's instructions.
RNA-seq libraries were prepared using a SureSelect Strand Specific RNA Reagent Kit (Agilent Technologies) according to the manufacturer's protocol.

value: skin


title: Control,311,DIV 38,rep_1

description: HiSeq paired-end, 100 bp

data_processing:
Sequence reads were trimmed for adaptor sequence using Trimmomatic (version: 0.39, ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:36)
Trimmed sequence reads were mapped to hg38 using STAR (version: 2.7.9)
Duplicates were removed using picard (version: 2.25.6, VALIDATION_STRINGENCY: LENIENT)
Read count extraction was performed using featureCounts from the Subread library (version: 2.0.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: meninge fibroblast

extract_protocol:
Total RNA was collected on day 8, 17, 32, 38 from NSCs/neurons, or from PS2, PS4 and PS8, after exposing cells to 0.1, or  20 ng/mL FGF2 for 6 days. RNA was collected from 3 different wells-replicates using RNeasy Mini Kit (Qiagen, 74104).
mRNA was purified from 200 ng of total RNA with oligodT beads and sheared by incubation at 94°C in the presence of Mg (RocheKapamRNAHyper Prep Cat. KR1352).

treatment_protocol:
Differentation protocol: iPSC were seeded in mTesR medium + ROCK inhibitor then switched to N2-B27 medium +  2 mM XAV939, LDN193189 (100 nM) and SB431542 (10 mM) (XLSB) for 12 days. NSCs were passaged and differentiated in NB + B27 until day 38.
Passaging protocol: iPSCs were plated with mTeSR1 plus ROCK inhibitor and then to N2 + B27+ 100 nM LDN193189 and 2 mM SB431542 for 8 days (passage 1). From passage 2 hNSCs were cultured in N2 medium + 20 ng/mL FGF2 and serially passaged every 6 days. NSCs were exposed to 0.1 or  20 ng/mL FGF2 for 6 days.

value: meninge fibroblast

value: Female

tag: fgf2 concentration_(ng/ml)

value: No FGF2

tag: time (days_in_vitro)_or_passage

value: DIV 38

value: Unaffected

value: N2-B27 + XLSB-induced neuronal differentiation of the iPSCs for 12 days. NSCs were passaged and differentiated in NB + B27


title: Slide2_WT_Replicate2

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: Illumina

data_processing:
We used Space Ranger (v2.1.0) by 10X Genomics to map the spatial RNA-seq reads to the modified B73 v5 reference genome and to count gene expression. After normalizing the gene expression data using sc.pp.normalize_total function (targeting a total count of 10,000 per spot) and applying log transformation in Scanpy (v1.10.2), the spatial expression values were visualized using sc.pl.spatial function in Scanpy, overlaying the expression data on the corresponding tissue images 73.
Assembly: B73 v5
Supplementary files format and content: processed scanpy objects
Library strategy: spatial transcriptomics

organism: Zea mays

source_name: early ear

extract_protocol:
For the spatial RNA-seq experiment, the early maize ear, matching the stages of the single-cell datasets, were sampled. The tissues were embedded in the Optimal Cutting Temperature (OCT) compound, snap-frozen in a cold 2-methylbutane bath merged in liquid nitrogen, and cryosectioned into 12 um thick slices.
We used the Visium Spatial Gene Expression Kit (10X Genomics, USA) to construct the spatial RNA-seq libraries following the manufacturer’s instructions. The tissue sections were mounted onto the spatial slides, fixed by cold methanol, and stained by 0.05% toluidine blue. The stained tissue sections were imaged using the BZ-X800 fluorescent microscope (Keyence, Japan). To determine the optimal tissue permeabilization time, we performed the Tissue Optimization workflow on a series of digestion times for each tissue type. For the spatial RNA-seq libraries, mRNA was first released according to the optimal permeabilization time, then the spatially barcoded cDNA were synthesized on the slides. Finally, cDNA were released from the slide and subjected to amplification and library construction, following the manufacturer’s specifications

value: early ear


title: Psoriasis skin 4

description: Library name: PSO4


title: iPSC, ASD, donor 4, rep 2

description: D8_ASD_375_filtered_feature_bc_matrix.h5

value: male

value: 8 days in vitro

value: N2-B27 + XLSB-induced neuronal differentiation of the iPSCs.


title: Control,290,DIV 38,rep_1

description: HiSeq paired-end, 100 bp

value: iPSC

value: Male


title: 2341, DMSO, 72hrs, biol rep 2

description:
Library name: Sample 2
C3A_2

value: Murine glioma cell line

value: Glioma cell line

value: BRAF V600E mutation

value: DMSO


title: iPSC, control, donor 3, rep 2

description: D8_Ctrl_317_filtered_feature_bc_matrix.h5

source_name: skin fibroblast

value: skin fibroblast

value: Neural Stem Cells

value: female


title: 2341, DMSO, 72hrs, biol rep 1

description:
Library name: Sample 1
C2A_1


title: ASD,434,DIV 30,rep_1

description: HiSeq paired-end, 100 bp

value: fibroblast

value: No FGF2

value: DIV 30

value: Idiophatic  ASD


title: Slide1_WT_Replicate1

description: Illumina

value: early ear


title: iPSC, control, donor 2, rep 2

description: D8_Ctrl_311_filtered_feature_bc_matrix.h5

value: meninge fibroblast

value: Unaffected


title: Bif3, replicate 2, scATAC-seq

description: 10X Genomics

library_source: genomic single cell

data_processing:
BWA alignment 5',3' coordinate adjustment MACS2 peak calling Tn5 integration site intersection with ACRs
Assembly: B73 v5
Supplementary files format and content: Position of ACR - Chromosome_Start position_End position (column 1), Barcode ID (column 2), The number of Tn5 insertion (column 3)

molecule: genomic DNA

source_name: Immature ears

extract_protocol:
Approximately 5 μL of nuclei were diluted 10 times, stained with DAPI (Sigma Cat. D9542), and then assessed for quality and density with a hemocytometer under a microscope. The original nuclei were diluted with DNB buffer to a final concentration of 3,200 nuclei per uL. Finally, 5 uL of nuclei (16,000 nuclei in total) were used as input for scATAC-seq library preparation.
scATAC-seq libraries were generated using the Chromium scATAC v1.1 (Next GEM) kit from 10X Genomics (Cat# 1000175), following the manufacturer's instructions (10xGenomics, CG000209_Chromium_NextGEM_SingleCell_ATAC_ReagentKits_v1.1_UserGuide_RevE).

value: Immature ears


title: ASD,384,DIV 30,rep_1

description: HiSeq paired-end, 100 bp

value: iPSC

value: N2-B27 + XLSB-induced neuronal differentiation of the iPSCs for 12 days. NSCs were passaged and differentiated in NB + B27


title: Slide5_Bif3_Replicate3

description: Illumina


title: iPSC, control, donor 1, rep 2

description: D8_Ctrl_290_filtered_feature_bc_matrix.h5

value: male

value: 8 days in vitro

value: N2-B27 + XLSB-induced neuronal differentiation of the iPSCs.


title: Slide3_WT_Replicate3

description: Illumina


title: A619, replicate 2, scATAC-seq

description: 10X Genomics


title: iPSC, ASD, donor 6, rep 1


title: Bif3, replicate 1, scATAC-seq

description: 10X Genomics


title: Control,317,DIV 38,rep_1

description: HiSeq paired-end, 100 bp

value: Female

value: DIV 38


title: trunk NCCs, control, E10.5

city: Ann Arbor

first: Hiroki

last: Ueharu

state: Michigan

address: 1011 N. Univ. Ave.,

department: Biologic and Material Sciences & Prosthodontics

institute: The University of Michigan School of dentistry

description:
10XGenomics
Control trunk at E10.5

data_processing:
Obtained data were processed by Cell Ranger software v3.0.0
Assembly: mm10
Supplementary files format and content: barcodes file, features file, matrix file

source_name: Trunk regions

extract_protocol:
We harvested embryos at E10.5. We isolated and transferred the BA1 and the trunk region to 1.5 ml tubes, respectively. Tissues were diggested with TrypLE at room temperature for 5 min to make single cell suspensions. Cells were washed with PBS twice.
Single cell RNA libraries were prepared according to the manufacture's protocol by loading onto the Chromium Single Cell 3’ v3 microfluidics chip.

value: Trunk regions

value: Neural crest cells

value: Control mice:P0-Cre(-)caAcvr1(+)

tag: developmental stage


title: cranial NCCs, caAcvr1 mut, E10.5

description:
10XGenomics
Mutant BA1 at E10.5

source_name: First branchial arch (BA1)

value: First branchial arch (BA1)

value: caAcvr1 mut mice:P0-Cre(+)caAcvr1(+)


title: ASD,375,DIV 30,rep_1

description: HiSeq paired-end, 100 bp

value: fibroblast

value: Neural Stem Cells

value: Male

value: No FGF2

value: DIV 30

value: Idiophatic  ASD


title: Control,317,DIV 30,rep_1

description: HiSeq paired-end, 100 bp

value: skin fibroblast

value: iPSC

value: Unaffected

value: N2-B27 + XLSB-induced neuronal differentiation of the iPSCs for 12 days. NSCs were passaged and differentiated in NB + B27


title: iPSC, ASD, donor 5, rep 1

value: male

value: 8 days in vitro

value: N2-B27 + XLSB-induced neuronal differentiation of the iPSCs.


title: A619, replicate 1, scATAC-seq

description: 10X Genomics

value: Immature ears


title: cranial NCCs, control, E10.5

description:
10XGenomics
Control BA1 at E10.5

value: Neural crest cells

value: Control mice:P0-Cre(-)caAcvr1(+)


title: iPSC, ASD, donor 4, rep 1


title: SJRH30 TLE3KO replicate 5 [269]

city: Faridabad

first: Sam

last: Mathew

state: Haryana

address: NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway,

department: Developmental Genetics

country: India

institute: Regional Centre for Biotechnology

data_processing:
The quality of sequence data was checked using using fastqc. The data was processed to remove low quality bases and adapter sequences using fastp v 0.20.1 with default parameters.
The presence of rRNA reads were checked and removed using bbduk package in bbmap software and sortmeRNA rRNA database.
The reads were mapped onto indexed Human reference genome (GRCh38.p7) using STAR aligner v2.7. Gene level expression values were obtained as read counts using featureCounts.
Expression similarity between biological replicates was checked by spearman correlation and Principal Components Analysis using R. Differential expression analysis was carried out using edgeR package after normalizing the data based on trimmed mean of M (TMM) values. Genes with absolute log2 fold change ≥ 2 and adjusted P value ≤ 0.05 were considered significant.
The genes that showed significant differential expression were used for Gene Ontology and pathway enrichment analysis.
Assembly: Human reference genome (GRCh38.p7)
Supplementary files format and content: Excel files with counts

source_name: SJRH30 Rhabdomyosarcoma cells

growth_protocol: Non-targeting control and TLE3 knockout RD and SJRH30 cells were cultured and xenografted into NOD/SCID mice. They were excised when control tumors reached the maximum permitted size.

extract_protocol:
Total RNA extracted using RNEasy mini kit (Qiagen) or Zymo research RNA kit. RNA quality was assessed using Tapestation (Agilent) and quantified using Qubit (ThermoFisher Scientific).
250ng of Total RNA was used to enrich the mRNA using NEBNext Poly (A) mRNA magnetic isolation module (Catalog: E7490, New England Biolabs) by following the manufacturers’ protocol. The enriched mRNAs were further taken for the library preparation using the NEBNext Ultra II RNA Library Prep Kit for Illumina (Catalog: E7775S, New England Biolabs).

treatment_protocol: Tumors were flash frozen in liquid nitrogen.

value: Xenograft

tag: strain

value: NOD/SCID mice

tag: cell line genotype

value: TLE3 knockout


title: Control,311,DIV 30,rep_1

description: HiSeq paired-end, 100 bp

value: meninge fibroblast

value: Neural Stem Cells

value: Female


title: MASH+RvD1 liver scRNA rep2

city: Los Angeles

first: Bishuang

last: Cai

address: 675 Charles E. Young Dr South, Rm 1220

department: Medicine

institute: University of California, Los Angeles

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1
The scRNA-seq filtered raw counts matrices were analyzed in Seurat (v5.0.1) using R (v4.3.2).
Assembly: mm10
Supplementary files format and content: cell barcodes (barcodes.tsv), genes (genes.tsv),  and count matrix (matrix.mtx)

source_name: liver

extract_protocol:
Mouse liver non-parenchymal cells (NPC) for scRNA-seq were isolated. Briefly, the liver was perfused in situ with HBSS buffer (without calcium & magnesium) containing 0.2 mg/mL EDTA, followed by sequential perfusion with HBSS buffer (with calcium & magnesium) containing 0.4 mg/mL pronase (Sigma, P5147) and 0.2% collagenase type II (Worthington, LS004196). The liver was minced and further digested with HBSS buffer (with calcium & magnesium) containing 0.2% collagenase type II, 0.4 mg/mL pronase and 0.1mg/mL DNase I (Roche, R104159001) in 37 C incubator with shaking for 30 min. Digestion was then stopped with DMEM containing 10% serum. The resulting liver cell suspension was passed through 100 mm nylon cell strainer and centrifuged at 50 g for 3 min three times to remove hepatocytes. This NPC suspension was centrifuged at 800 g for 5 min. The NPC cell pellet was subjected to red blood cell lysis buffer for 2 min. Upon the removal of red blood cells, the NPC cells were resuspended in HBSS, and subjected to density gradient centrifugation using 20% Optiprep (Axis Shield, # 1114542) to remove dead cells. Cell viability was confirmed by trypan blue exclusion.
scRNA-seq libraries were prepared using a Chromium Single Cell 3’ Reagent kit (10x Genomics) according to the manufacturer’s instructions.

value: liver

value: Male

tag: age

value: 18 weeks

value: FAT-MASH diet and RvD1 treatment


title: SJRH30 TLE3KO replicate 4 [268]

tag: tissue


title: trunk NCCs, caAcvr1 mut, E10.5

description:
10XGenomics
Mutant trunk  at E10.5

value: Trunk regions

tag: cell line

value: caAcvr1 mut mice:P0-Cre(+)caAcvr1(+)


title: iPSC, control, donor 3, rep 1

value: skin fibroblast

value: iPSC

tag: cell type

value: female

tag: time

value: 8 days in vitro

value: Unaffected


title: MASH+RvD1 liver scRNA rep1

description: 10x Genomics

tag: treatment


title: iPSC, control, donor 2, rep 1

tag: line

value: N2-B27 + XLSB-induced neuronal differentiation of the iPSCs.


title: SJRH30 TLE3KO replicate 3 [267]

value: Xenograft

value: NOD/SCID mice


title: SJRH30 TLE3KO replicate 2 [266]

value: TLE3 knockout


title: MASH liver scRNA rep2

description: 10x Genomics

tag: Sex

value: FAT-MASH diet and vehicle  treatment


title: ASD,384,DIV 17,rep_1

description: HiSeq paired-end, 100 bp

value: fibroblast

value: Neural Stem Cells

value: No FGF2

value: DIV 17

tag: disease

value: Idiophatic  ASD

value: N2-B27 + XLSB-induced neuronal differentiation of the iPSCs for 12 days. NSCs were passaged and differentiated in NB + B27


title: SJRH30 non-targeting control replicate 5 [254]

value: Non-targeting control


title: MASH+RvD1 liver 4

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality. Reads were pre-processed by Trim Galore (v.0.6.3) and Cutadapt programs.
Reads were aligned to the mouse genome mm10 using STAR (v2.7.6a) with the default settings.
Transcript assembly and differential expression analysis were performed using Cufflinks (v2.2.1). Assembling of novel transcripts was not allowed (-G), other parameters of Cufflinks followed the default setting.
A tab-delimited matrix file containing FPKM values for RefSeq genes in each sample generated using Cufflinks.
Assembly: mm10
Supplementary files format and content: tab-delimited text file

extract_protocol:
Total liver RNA from FAT-MASH diet and RvD1-treated mice was extracted using the RNeasy kit (Qiagen) according to the manufacturer’s instructions
RNA-seq library construction was performed at Innomics Inc. with a standard polyA-enrichment protocol.

value: liver

value: Male

value: 18 weeks

value: FAT-MASH diet and RvD1 treatment


title: MASH+RvD1 liver 3


title: ASD,375,DIV 17,rep_1

description: HiSeq paired-end, 100 bp

value: iPSC


title: SJRH30 TLE3KO replicate 1 [265]


title: iPSC, control, donor 1, rep 1

value: meninge fibroblast

value: male

value: 8 days in vitro

value: Unaffected

value: N2-B27 + XLSB-induced neuronal differentiation of the iPSCs.


title: MASH liver scRNA rep1

description: 10x Genomics

value: FAT-MASH diet and vehicle  treatment


title: Control,311,DIV 17,rep_1

description: HiSeq paired-end, 100 bp

value: Neural Stem Cells

value: Female


title: MASH+RvD1 liver 2


title: SJRH30 non-targeting control replicate 3 [252]

value: Xenograft

value: NOD/SCID mice


title: Brain, old, rep3

city: Jena

first: Alessandro

last: Ori

address: Beutenbergstraße 11

institute: The Leibniz Institute on Aging – Fritz Lipmann Institute

description: 150 bp sequencing

data_processing:
Read counts and  normalization was done using DeSeq2 benchwork
Assembly: mm10
Supplementary files format and content: Comma-separated valuesfile includes raw counts for each Sample
Supplementary files format and content: Comma-separated valuesfile includes normalized counts for each Sample
Supplementary files format and content: Comma-separated valuesfile includes TPM values for each Sample

source_name: Brain

extract_protocol:
Total RNA was extracted using Qiazol (Qiagen, 79306) according to the manufacturer's instructions
PolyA selection with ERCC spike-in

value: Brain

value: Whole tissue

tag: genotype

value: WT

value: 33 months


title: Control,317,DIV 17,rep_1

description: HiSeq paired-end, 100 bp

value: skin fibroblast

value: No FGF2

value: DIV 17

value: N2-B27 + XLSB-induced neuronal differentiation of the iPSCs for 12 days. NSCs were passaged and differentiated in NB + B27


title: Brain, old, rep4

description: 150 bp sequencing


title: Chow liver scRNA

description: 10x Genomics

value: liver

value: Male

value: 18 weeks

value: Chow diet


title: SJRH30 non-targeting control replicate 2 [251]

value: Non-targeting control


title: Control,290,DIV 30,rep_1

description: HiSeq paired-end, 100 bp

value: meninge fibroblast

value: iPSC

value: Neural Stem Cells

value: DIV 30

value: Unaffected


title: ASD,434,DIV 17,rep_1

description: HiSeq paired-end, 100 bp

value: fibroblast

value: Idiophatic  ASD


title: Vibrio cholerae C6706, Expressing TseVs, rep3

city: Shen Zhen

first: Ming

last: Liu

address: 1088 Xueyuan Blvd, Nan Shan Qu

country: China

institute: Southern University of Science and Technology

description: Library name: VCT3

data_processing:
Raw RNA-seq reads were trimmed and filtered using Trim Galore v0.6.10 with default settings: adapter removal, Phred quality score cutoff of 20, minimum read length of 20 bp. The quality of clean reads was assessed using FastQC v0.12.1.
Clean reads were aligned to the Vibrio cholerae reference genome using STAR v2.7.11b, allowing up to 10 mismatches per pair (--outFilterMismatchNmax 10) and outputting only uniquely mapped reads (--outFilterMultimapNmax 10).
Gene-level read counts were obtained using featureCounts v2.0.8.
Read counts were normalized using DESeq2 v1.42.1 based on the median-of-ratios method, which corrects for differences in sequencing depth and RNA composition across samples.
Assembly: GCA_000006745.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include DESeq2-normalized read counts for each Sample

organism: Vibrio cholerae C6706

source_name: strain

extract_protocol:
RNA was harvested using HiPure Universal RNA Mini Kit. 1.5 ug of total RNA was used for the construction of seguencing libraries
RNA libraries for RNA-seq were prepared using ALFA-SEQ RNA Library Prep Kit II follwing manufacturer's protocols

value: strain


title: ASD,434,DIV 8,rep_1

description: HiSeq paired-end, 100 bp

value: DIV 8


title: SJRH30 non-targeting control replicate 1 [250]

value: Xenograft

value: NOD/SCID mice


title: Brain, old, rep1

description: 150 bp sequencing

value: Brain

value: Whole tissue

value: WT

value: 33 months


title: Brain, young, rep5

description: 150 bp sequencing

value: 3 months


title: Vibrio cholerae C6706, Expressing TseVs, rep2

description: Library name: VCT2


title: RD TLE3KO replicate 5 [119]

source_name: RD Rhabdomyosarcoma cells

value: TLE3 knockout


title: ASD,375,DIV 8,rep_1

description: HiSeq paired-end, 100 bp

value: Male

value: No FGF2

value: N2-B27 + XLSB-induced neuronal differentiation of the iPSCs for 12 days. NSCs were passaged and differentiated in NB + B27


title: Brain, old, rep5

description: 150 bp sequencing


title: SJRH30 non-targeting control replicate 4 [253]

value: Non-targeting control


title: Vibrio cholerae C6706, Expressing TseVs, rep1

description: Library name: VCT1


title: Control,317,DIV 8,rep_1

description: HiSeq paired-end, 100 bp

value: skin fibroblast

value: iPSC

value: Neural Stem Cells

value: Female

value: Unaffected


title: RD TLE3KO replicate 4 [118]

value: Xenograft


title: Brain, young, rep3

description: 150 bp sequencing


title: RD TLE3KO replicate 3 [117]

value: NOD/SCID mice


title: Vibrio cholerae C6706, Carrying empty vector, rep2

description: Library name: VC2

value: strain


title: Control,290,DIV 8,rep_1

description: HiSeq paired-end, 100 bp

value: meninge fibroblast

value: DIV 8


title: Brain, young, rep1

description: 150 bp sequencing

value: Brain

value: Whole tissue

value: WT


title: RD TLE3KO replicate 1 [115]

value: TLE3 knockout


title: RD TLE3KO replicate 2 [116]


title: Brain, young, rep2

description: 150 bp sequencing

value: 3 months


title: Control,311,DIV 8,rep_1

description: HiSeq paired-end, 100 bp

value: No FGF2

value: N2-B27 + XLSB-induced neuronal differentiation of the iPSCs for 12 days. NSCs were passaged and differentiated in NB + B27


title: MASH+RvD1 liver 1

value: liver

value: Male

value: 18 weeks

value: FAT-MASH diet and RvD1 treatment


title: Vibrio cholerae C6706, Carrying empty vector, rep1

description: Library name: VC1


title: ASD,384,DIV 8,rep_1

description: HiSeq paired-end, 100 bp

value: fibroblast

value: iPSC

value: Neural Stem Cells

value: Idiophatic  ASD


title: RD non-targeting control replicate 5 [104]

value: Xenograft

value: NOD/SCID mice

value: Non-targeting control


title: EMC4 KO 2

city: Zürich

first: Sandesh

last: Neupane

address: Schmelzbergstrasse 12

country: Switzerland

institute: University Of Zurich

description:
Library name: Sample11
KO_EMC5

data_processing:
Transcript quantification was performed with kallisto using the GRCh38.p13 reference transcriptome (Annotation Release 42, downloaded on 2023-01-30, doi:10.1038/nbt.3519). Differential gene expression analysis was conducted using EdgeR (Robinson, McCarthy, and Smyth 2010). All computational analyses, including Gene Set Enrichment Analysis (GSEA) and Over-Representation Analysis (ORA), were executed via the SUSHI platform at the Functional Genomics Center Zurich (Hatakeyama et al. 2016).
Assembly: GRCh38.p13

source_name: Cell-culture

growth_protocol: Normal HEK Cell DMEM complete media

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit following the manufacturer’s protocol. RNA integrity and purity were assessed using a Qubit® Fluorometer (Life Technologies) and a Fragment Analyzer (Agilent). Samples with a 260/280 nm ratio between 1.8 and 2.1 and a 28S/18S ratio between 1.5 and 2 were considered suitable for sequencing. RNA samples (100–1000 ng) underwent poly(A) enrichment and were reverse transcribed into double-stranded cDNA using the TruSeq Stranded mRNA Kit (Illumina).   cDNA libraries were enzymatically fragmented, end-repaired, adenylated, and ligated with TruSeq adapters containing unique dual indices (UDI). Adapter-ligated fragments were enriched by PCR amplification, and final libraries were assessed for quality and quantity using a Qubit® Fluorometer and Fragment Analyzer. The final product had an average fragment size of ~260 bp and was normalized to 10 nM in Tris-Cl (10 mM, pH 8.5, 0.1% Tween-20) before sequencing. Sequencing was performed on an Illumina NovaSeqX platform using a paired-end 2 × 150 bp strategy. Raw reads were pre-processed using fastp (S. Chen et al. 2018) with the following parameters: --trim_front1 1 --cut_tail 20 --trim_poly_x --poly_x_min_len 10 --length_required 18.  Transcript quantification was performed with kallisto using the GRCh38.p13 reference transcriptome (Annotation Release 42, downloaded on 2023-01-30, doi:10.1038/nbt.3519). Differential gene expression analysis was conducted using EdgeR (Robinson, McCarthy, and Smyth 2010). All computational analyses, including Gene Set Enrichment Analysis (GSEA) and Over-Representation Analysis (ORA), were executed via the SUSHI platform at the Functional Genomics Center Zurich (Hatakeyama et al. 2016).
cDNA libraries were enzymatically fragmented, end-repaired, adenylated, and ligated with TruSeq adapters containing unique dual indices (UDI). Adapter-ligated fragments were enriched by PCR amplification, and final libraries were assessed for quality and quantity using a Qubit® Fluorometer and Fragment Analyzer. The final product had an average fragment size of ~260 bp and was normalized to 10 nM in Tris-Cl (10 mM, pH 8.5, 0.1% Tween-20) before sequencing. Sequencing was performed on an Illumina NovaSeqX platform using a paired-end 2 × 150 bp strategy. Raw reads were pre-processed using fastp (S. Chen et al. 2018) with the following parameters: --trim_front1 1 --cut_tail 20 --trim_poly_x --poly_x_min_len 10 --length_required 18.

value: Cell-culture

value: Dividing

value: CRISPR


title: EMC4 KO 3

description:
Library name: Sample12
KO_EMC6


title: mouse TA muscle, KO, rep7

city: Toon

first: Mamoru

last: Aoto

state: Ehime

address: 454 Shitsukawa

department: Department of Circulatory Physiology

country: Japan

institute: Ehime University Graduate School of Medicine

data_processing:
For analysis of DEGs, raw sequencing data were quality-checked and trimmed using FastQC v.12.0 and Trimmomatic v0.39. The resulting high-quality reads were aligned to the mouse reference genome (GRCm39/mm39) using STAR v2.7.9a. Subsequently, RSEM v1.3.3 was employed to quantify gene expression levels. Differentially expressed genes (DEGs) were identified using iDEP v0.96.
Alternative splicing events were identified using two independent software packages: rMATS turbo v4.1.2 and CASH v2.2.1.
Assembly: mm39
Supplementary files format and content: Excel file containing alternative splicing data analyzed using rMATs v4.1.2
Supplementary files format and content: Excel file containing alternative splicing data analyzed using CASH v2.2.1

source_name: tibialis anterior muscle

extract_protocol:
RNA was harvested using the Rneasy mini plus kit (Qiagen). 0.3 ug of total RNA was used to construct sequencing libraries.
RNA libraries for RNA-seq were prepared using the MGIEasy RNA Directional Library Prep Set following the manufacturer’s protocols.

value: tibialis anterior muscle

value: HSA-Cre Tg/+; Acin1 F/F


title: RD non-targeting control replicate 4 [103]


title: mouse TA muscle, KO, rep8


title: EMC4 KO 1

description:
Library name: Sample10
KO_EMC4


title: PEA1 rAREG 3

type: RNA

city: Providence

first: Payton

last: De La Cruz

state: Rhode Island

address: 200 Chestnut St

department: Division of Biology and Medicine

institute: Brown University

description:
low count genes were filtered out for a total of 750 genes detected on the panel
SAMPLE 12

hyb_protocol: The reporter code set and capture probe set tubes were removed from -80C and thawed on ice, prior to mixing by tapping and pulse centrifugation. 70 µl hybridization buffer was added to the tube containing the reporter probe set and mixed by tapping, followed by pulse centrifugation. 8 µl of the diluted reporter probe was added to a PCR tube. Each RNA sample was diluted in water to 25 ng/µl and 2 µl final volume for 50 ng total input per sample. 5 µl RNA sample was added to each tube containing the reporter probe set and mixed by tapping, followed by pulse centrifugation. 2 µl Capture Probe Set was added to each tube, mixed by tapping, and the sample was collected by pulse centrifugation and then immediately placed in a pre-heated PCR machine, with the lid set to 70 °C and the block set to 65 °C. The hybridization was performed for 18 h at 65 °C. Samples were cooled to 4 °C and any condensation was collected by pulse centrifugation. Each sample was diluted with 18 µl hybridization buffer.

scan_protocol: An nCounter Sprint cartridge was calibrated to room temperature for 15 min prior to injection of 33 µl of each sample into one of the 12 injection ports of the cartridge, followed by the introduction of an air seal. The sample injection cartridge was sealed with provided tape and the reagent supply ports were unsealed prior to loading on the nCounter Sprint profiler. The analysis run was started immediately after loading.

data_processing: The resulting data fole in RCC format was used for data analysis in the ROSALIND analysis platform. Raw data in RCC format was uploaded in ROSALIND for automated normalization, background subtraction, and quality control (QC) check.

label: fluorescent barcode

source_name: PEA1 cell line

growth_protocol: OVCR8WT cells were cultured in Dulbecco Modified Eagle Medium supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin. PEA1 cells were grown in RPMI 1640 supplemented with 2mM of glutamine, 2mM of sodium pyruvate, 10% FBS, and 1% penicillin/streptomycin. Cells were maintained in a 37°C/5% CO2 humidified chamber.

extract_protocol: RNA was isolated using Trizol / LiCL extraction/precipitation protocol.

treatment_protocol: OVCAR8WT and PEA1 cells were treated with either BSA control (samples 1-3 and samples 7-9) or 200ng/ml of rAREG (samples 4-6 and samples 10-12) for 2 hours .

value: PEA1 cell line

value: rAREG


title: mouse TA muscle, KO, rep5


title: Vibrio cholerae C6706, Carrying empty vector, rep3

description: Library name: VC3

value: strain


title: PEA1 rAREG 2

description:
low count genes were filtered out for a total of 750 genes detected on the panel
SAMPLE 11


title: Brain, young, rep4

description: 150 bp sequencing

value: Brain

value: Whole tissue

value: WT

value: 3 months


title: RD non-targeting control replicate 3 [102]


title: OXR1 1 activation 3

description:
Library name: Sample9
HA_OXR


title: mouse TA muscle, control, rep3

value: HSA-Cre Tg/+; Acin1 +/+


title: RD non-targeting control replicate 2 [101]


title: PEA1 rAREG 1

description:
low count genes were filtered out for a total of 750 genes detected on the panel
SAMPLE 10


title: OXR1 1 activation 2

description:
Library name: Sample8
HA_OXR


title: mouse TA muscle, control, rep2


title: PEA1 control 3

description:
low count genes were filtered out for a total of 750 genes detected on the panel
SAMPLE 9

value: control


title: mouse TA muscle, control, rep1


title: hippocampus, control_3

city: Cambridge

first: Li-Huei

last: Tsai

address: 43 Vassar Street

institute: Massachusetts Institute of Technology

data_processing:
instrument model: nextseq500/550
data processing was performed using Seurat.
Assembly: mm10
Supplementary files format and content: annotated_seurat_data.RData contains the processed seurat data

source_name: hippocampus

extract_protocol:
Mice were sacrificed and and whole hippocampal region was microdissected, snap frozen and stored at -80°c. Nuclei were then isolated from tisssues
Libraries were prepared using the Chromium Single Cell 3′ Reagent Kits v.3.1 (Dual Index) according to the manufacturer’s protocol (10X Genomics, Pleasanton, CA).
The snRNA-seq libraries were sequenced using NextSeq 500/550 High Output (150 cycles).

treatment_protocol: we exposed one group of Ts65Dn mice (ST group) to one hour of 40 Hz auditory and visual stimulation per day, while a parallel control group of Ts65Dn mice (NS group) was exposed to ambient light and sound. After three weeks of treatment period, hippocampal nuclei were subjected to single nuclei RNAseq using 10x Genomics.

value: hippocampus

tag: condition

value: NS

tag: sample type

value: single nuclei RNA


title: Control,290,DIV 17,rep_1

description: HiSeq paired-end, 100 bp

value: meninge fibroblast

value: iPSC

value: Neural Stem Cells

value: Male

tag: fgf2 concentration_(ng/ml)

value: No FGF2

value: DIV 17

value: Unaffected

value: N2-B27 + XLSB-induced neuronal differentiation of the iPSCs for 12 days. NSCs were passaged and differentiated in NB + B27


title: NTG control KO 3

description:
Library name: Sample6
KO_NTG3

value: Cell-culture

value: Dividing

value: CRISPR


title: MC-LR-Extracellular Vesicles3

city: Nanjing

first: Meihong

last: Guo

state: None Selected

address: 南京市鼓楼区汉口路22号南京大学

institute: Nanjing University

data_processing:
V2-Dr.TOM II
Assembly: Hg38
Supplementary files format and content: tab-delimted text files include raw counts for each sample

source_name: placenta

growth_protocol: HTR-8/Svneo (Human Trophoblast Cell) were cultured in RPMI 1640 medium containing 10% FBS at 37°C with 5% CO2.

extract_protocol:
700 μL QIAzol was added into exoexotic body weight suspension and swirled for 10s-Centrifuge briefly and incubate at room temperature for 5min-Add 140μL chloroform/isoamyl alcohol (24:1), violently upside down for 15s, and incubate at room temperature for 2~3min-Centrifuge at 4℃ at 12,000×g for 8min. Drain the supernatant into the new tube-Add two times the supernatant volume of anhydrous ethanol, mix well-All the mixture was purified by column-Add 700μL RWT buffer to wash once-Add 500μL RPE buffer and wash twice-Centrifuge 12,000×g for 2min to dry the film and discard the collection tube-The purification column was moved to a new collection tube and 20μL RNA-Free water was added. The RNA was incubated at room temperature for 1min, and centrifuged at 12,000×g for 2min to eluate RNA, and about 15μL eluted product was obtained.
RNA libraries for RNA-seq were prepared using DNBSEQ According to following manufacturer's protocols.

treatment_protocol: HTR-8/Svneo cells cultured in exosomes free medium were treated with 0 or 1 μM MC-LR (A-LR-M001, TAIWAN ALGAL SCIENCE INC) for 24 h

value: placenta

value: Human Trophoblast Cell

value: WT


title: NTG control KO 2

description:
Library name: Sample5
KO_NTG2


title: MC-LR-Extracellular Vesicles2

address: 南京市鼓楼区汉口路22号南京大学


title: PEA1 control 2

description:
low count genes were filtered out for a total of 750 genes detected on the panel
SAMPLE 8

value: PEA1 cell line

value: control


title: PEA1 control 1

description:
low count genes were filtered out for a total of 750 genes detected on the panel
SAMPLE 7


title: MC-LR-Extracellular Vesicles1

address: 南京市鼓楼区汉口路22号南京大学


title: hippocampus, control_2

value: hippocampus

value: NS

value: single nuclei RNA


title: NTG control KO 1

description:
Library name: Sample4
KO_NTG1


title: hippocampus, control_1


title: OVCAR8 rAREG 3

description:
low count genes were filtered out for a total of 750 genes detected on the panel
SAMPLE 6

source_name: OVCAR8WT cell line

value: OVCAR8WT cell line

value: rAREG


title: hippocampus, stimulation_3

value: ST


title: OVCAR8 rAREG 2

description:
low count genes were filtered out for a total of 750 genes detected on the panel
SAMPLE 5


title: Normal-Extracellular Vesicles3

address: 南京市鼓楼区汉口路22号南京大学

value: Normal-control


title: hippocampus, stimulation_2


title: NTG control HA 3

description:
Library name: Sample3
HA_NTG3


title: OVCAR8 control 3

description:
low count genes were filtered out for a total of 750 genes detected on the panel
SAMPLE 3


title: OVCAR8 rAREG 1

description:
low count genes were filtered out for a total of 750 genes detected on the panel
SAMPLE 4


title: hippocampus, stimulation_1


title: RD non-targeting control replicate 1 [100]

value: Xenograft

value: NOD/SCID mice

value: Non-targeting control


title: NTG control HA 1

description:
Library name: Sample1
HA_NTG1

value: Cell-culture

value: Dividing


title: OXR1 1 activation 1

description:
Library name: Sample7
HA_OXR

value: CRISPR


title: Normal-Extracellular Vesicles2

address: 南京市鼓楼区汉口路22号南京大学

value: placenta

value: Human Trophoblast Cell


title: Sen_DMSO

status: Public on Apr 24 2025

city: Heidelberg

first: Andres

last: Elia

state: Baden-Württemberg

address: Im Neuenheimer Feld 223

institute: DKFZ

data_processing:
Data was demultiplexed and UMI-sequences were extracted.
rRNA depletion was performed based on custom human rRNA reference files
Genomic bam files were obtained using STAR v2.5.3a (Dobin et al., 2013) to hg19 with --outSAMtype BAM Unsorted --readFilesCommand zcat  --quantMode TranscriptomeSAM GeneCounts --outSAMmapqUnique 0
Count tables were created with featureCounts v1.5.1 with -g gene_id
Assembly: hg19
Supplementary files format and content: TSV files contain featureCounts v1.5.1 ouput of genomic bam files.
Library strategy: Ribo-Seq

molecule: cytoplasmic RNA

source_name: BJ

extract_protocol:
Cytoplasmic RNA from ribosome protected fragments (RPFs) were isolated from RNaseI-treated, purified monosomes using TRIzol reagent.
Libraries were constructed according to McGlincy NJ and Ingolia NT.  Methods. 2017

value: BJ


title: Sen_GC7


title: BJ_DMSO

value: DMSO


title: ATP_CLM_3; THP-1, CLM+ATP, 3h

city: Bethesda

first: Bibi

last: Bielekova

state: MD

address: 10 Center Dr, Bethesda

institute: NIH

data_processing:
Paired end FASTQ files were generated and concatenated by cat package. Preprocessing for FASTQ files (quality control, adapter trimming, quality filtering, per-read quality pruning of data) was performed by fastp package.
The expression of transcripts was quantified based on GRCh38.p14 by using Salmon package.
Preprocess for FASTQ files and quantifying of gene expression were performed by cloud based Galaxy (v0.23.2)
Raw reads count data was normalized and comparison was performed by DESeq2 in iDEP 0.96.
K-means clustering, principal component analysis was done in iDEP.
Assembly: GRCh38/hg38
Supplementary files format and content: normalized_counts.txt

extract_protocol:
Total RNA extraction was performed using Trizol LS reagent (Invitrogen) followed by purification using the AllPrep DNA/RNA kit, including the on-column DNAse treatment (Qiagen).
The Stranded mRNA Prep kit (Illumina) was used to generate sequencing libraries according to the manufacture’s reference guide #1000000124518, v02. Briefly, 10 ng (MDMs_ATP+CLM_6hr) or 25 ng (all others) total RNA was used as template for library preparation.

value: leukemia monocytic cell line

value: WT

value: LPS+CLM+ATP


title: OVCAR8 control 1

description:
low count genes were filtered out for a total of 750 genes detected on the panel
SAMPLE 1

value: OVCAR8WT cell line

value: control


title: ATP_3; THP-1, ATP, 3h

value: LPS+ATP


title: CON_3; THP-1, Ctrl, 3h

value: LPS


title: ATP_CLM_2; MDMs, CLM+ATP, 6h

value: primary monocyte-drived macrophages


title: CON_2; MDMs, Ctrl, 6h


title: ATP_CLM_1; MDMs, CLM+ATP, 3h


title: CON_1; MDMs, Ctrl, 3h


title: ATP_2; MDMs, ATP, 6h


title: ATP_1; MDMs, ATP, 3h


title: NTG control HA 2

description:
Library name: Sample2
HA_NTG2


title: OVCAR8 control 2

description:
low count genes were filtered out for a total of 750 genes detected on the panel
SAMPLE 2


title: FT190,shA4,S9.6 DRIP+RNH

city: Montreal

first: Sidong

last: Huang

address: McIntyre Medical Sciences Building 3655 promenade Sir-William-Osler

country: Canada

institute: McGill University

description: Library name: shA4_S9.6+RNH

library_source: genomic

data_processing:
Sequencing data were mapped to the hg38 genome using bowtie with default parameters. Duplicate reads were removed using samtools. Peaks were calculated using MACS2. Metaplots of ChIP-seq data were generated using ngsplot and heat maps of ChIP-seq data were generated using Deeptools.
Assembly: HG38
Supplementary files format and content: BigWig
Library strategy: CUT&Tag

source_name: Ovary

growth_protocol: FT190 cells were cultured in Roswell Park Memorial Institute 1640 Medium (RPMI, Thermo Fisher Scientific, Cat# 11875-093; no pyruvate) with 6% fetal bovine serum (Sigma, Cat# F1051), 1% penicillin/streptomycin (Thermo Fisher Scientific, Cat# 15140-122), and 2 mM L-glutamine (Thermo Fisher Scientific, Cat# 25030-081). Cells were maintained in a humidified 5% CO2-containing incubator at 37°C and regular Mycoplasma test was performed using Mycoalert Detection Kit (Lonza, Cat# LT07-318).

extract_protocol:
Experiments for CUT&Tag was performed using the CUT&Tag-IT™ R-loop Assay Kit (Active Motif, 53167) according to the manufacturer’s protocol. FT190 control and SMARCA4 knockdown cells were seeded overnight, and 200,000 cells per condition were harvested, washed, and immobilized on Concanavalin A-coated magnetic beads. Cells were treated with RNase A or water (control) for 30 minutes at 37°C, followed by incubation overnight at 4°C with either the Active Motif DNA-RNA hybrid (Clone S9.6) primary antibody or BRCA1 antibody (Millipore, cat: OP92). The following day, a rabbit anti-mouse secondary antibody was added, followed by binding of pAG-Tn5 Transposome for targeted tagmentation at R-loop-enriched regions (S9.6) or BRCA1-enriched regions.
DNA was extracted and libraries were prepared using indexed primers according to the kit instructions. The libraries were PCR-amplified, purified, and quality-checked using a Bioanalyzer. Sequencing was performed on the NextSeq 2000 using paired-end 100 bp reads.

value: Ovary

value: epithelial cell

tag: chip antibody


title: U2OS WT, Asynchronous, Synchronization Control

description: Library name: Sample34

data_processing:
The adaptor sequences were trimmed using cutadapt (v3.4).
rRNA reads were discarded with BLAST-Like Alignment Tool (BLAT, v36x2) and
Remaining reads were aligned to GRCh37/hg19 human genome by Spliced Transcripts Alignment to a Reference (STAR, v2.5.3a). rRNA index for RNA18S5, RNA28S5, RNA5-8S5 was constructed manually from NCBI RefSeq annotation.
Raw counts were determined with a custom script quantifying sorted, genome-based BAM files from RiboSeq. Data were inferred for transcript ID and counts, as obtained with STAR “--quantmode GeneCounts”.
Assembly: hg19
Supplementary files format and content: tab-delimited text file with raw counts
Library strategy: Ribo-seq

source_name: Osteosarcoma

growth_protocol: U2OS were cultured in DMEM supplemented with 10 % FBS and 1 % Pen/Strep and maintained at 37 °C and 5 % CO2

extract_protocol:
Cytoplasmic RNA from ribosome protected fragments (RPFs) were isolated from cytosolic cell lysate. Isolates were RNaseI-treated  and monosomes were purified using TRIzol reagent and chloroform.
Libraries were constructed according to McGlincy NJ and Ingolia NT.  Methods. 2017

treatment_protocol: U2OS cells were treated with different mitosis-arresting drugs for 16 h. Mitotically-arrested cells were harvested by physical disruption, whereas asynchronous cells were gently scraped in PBS with Cycloheximide.

value: Osteosarcoma


title: U2OS WT, G2 enrichment, RO3306 6 µM, 18h

description: Library name: Sample36


title: RPE1 WT, Asynchronous, Nocodazole 16h

description: Library name: Sample39

source_name: Retinal epithelium

value: Retinal epithelium

value: Nocodazole


title: FT190,PLKO,S9.6 DRIP+RNH

description: Library name: PLKO_S9.6+RNH

value: Active Motif DNA-RNA hybrid (Clone S9.6)

value: Ctrl+RNH


title: U2OS WT, Mitosis enrichment, 45 min after G2 enrichment

description: Library name: Sample37


title: U2OS WT, G1 enrichment, 3h after mitosis enrichment

description: Library name: Sample35


title: FT190,PLKO,S9.6 DRIP

description: Library name: PLKO_S9.6

value: Ctrl


title: Normal-Extracellular Vesicles1

address: 南京市鼓楼区汉口路22号南京大学

value: placenta

value: Human Trophoblast Cell

value: Normal-control


title: FT190,shA4,S9.6 DRIP

description: Library name: shA4_S9.6


title: FT190,shA4,BRCA1 CUT&RUN+RNH

description: Library name: shA4_BRCA1+RNH

value: BRCA1 (Millipore, cat:OP92)


title: FT190,shA4,BRCA1 CUT&RUN

description: Library name: shA4_BRCA1


title: BJ_GC7

value: BJ

value: DMSO


title: FT190,PLKO,BRCA1 CUT&RUN

description: Library name: PLKO_BRCA1


title: FT190,PLKO,BRCA1 CUT&RUN+RNH

description: Library name: PLKO_BRCA1+RNH


title: MDA-MB-231 WT, STLC 16h, Harringtonine 10min

description: Library name: Sample33

data_processing:
The adaptor sequences were trimmed using cutadapt (v3.4).
rRNA reads were discarded with BLAST-Like Alignment Tool (BLAT, v36x2) and
Remaining reads were aligned to GRCh37/hg19 human genome by Spliced Transcripts Alignment to a Reference (STAR, v2.5.3a). rRNA index for RNA18S5, RNA28S5, RNA5-8S5 was constructed manually from NCBI RefSeq annotation.
Raw counts were determined with a custom script quantifying sorted, genome-based BAM files from RiboSeq. Data were inferred for transcript ID and counts, as obtained with STAR “--quantmode GeneCounts”.
Assembly: hg19
Supplementary files format and content: tab-delimited text file with raw counts
Library strategy: Ribo-Seq

source_name: Breast Adenocarcinoma

value: Breast Adenocarcinoma

value: WT

value: STLC, Harringtonine


title: MDA-MB-231 WT, STLC 16h, Harringtonine 2min

description: Library name: Sample31


title: RPE1 WT, Asynchronous, DMSO 16h

description: Library name: Sample38


title: MDA-MB-231 WT, DMSO 16h, Harringtonine 10min

description: Library name: Sample29

value: DMSO, Harringtonine


title: MDA-MB-231 WT, STLC 16h, Harringtonine 5min

description: Library name: Sample32


title: MDA-MB-231 WT, DMSO 16h, Harringtonine 2min

description: Library name: Sample27


title: MDA-MB-231 WT, STLC 16h, Harringtonine 0min

description: Library name: Sample30


title: U2OS WT, Salubrinal, 16 h, ISR-control

description: Library name: Sample25

value: Salubrinal


title: PC3 WT, DMSO, 16 h

description: Library name: Sample22

source_name: Prostate Adenocarcinoma

value: Prostate Adenocarcinoma


title: U2OS WT, DMSO, 16 h, ISR-control

description: Library name: Sample24

value: Osteosarcoma


title: MDA-MB-231 WT, Nocodazole, 16 h

description: Library name: Sample21

value: Nocodazole


title: PC3 WT, Nocodazole, 16 h

description: Library name: Sample23


title: MDA-MB-231 WT, DMSO 16h, Harringtonine 5min

description: Library name: Sample28


title: U2OS WT, Nocodazole, 16 h, Rep2

description: Library name: Sample17


title: MDA-MB-231 WT, DMSO, 16 h

description: Library name: Sample20


title: U2OS WT, STLC 16h, Harringtonine 5min

description: Library name: Sample12


title: U2OS WT, DMSO 16h, Harringtonine 10min

description: Library name: Sample9


title: U2OS WT, STLC 16h, Harringtonine 10min

description: Library name: Sample13


title: U2OS WT, Nocodazole, 16 h, Rep1

description: Library name: Sample15


title: U2OS WT, DMSO, 16 h, Rep1

description: Library name: Sample14


title: U2OS WT, DMSO, 16 h, Rep2

description: Library name: Sample16


title: U2OS WT, STLC 16h, Harringtonine 2min

description: Library name: Sample11


title: U2OS WT, STLC 16h, Harringtonine 0min

description: Library name: Sample10


title: U2OS WT, DMSO 16h, Harringtonine 0min

description: Library name: Sample6


title: U2OS WT, S-trityl-L-cysteine (STLC), 16 h

description: Library name: Sample5

value: osteosarcoma

value: S-trityl-L-cysteine


title: U2OS WT, DMSO 16h, Harringtonine 5min

description: Library name: Sample8


title: U2OS WT, DMSO, 16 h

description: Library name: Sample1


title: U2OS WT, Nocodazole, 16 h

description: Library name: Sample3


title: U2OS WT, BI2536, 16 h

description: Library name: Sample2


title: THZ treated group

city: Nanchong

first: Min

last: Yong

state: Sichuan

address: Wen hua Road

department: Center for Reproductive Medicine, Department of Obstetrics and Gynecology

institute: Affiliated Hospital of North Sichuan Medical College,

description: Library name: Sample 2

data_processing:
Quality control: The quality of raw reads was first assessed using the FastQC. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Genomic alignment and quantification: Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2. HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz. The CIRCexplorer program (v2.3.8) was used to identify both the circularizing junction and the spliced sequence of circRNAs. All circRNA candidates with junction reads less than 2 were discarded. The remaining circRNA candidates were considered bonafide circRNAs.
DESeq2 (v2) was applied for the detection of differentially expressed mRNAs between tumor and non-tumor samples, the limma R package (3.40.6) was used for differentially expressed circRNAs.
Assembly: GRCh38
Supplementary files format and content: Count and FPKM values for each sample

growth_protocol: A2780 and SKOV3 ovarian cancer cell lines obtained from Translational Medicine ResearchCenter, North Sichuan Medical College. The cells were successfully recovered and subsequently cultured in RPMI 1640 medium (Gibco, C11875-500B'T) supplemented with 1% penicillin-streptomycin and 10% fetalbovine serum (FBS)(Gibco, 10099-141 C), under 5% CO2 at 37 °C in a humidified incubator.

extract_protocol:
After being treated with 15μM thioridazine for 24h, the SKOV3 cells were lysed with Trizol (Invitrogen, USA) and total RNA was extracted using Trizol reagentaccording to the manufacturer’s instructions.RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly,ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: The SKOV3 cells was treated with 15μM thioridazine for 24h.

value: Ovarian cancer cells

value: 15μM thioridazine


title: U2OS WT, Paclitaxel, 16 h

description: Library name: Sample4

value: Paclitaxel


title: negative control roup

description: Library name: Sample 1


title: E1A.289R.YCD.biol.rep.2

city: Winnipeg

first: Peter

last: Pelka

state: Manitoba

address: 45 Chancellors Cir

department: Microbiology

institute: University of Manitoba

description:
Library name: E1A.289R.YCD.biol.rep.2
Column name in raw_counts: E1A.289R.YCD.2

data_processing:
Base calls were made using the Illumina CASAVA pipeline.
Trimmomatic was used to remove Illumina sequencing adapters and to trim and clip low quality reads
The reads were aligned to the Homo sapiens reference genome GRCh37 using the STAR aligner
Cufflinks were used to assemble aligned RNA-seq reads into transcripts and generate raw read counts
Assembly: GRCh37
Supplementary files format and content: csv file includes raw counts for each sample

source_name: E1A.289R.YCD.biol.rep.2, IMR-90 cells, 16 hpi

growth_protocol: IMR-90 (ATCC# CCL-186) cells were grown in Dulbecco’s Modified Eagle’s Medium (MilliporeSigma) supplemented with 10% fetal bovine serum, streptomycin and penicillin (Corning).

extract_protocol:
Total cellular RNA was extracted from infected cells 16 hours after infection using the TRIzol method
Libraries were prepared using the first strand TrueSeq mRNA protocol for paired reads.

treatment_protocol: Virus infections were carried out at a multiplicity of infection (MOI) of 10 in serum-free medium for 1 hour after which fresh complete media was added without removal of the infection media.

value: Lung

value: IMR 90

value: fibroblast

value: Infection, harvest after 16 hours


title: U2OS WT, DMSO 16h, Harringtonine 2min

description: Library name: Sample7


title: E1A.289R.YCD.biol.rep.1

description:
Library name: E1A.289R.YCD.biol.rep.1
Column name in raw_counts: E1A.289R.YCD.1

source_name: E1A.289R.YCD.biol.rep.1, IMR-90 cells, 16 hpi


title: E1A.243R.dl520.biol.rep.1

description:
Library name: E1A.243R.dl520.biol.rep.1
Column name in raw_counts: dl520.1

source_name: E1A.243R.dl520.biol.rep.1, IMR-90 cells, 16 hpi


title: E1A.243R.dl520.biol.rep.2

description:
Library name: E1A.243R.dl520.biol.rep.2
Column name in raw_counts: dl520.2

source_name: E1A.243R.dl520.biol.rep.2, IMR-90 cells, 16 hpi


title: E1A.289R.pm975.biol.rep.1

description:
Library name: E1A.289R.pm975.biol.rep.1
Column name in raw_counts: pm975.1

source_name: E1A.289R.pm975.biol.rep.1, IMR-90 cells, 16 hpi


title: E1A.289R.pm975.biol.rep.2

description:
Library name: E1A.289R.pm975.biol.rep.2
Column name in raw_counts: pm975.2

source_name: E1A.289R.pm975.biol.rep.2, IMR-90 cells, 16 hpi


title: Lung Tumor TAT-CRE

city: Erlangen

first: Lydia

last: Meder

address: Glückstraße 6

department: Department of Experimental Medicine 1

description:
Library name: SAMPLE 1
10x Genomics

data_processing:
Base calling was performed using the Illumina platform.
Demultiplexing, adapter trimming, UMI-based error corrections done with Singleron’s pipeline.
Gene expression matrices were analyzed in R (v4.3.2) using Seurat- package 5.0.1.
Data were normalized, scaled and analyzed for variable features using the function SCTtransform within Seurat .
PCA was performed on the integrated data set with the number of considered PCA determined by the Elbow-method.
Individual cell clustering was obtained using the Leiden-clustering algorithm with subsequent application of Uniform manifold approximation and projection (UMAP) for data visualization.
Major cell types of the identified clusters were determined by automatic cell type detection by Sctype.
Assembly: mm39
Supplementary files format and content: Tab-Separated Values and Matrix Market Format files

source_name: Lung

growth_protocol: Tumor growth in vivo was monitored until a human end-point according to the approved score sheet was reached.

extract_protocol:
A piece of the tumor tissue with a diameter of 3-5 mm was embedded in Sample Preparation Buffer (Singleron Biotechnologies) stable for up to 72 hours prior processing. Single cell suspension from tumor tissue were processed in sCelLiVETM Tissue Dissociation Buffer.
Single cells were loaded into the microfluidic SCOPE-chipTM and cell identifying tags were flowed in and allowed to settle in the wells on top. mRNA from each lysed cell was hybridized to the barcode sequences on the bead in the same well. Then, reverse transcription of primed RNA and cDNA amplification take place. The amplified cDNA was fragmented, adapter ligated and amplified to construct a sequencing library suitable for the Illumina sequencing platform.

treatment_protocol: Mice were inhaled by TAT-CRE or AD-CRE, respectively.

value: KRAS-G12D/+, Trp53 flox/flox

value: TAT-CRE inhalation

tag: batch


title: MCN-L_06

type: genomic

city: Berlin

first: Mihnea

middle: P.

last: Dragomir

state: Berlin

address: 1 Charitéplatz

department: Pathology

institute: Charité - Universitätsmedizin

hyb_protocol: Standard Illumina Protocol (see manufacturer instructons)

data_processing:
Various R packages as implemented in ChAMP were used for the DNA methylation analysis.
raw .idat files processed as Beta values

label: Cy3 and Cy5

source_name: Liver

extract_protocol: Semi-automated DNA extraction was performed according to the manufacturer’s instructions (Maxwell RSC FFPE Plus DNA Purification Kit, Custom, Promega).

value: Liver

value: partial hepatectomy

value: Female

value: FFPE

tag: sample group

value: MCN-L


title: MCN-P_13

scan_protocol: Standard Illumina Protocol (see manufacturer instructons)

source_name: Pancreas

value: Pancreas

value: distal pancreatectomy

value: MCN-P


title: MCN-P_14

label_protocol: Standard Illumina Protocol (see manufacturer instructons)


title: MCN-P_09


title: MCN-L_03

value: left hepatectomy


title: E1A.WT.dl309.biol.rep.2

description:
Library name: E1A.WT.dl309.biol.rep.2
Column name in raw_counts: dl309.2

source_name: HAdV-C5-dl309.biol.rep.2, IMR-90 cells, 16 hpi


title: MCN-L_01


title: Lung Tumor AD-CRE

description:
Library name: SAMPLE 2
10x Genomics

value: AD-CRE inhalation


title: OVCAR3CIS cells, siMMP3+CIS, rep4

city: San Juan

first: Mariela

last: Rivera-Serrano

state: PR

address: 601 Ave Universidad

institute: University of Puerto Rico Rio Piedras

data_processing:
The library was quantified with KAPA SYBR® FAST qPCR and then sequenced using the Illumina HiSeq platform (2 × 150 bp) with a sequencing depth of approximately 100 million reads per sample. Sequence reads were trimmed to remove possible adapter sequences and nucleotides of poor quality via Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene counts were calculated via featureCounts from the Subread package (version 1.5.2, Parkville, Victoria, Australia), and initial gene expression analysis was performed using the DESeq2 (version 1.28.1) package in the R version 4.0.1 package.
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: tab-delimeted text file include raw counts for each sample

extract_protocol:
Controls, including untreated cells and cells treated with only cisplatin (four biological replicates of each condition), were extracted with the Mirvana RNA Isolation Kit (Fisher, Grand Island, NY, USA). The integrity of the RNA samples was evaluated via an Agilent Bioanalyzer 2100, and 1.0 µg of high-quality RNA was used for the sequencing protocol.
The RNA was enriched, and the library was prepared via GENEWIZ® Strand-specific RNA sequencing with rRNA depletion (GENEWIZ, Inc. South Plainfield, NJ, USA).

value: epithelial cells resistant to cisplatin

value: MMP3 knockdown

value: 50nM siMMP3+2uM cisplatin


title: MCN-P_10


title: MCN-P_12


title: Mock.biol.rep.1

description:
Library name: Mock.biol.rep.1
Column name in raw_counts: Mock.1

source_name: Mock.biol.rep.1, IMR-90 cells,

value: Lung

value: IMR 90

value: fibroblast

value: Mock

value: Mock Infection


title: Mock.biol.rep.2

description:
Library name: Mock.biol.rep.2
Column name in raw_counts: Mock.2

source_name: Mock.biol.rep.2, IMR-90 cells,


title: MCN-P_11


title: MCN-L_04

value: Liver

value: partial hepatectomy


title: E1A.WT.dl309.biol.rep.1

description:
Library name: E1A.WT.dl309.biol.rep.1
Column name in raw_counts: dl309.1

source_name: HAdV-C5-dl309.biol.rep.1, IMR-90 cells, 16 hpi

value: Infection, harvest after 16 hours


title: OVCAR3CIS cells, siMMP3+CIS, rep2


title: MCN-L_02

value: Female

value: FFPE

value: MCN-L


title: MCN-P_06

value: Pancreas

value: distal pancreatectomy

value: MCN-P


title: MCN-P_05


title: MCN-P_08

value: cystectomy


title: MCN-P_07


title: OVCAR3CIS cells, siMMP3+CIS, rep3

value: epithelial cells resistant to cisplatin

value: MMP3 knockdown


title: OVCAR3CIS cells, siMMP3+CIS, rep1

value: 50nM siMMP3+2uM cisplatin


title: MCN-P_03


title: MCN-P_02


title: OVCAR3CIS cells, NC+CIS, rep4

value: WT

value: 50nM NC-siRNA+2uM cisplatin


title: MCN-P_01


title: gIPMN

value: gIPMN


title: OVCAR3CIS cells, NC+CIS, rep2


title: OVCAR3CIS cells, NC+CIS, rep1


title: sh-PURB#1

city: MANHATTAN

first: Zhangchuan

last: Xia

state: NY

address: 1130 St. Nicholas Ave, Rm 608

department: Institute for Cancer Genetics

institute: Columbia University Medical Center

description: Library name: zxgu4_sh-PURB#1

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0).
We test for differentially expressed genes under various conditions using Sleuth or DESeq2, R packages designed to test differential expression between two experimental groups from RNA-seq counts data.
Assembly: Human: GRCh38
Supplementary files format and content: xlsx file includes TPM values for each sample

source_name: Bone

growth_protocol: U2OS cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Extraction of total RNA was using TRIzol reagent according to the manufacturer’s protocol. 1.0 ug of total RNA was used for the construction of sequencing libraries.
We use ribosomal depletion to remove rRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry following manufacturer's protocols.

treatment_protocol: PURB knockdown was induced by treatment of doxycycline (5.0 μg/ml) for indicated time.Control cells were treated with DMSO.

value: Bone

value: Cancer cells


title: P56R cells, Combination, 2Day, rep3

city: Ganzhou

first: zhou

last: dongdong

address: hexie avenue

institute: Gannan Medical University

description: Library name: P43

data_processing:
The clustering of the index-coded samples was performed on a cBotCluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia)according to the manufacturer’s instructions
After cluster generation, the librarypreparations were sequenced on an Illumina Novaseq platform and 150 bppaired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through fastpsoftware.
Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean reads were aligned to the referencegenome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped toeach gene.
Differential expression analysis oftwo conditions/groups (two biological replicates per condition) was performedusing the DESeq2 R package (1.20.0), Genes with an adjusted P-value <=0.05 found by DESeq2 wereassigned as differentially expressed
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes fpkm counts for each sample

source_name: cell line

growth_protocol: P53R cells were incubated in MEM with 10% fetal bovine serum and 1% penicillin-streptomycin at 37 °C under 5% CO2

extract_protocol:
TRIzol(Thermo Fisher)
AMPure XP system and Agilent Bioanalyzer2100 system

treatment_protocol: P53R cells were treated with 1μg/ml Oba01 、1μM Abemaciclib and combanition for 48 h

value: cell line

value: Colorectal cancer cells

value: Combination


title: sh-PURB#2

description: Library name: zxgu6_sh-PURB#2


title: sh-NC#2

description: Library name: zxgu5_sh-NC#2


title: OVCAR3CIS cells, NC+CIS, rep3


title: OVCAR3CIS cells, cisplatin (CIS) treated, rep2

value: 2uM cisplatin


title: P56R cells, Abemaciclib, 2Day, rep3

description: Library name: P33

value: Abemaciclib


title: P56R cells, Combination, 2Day, rep1

description: Library name: P41


title: P56R cells, Abemaciclib, 2Day, rep2

description: Library name: P32


title: P56R cells, Abemaciclib, 2Day, rep1

description: Library name: P31


title: U2OS WT, Nocodazole, 16 h, RNAseq

description: Library name: Sample43

data_processing:
The adaptor sequences were trimmed using cutadapt (v3.4).
RiboSeq: rRNA reads were discarded with BLAST-Like Alignment Tool (BLAT, v36x2) and
RiboSeq: Remaining reads were aligned to GRCh37/hg19 human genome by Spliced Transcripts Alignment to a Reference (STAR, v2.5.3a). rRNA index for RNA18S5, RNA28S5, RNA5-8S5 was constructed manually from NCBI RefSeq annotation.
RiboSeq: Raw counts were determined with a custom script quantifying sorted, genome-based BAM files from RiboSeq. Data were inferred for transcript ID and counts, as obtained with STAR “--quantmode GeneCounts”.
RNA-seq:Alignment was performed against mm10 using STAR with “--twopassMode Basic --twopass1readsN -1 --outSAMtype BAM Unsorted SortedByCoordinate --limitBAMsortRAM 100000000000 --outBAMsortingThreadN=1 --outSAMstrandField intronMotif --outSAMunmapped Within KeepPairs --outFilterMultimapNmax 1 --outFilterMismatchNmax 5 --outFilterMismatchNoverLmax 0.3 --chimSegmentMin 15 --chimScoreMin 1 --chimScoreJunctionNonGTAG 0 --chimJunctionOverhangMin 15  --chimSegmentReadGapMax 3 --alignSJstitchMismatchNmax 5 -1 5 5 --alignIntronMax 1100000 --alignMatesGapMax 1100000 --alignSJDBoverhangMin 3 --alignIntronMin 20 --quantMode TranscriptomeSAM GeneCounts --outSAMmapqUnique 0”
RNA-seq:Raw counts were determined with a custom script quantifying sorted, transcriptome-based BAM files from RNAseq. Data were inferred for transcript ID and counts, as obtained with STAR “--quantmode GeneCounts”.
Assembly: hg19
Supplementary files format and content: tab-delimited text file with raw counts

source_name: Osteosarcoma

extract_protocol:
RiboSeq: Cytoplasmic RNA from ribosome protected fragments (RPFs) were isolated from cytosolic cell lysate. Isolates were RNaseI-treated  and monosomes were purified using TRIzol reagent and chloroform.
RNA-seq:Cytoplasmic RNA was isolated from cytosolic cell lysate. RNA was extracted by Trizol-chloroform extraction and isopropanol precipitation.
RiboSeq: Libraries were constructed according to McGlincy NJ and Ingolia NT.  Methods. 2017
RNA-seq:Libraries were constructed according Loayza-Puch, F., Drost, J., Rooijers, K. et al.   Genome Biology 2013

value: Osteosarcoma

value: Nocodazole


title: P56R cells, Oba01, 2Day, rep3

description: Library name: P23


title: OVCAR3CIS cells, cisplatin (CIS) treated, rep4


title: P56R cells, Combination, 2Day, rep2

description: Library name: P42


title: OVCAR3CIS cells, cisplatin (CIS) treated, rep1


title: OVCAR3CIS cells, cisplatin (CIS) treated, rep3


title: MCN-P_04

value: Pancreas

value: distal pancreatectomy

value: Female

value: FFPE

value: MCN-P


title: P56R cells, Oba01, 2Day, rep2

description: Library name: P22


title: U2OS WT, DMSO, 16 h, RNAseq

description: Library name: Sample42

value: WT

value: DMSO


title: P56R cells, Oba01, 2Day, rep1

description: Library name: P21


title: OVCAR3CIS cells, MMP3-targeted siRNA (siMMP3), rep4

value: epithelial cells resistant to cisplatin

value: MMP3 knockdown

value: 50nM MMP3-targeted siRNA


title: P53R cells, Control, 2Day, rep3

description: Library name: P13

value: cell line

value: Control


title: U2OS WT, Nocodazole, 16 h, RiboSeq

description: Library name: Sample41

data_processing:
*library strategy: Ribo-seq
The adaptor sequences were trimmed using cutadapt (v3.4).
RiboSeq: rRNA reads were discarded with BLAST-Like Alignment Tool (BLAT, v36x2) and
RiboSeq: Remaining reads were aligned to GRCh37/hg19 human genome by Spliced Transcripts Alignment to a Reference (STAR, v2.5.3a). rRNA index for RNA18S5, RNA28S5, RNA5-8S5 was constructed manually from NCBI RefSeq annotation.
RiboSeq: Raw counts were determined with a custom script quantifying sorted, genome-based BAM files from RiboSeq. Data were inferred for transcript ID and counts, as obtained with STAR “--quantmode GeneCounts”.
RNA-seq:Alignment was performed against mm10 using STAR with “--twopassMode Basic --twopass1readsN -1 --outSAMtype BAM Unsorted SortedByCoordinate --limitBAMsortRAM 100000000000 --outBAMsortingThreadN=1 --outSAMstrandField intronMotif --outSAMunmapped Within KeepPairs --outFilterMultimapNmax 1 --outFilterMismatchNmax 5 --outFilterMismatchNoverLmax 0.3 --chimSegmentMin 15 --chimScoreMin 1 --chimScoreJunctionNonGTAG 0 --chimJunctionOverhangMin 15  --chimSegmentReadGapMax 3 --alignSJstitchMismatchNmax 5 -1 5 5 --alignIntronMax 1100000 --alignMatesGapMax 1100000 --alignSJDBoverhangMin 3 --alignIntronMin 20 --quantMode TranscriptomeSAM GeneCounts --outSAMmapqUnique 0”
RNA-seq:Raw counts were determined with a custom script quantifying sorted, transcriptome-based BAM files from RNAseq. Data were inferred for transcript ID and counts, as obtained with STAR “--quantmode GeneCounts”.
Assembly: hg19
Supplementary files format and content: tab-delimited text file with raw counts


title: sh-NC#1

description: Library name: zxgu3_sh-NC#1

value: Bone

value: Cancer cells


title: P53R cells, Control, 2Day, rep2

description: Library name: P12

value: Colorectal cancer cells


title: Tumour, Oba01, 2Day, rep11

description: Library name: PDX_196_5

data_processing:
Illumina NovaSeq 6000
The clustering of the index-coded samples was performed on a cBotCluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia)according to the manufacturer’s instructions
After cluster generation, the librarypreparations were sequenced on an Illumina Novaseq platform and 150 bppaired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through fastpsoftware.
Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean reads were aligned to the referencegenome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped toeach gene.
Differential expression analysis oftwo conditions/groups (two biological replicates per condition) was performedusing the DESeq2 R package (1.20.0), Genes with an adjusted P-value <=0.05 found by DESeq2 wereassigned as differentially expressed
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes fpkm counts for each sample

source_name: tissue

growth_protocol: CRC082、CRC090、CRC114 and CRC196 PDXs were implanted subcutaneously in NOD-SCID mice

extract_protocol:
Freezed
AMPure XP system and Agilent Bioanalyzer2100 system

treatment_protocol: PDXs were treated with 5μg/ml Oba01 for  72h

value: tissue

value: Tumour

value: Patient derived xenograft tumor


title: P53R cells, Control, 2Day, rep1

description: Library name: P11


title: Tumour, Oba01, 2Day, rep12

description: Library name: PDX_196_6


title: OVCAR3CIS cells, MMP3-targeted siRNA (siMMP3), rep3


title: OVCAR3CIS cells, MMP3-targeted siRNA (siMMP3), rep2


title: U2OS WT, Nocodazole, 16 h, Rep3

description: Library name: Sample19

value: Osteosarcoma

value: Nocodazole


title: U2OS WT, DMSO, 16 h, Riboseq

description: Library name: Sample40


title: OVCAR3CIS cells, MMP3-targeted siRNA (siMMP3), rep1


title: Tumour, Oba01, 2Day, rep10

description: Library name: PDX_196_4


title: OVCAR3CIS cells, Negative control (NC) siRNA, rep4

value: 50nM NC siRNA


title: OVCAR3CIS cells, Negative control (NC) siRNA, rep3


title: MCF-7_H3K27ac_Nutlin-3a_2

city: Jena

first: Martin

last: Fischer

state: Thuringia

department: Computational Biology

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

data_processing:
After initial data quality inspection using FastQC v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), we applied Trimmomatic v0.39 (5nt sliding window approach, mean quality cutoff 22) for read quality trimming.
Nextera transposase adapter sequence content was clipped using Cutadapt v2.10. Potential sequencing errors were detected and corrected using Rcorrector v1.0.4.
Reads were aligned to hg38 using the mapping software segemehl 72,73 v0.3.4 with adjusted accuracy (95 %) and split-read option disabled. Non-mitochondrial alignments were selected and filtered for uniqueness and properly aligned mate pairs with Samtools v1.14 74 as well as subsequently dedubplicated by Picard MarkDuplicates v2.23.8 (https://broadinstitute.github.io/picard/). To account for Tn5 transposase cutting sites, 4bp were clipped off from 5’-end of positive strand aligned reads, 5bp otherwise, utilizing fgbio ClipBam v1.5.1 (https://fulcrumgenomics.github.io/fgbio).
Aligned data was further filtered for fragments >120bp and cleaned from reads overlapping ENCODE blacklisted regions (ENCFF356LFX) before subjected to peak calling on sparse data using Macs2 without local lambda estimates (-f BED --nolambda -q 0.00001 --min-length 150 --max-gap 100 --broad --broad-cutoff 0.00001 --fe-cutoff 8 --nomodel --shift 0 --extsize 200)
Assembly: hg38
Supplementary files format and content: MACS2 narrowPeaks
Library strategy: CUT&Tag

source_name: breast

growth_protocol: MCF-7 cells (ATCC, Manassas, Virginia, USA) were grown in high glucose Dulbecco's modified Eagle's media (DMEM) with pyruvate (Thermo Fisher Scientific, Darmstadt, Germany). Culture media were supplemented with 10 % fetal bovine serum (FBS; Thermo Fisher Scientific), penicillin/streptomycin (Thermo Fisher Scientific), and non-essential amino acids (Thermo Fisher Scientific).

extract_protocol:
Biological duplicates of 100 000 MCF-7 cells treated with Nutlin-3a and DMSO control were used for CUTANA CUT&Tag assay (EpiCypher) according to the manufacturer protocol version 1.5. Antibodies against H3K4me1 (#5326) and H3K27ac (#8173) were purchased from Cell Signaling Technology.
Libraries were constructed using the CUTANA CUT&Tag assay (EpiCypher) according to the manufacturer protocol version 1.5.
The libraries were pooled and sequenced on a NextSeq 500 using a high output kit v2.5 with 75 cycles (37 pb paired-end) run (Illumina)

treatment_protocol: Cells were treated with DMSO solvent control (0.15 %; Carl Roth, Karlsruhe, Germany) or Nutlin-3a (10 µM; Sigma Aldrich) for 24 h

value: breast

value: epithelial cells

value: wild-type

value: Nutlin-3a 10 µM 24 h


title: Tumour, Oba01, 2Day, rep8

description: Library name: PDX_114_5


title: Tumour, Oba01, 2Day, rep7

description: Library name: PDX_114_4


title: MCF-7_H3K27ac_Nutlin-3a_1


title: Tumour, Control, 2Day, rep11

description: Library name: PDX_196_2


title: Tumour, Control, 2Day, rep10

description: Library name: PDX_196_1


title: Tumour, Oba01, 2Day, rep9

description: Library name: PDX_114_6


title: Tumour, Control, 2Day, rep9

description: Library name: PDX_114_3


title: Tumour, Control, 2Day, rep8

description: Library name: PDX_114_2


title: OVCAR3CIS cells, Negative control (NC) siRNA, rep1

value: epithelial cells resistant to cisplatin

value: WT


title: U2OS WT, DMSO, 16 h, Rep3

description: Library name: Sample18

value: DMSO


title: MCF-7_H3K27ac_DMSO_2

value: DMSO 24 h


title: OVCAR3CIS cells, Negative control (NC) siRNA, rep2


title: MCF-7_H3K27ac_DMSO_1


title: Tumour, Control, 2Day, rep7

description: Library name: PDX_114_1

value: Control


title: Tumour, Oba01, 2Day, rep6

description: Library name: PDX_90_6


title: Tumour, Control, 2Day, rep12

description: Library name: PDX_196_3


title: MCN-L_05

value: Liver

value: partial hepatectomy

value: Female

value: FFPE

value: MCN-L


title: Tumour, Oba01, 2Day, rep5

description: Library name: PDX_90_5

value: tissue

value: Tumour

value: Patient derived xenograft tumor


title: MCF-7_H3K4me1_Nutlin-3a_2

value: breast


title: OVCAR3CIS cells, None-treated, rep3


title: Tumour, Oba01, 2Day, rep4

description: Library name: PDX_90_4


title: MCF-7_H3K4me1_Nutlin-3a_1

value: epithelial cells


title: Tumour, Control, 2Day, rep6

description: Library name: PDX_90_3


title: OVCAR3CIS cells, None-treated, rep2


title: Tumour, Control, 2Day, rep4

description: Library name: PDX_90_1


title: OVCAR3CIS cells, None-treated, rep1


title: Tumour, Control, 2Day, rep5

description: Library name: PDX_90_2


title: Tumour, Oba01, 2Day, rep2

description: Library name: PDX_82_5


title: MCF-7_H3K4me1_DMSO_1

value: wild-type


title: Tumour, Oba01, 2Day, rep1

description: Library name: PDX_82_4


title: Tumour, Oba01, 2Day, rep3

description: Library name: PDX_82_6


title: Tumour, Control, 2Day, rep3

description: Library name: PDX_82_3


title: MCF-7_H3K4me1_DMSO_2


title: Exp2, Rywal, roots, inoculated_PS-216_YFP_218_mKate_26h_48

city: Ljubljana

first: Marko

last: Petek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS873

data_processing:
filtering low quality reads (--quality 20) and trimming Ns (--trim-n) using Trim Galore
mapping filtered reads to reference potato genome using STAR v2.7.5c (parameters: --outFilterMultimapNmax 1 --outFilterMismatchNoverReadLmax 0.02 --quantTranscriptomeBan Singleend --outFilterType BySJout --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 10000 --alignMatesGapMax 10000)
generating raw counts table
taxonomic classification of reads using Centrifuge v1.0.4. Due to significant contamination observed in sample BS472, we have made the decision to exclude this sample from subsequent analysis.
differential expression analysis in R: filter genes with low expression, TMM normalization using edgeR v3.26.8 package, export of TMM normalized values using function cpm(log=TRUE, prior.count=0.5)
Assembly: Solanum tuberosum DM v4.04, GTF with merged PGSC and ITAG gene model annotations (https://doi.org/10.15490/fairdomhub.1.datafile.3408.1)
Supplementary files format and content: tab-delimited text files with raw count values and TMM-normalized count values for each Sample

organism: Solanum tuberosum

source_name: roots

growth_protocol: Potato plants cv. Rywal were grown in stem node tissue culture for two to four weeks after in-vitro micropropagation under controlled environmental conditions (22 ± 2°C in the light and 19 ± 2°C in the dark with 70–90 μmol/m2/s2 radiation with OSRAM L 58 W/77 FLUORA lamps and a 16-h photoperiod) as previously described by Lukan et al., 2022 (https://doi.org/10.1093/hr/uhac147).

extract_protocol:
Total RNA was isolated from roots and shoots by RNeasy Plant Mini Kit (Qiagen) and treated with RNA Clean & Concentrator-5, including DNase treatment (Zymo Research).
Poly-A selection and strand-specific Illumina RNA-Seq library preparation was performed by Novogene Ltd. using their standard procedure.

treatment_protocol: For Exp1, plants were added to bacterial culture after the culture reached 107 CFU/ml and were incubated for 2 or 26 h. For Exp2, when two strains were used, bacterial cultures were mixed in the ratio of 1:1. In both experiments, plant shoots were not in contact with bacterial culture. Noninoculated plants were incubated in media for the same time.

value: roots

tag: expt

tag: plant no.

tag: cultivar

value: Rywal

value: inoculated

tag: b.subtilis strain

value: PS-216-YFP & PS-218-mKate

tag: time (after biofilm formation)


title: shA4,PLKO,PolII,ChIP

data_processing:
ChIP-seq data were mapped to the hg38 genome using bowtie with default parameters. Duplicate reads were removed using samtools. ChIP-seq peaks were calculated using MACS2. Metaplots of ChIP-seq data were generated using ngsplot and heat maps of ChIP-seq data were generated using Deeptools.
Assembly: HG38
Supplementary files format and content: BigWig

source_name: Ovary

extract_protocol:
Cells were fixed in complete media with 0.3% formaldehyde for 30 minutes at 4°C, then quenched by adding 0.125 M glycine for 5 minutes at room temperature and 15 minutes on ice. Fixed cells were pelleted and washed once with 1× PBS before snap-freezing on dry ice. cell pellet was resuspended in 1 ml buffer A (25 mM HEPES-NaOH, pH 7.5; 10 mM KCl; 0.1% NP-40; 1.5 mM MgCl2) and homogenized. Nine volumes of buffer B (15 mM HEPES-NaOH, pH 7.9; 15 mM NaCl; 60 mM KCl; 0.5 mM PMSF; 0.32 M sucrose) were added, and the mixture was centrifuged at 2000 RPM (4°C, 7 minutes) to collect nuclei. The nuclei were resuspended in 1 ml buffer B and 3.3 µl of 1 M CaCl2, then prewarmed at 37°C for 15 minutes. MNase (1 µl, NEB, M0247SXXX) was added and incubated at 37°C for 15 minutes. The reaction was quenched with 10 µM EGTA on ice for 5 minutes. One volume of 2x buffer C (20 mM Tris-HCl, pH 8.0; 200 mM NaCl; 2 mM EDTA; 1 mM EGTA; 0.2% Na-Deoxycholate; 1% N-lauroylsarcosine) and Triton X-100 (final 1%) were added. Samples were then passed through a 21G needle five times and centrifuged at 13000g (4°C) for 15 minutes. Five micrograms of antibodies were added to the lysate for overnight incubation at 4°C. Protein G Magnetic Dynabeads® (ThermoFisher Scientific) were used for pulldown. Immunoprecipitated chromatin bound to Dynabeads was washed four times with RIPA buffer (50 mM HEPES-KOH, pH 7.5; 500 mM LiCl; 1 mM EDTA; 1% NP-40; 0.7% Na-Deoxycholate). Chromatin was eluted from Dynabeads in 100 µl elution buffer (50 mM Tris-HCl, pH 8.0; 10 mM EDTA; 1% SDS) by incubating at 65°C for 30 minutes. Immunoprecipitated samples and input were incubated overnight at 65°C to denature formaldehyde crosslinking. Samples were then treated with RNase A (ThermoFisher Scientific) followed by proteinase K (Sigma Aldrich) before extraction using a Zymo kit.
ChIP-sequencing (ChIP-seq) libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions.

tag: tissue

value: Ovary

tag: cell line

tag: cell type

value: epithelial cell

value: Pol II (Abcam, ab76123)


title: Tumour, Control, 2Day, rep1

description: Library name: PDX_82_1

tag: treatment

value: Control


title: Exp2, Rywal, roots, inoculated_PS-216_YFP_218_mKate_26h_47

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS872


title: Exp2, Rywal, roots, inoculated_PS-216_YFP_218_mKate_26h_46

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS871


title: IGF2BP1-KO_iMeLCs_rep2

city: Jiaxing

first: Yashi

last: Gu

address: No.718, HaiZhouEastRoad

institute: zje

description:
Library name: sample 2
CGS665

data_processing:
Quality assessment of the raw RNA-seq data was conducted using FastQC (v0.11.9), which examined the overall quality of the bulk RNA-seq fastq files. After that, cutadapt (v4.1) and trim-galore (v0.6.7) were used to remove low-quality bases and potential adapters. The processed reads were then aligned to the hg38 reference using STAR (v2.7.10a), sorted using samtools (v1.6), and the read counts per gene were quantified through featureCounts (v2.0.1) using the Gencode (v41) genomic annotation file.
Assembly: hg38
Supplementary files format and content: The processed data (counts) of RNA-seq data is stored in GSE266418_IGF2BP1-KO_iMeLCs_updated_count_matrix.xlsx.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen, 15596026). A part of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacturer's protocols.

value: embryonic stem cells induced incipient mesoderm-like cells

value: incipient mesoderm-like cells differentiation


title: IGF2BP1-KO_iMeLCs_rep1

description:
Library name: sample 1
CGS665


title: shA4,PLKO,Input

value: Input


title: OVCAR3CIS cells, None-treated, rep4

value: epithelial cells resistant to cisplatin

value: WT


title: mouse_774_cart19-taz [M_774_C]

city: Philadelphia

first: Marco

last: Ruella

state: PA

address: 3400 Civic Center Blv

department: Center for Cellular Immunotherapies

institute: University of Pennsylvania

data_processing:
gene counting and analysis with DESeq2 R library package
Assembly: hg38
Supplementary files format and content: excel file with raw gene counts

extract_protocol:
OCI-Ly18-GFP+ cells were sub-cutaneously implanted into NSG mice. 3 days later, mice were treated with tazemetostat (150 mg/kg/daily) or vehicle for 14 days. Mice were then infused with CART19 cells or UTD. 11 days post CART19 infusion, mice were sacrified, tumor were dissected and processed to prepare a single cell suspension. Cell sorting separated tumor-GFP+ cells from CART19 cells. Total RNA was extracted from tumor cells and submitted for bulk RNA sequencing.
NEB NEXT Ultra II RNA seq library kit

treatment_protocol: Tazemetostat (EPZ6438; 150 mg/kg/daily via oral gavage)

value: DLBCL


title: mouse_774_cart19-taz [M_774_B]


title: FT190,PLKO,PolII(S2),ChIP

value: Pol II phsopho S2 (Abcam, ab5095)

value: Ctrl


title: Exp2, Rywal, roots, inoculated_PS-218_YFP_218_mKate_26h_39

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS864

value: PS-218-YFP & PS-218-mKate


title: Exp2, Rywal, roots, inoculated_PS-218_YFP_218_mKate_26h_40

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS865

value: roots


title: mouse_768_cart19-taz [M_768_B]


title: Tumour, Control, 2Day, rep2

description: Library name: PDX_82_2

value: tissue

value: Tumour

value: Patient derived xenograft tumor


title: FT190,PLKO,PolII,ChIP

value: Ovary


title: Exp2, Rywal, roots, inoculated_PS-216_YFP_218_mKate_26h_45

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS870

value: Rywal

value: inoculated

value: PS-216-YFP & PS-218-mKate


title: Exp2, Rywal, roots, inoculated_PS-218_YFP_218_mKate_26h_38

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS863


title: shA4,PLKO,BRCA1,ChIP

value: epithelial cell

value: BRCA1 (Bethyl Lab, #A300-000A)


title: mouse_767_cart19-taz [M_767_C]


title: Exp2, Rywal, roots, inoculated_PS-218_YFP_218_mKate_26h_37

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS862


title: mouse_768_cart19-taz [M_768_C]


title: mouse_768_cart19-taz [M_768_A]


title: mouse_767_cart19-taz [M_767_B]


title: mouse_770_cart19 [M_770_B]


title: Exp2, Rywal, roots, inoculated_PS-218_26h_mKate_32

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS857


title: FT190,PLKO,BRCA1,ChIP


title: mouse_767_cart19-taz [M_767_A]


title: mouse_769_cart19 [M_769_C]


title: FT190,shSMARCA4,rep1

data_processing:
Sequencing files were trimmed with trimmoatic and mapped to the reference human genome sequence (hg38) with STAR (2.6.1c). Gene expressions were calculated by Homer with Gencode gene annotation GTF file. Differential expression genes were identified with DESeq2 (version 1.19.38).
Assembly: HG38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen, Hilden, Germany). 1ug total RNA was used for the library construction.
RNA libraries for RNA-Seq were prepared using the SMARTER mRNA-Seq library.

value: ovarian epithelial cell


title: FT190,shSMARCA4,rep2


title: mouse_770_cart19 [M_770_A]


title: Exp2, Rywal, roots, inoculated_PS-218_26h_mKate_31

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS856


title: MDA-MB-231 WT, DMSO 16h, Harringtonine 0min

description: Library name: Sample26

data_processing:
The adaptor sequences were trimmed using cutadapt (v3.4).
rRNA reads were discarded with BLAST-Like Alignment Tool (BLAT, v36x2) and
Remaining reads were aligned to GRCh37/hg19 human genome by Spliced Transcripts Alignment to a Reference (STAR, v2.5.3a). rRNA index for RNA18S5, RNA28S5, RNA5-8S5 was constructed manually from NCBI RefSeq annotation.
Raw counts were determined with a custom script quantifying sorted, genome-based BAM files from RiboSeq. Data were inferred for transcript ID and counts, as obtained with STAR “--quantmode GeneCounts”.
Assembly: hg19
Supplementary files format and content: tab-delimited text file with raw counts
Library strategy: Ribo-Seq

source_name: Breast Adenocarcinoma

value: Breast Adenocarcinoma

value: DMSO, Harringtonine


title: mouse_769_cart19 [M_769_B]

value: DLBCL


title: FT190,Ctrl,rep2

value: WT


title: mouse_774_cart19-taz [M_774_A]


title: FT190,PLKO,Input

value: Input

value: Ctrl


title: mouse_769_cart19 [M_769_A]


title: FT190,Ctrl,rep1


title: mouse_766_cart19 [M_766_C]


title: Exp2, Rywal, roots, inoculated_PS-218_26h_mKate_30

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS855

value: roots


title: mouse_766_cart19 [M_766_B]


title: Exp2, Rywal, roots, inoculated_PS-216_26h_YFP_24

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS849


title: SU-DHL-4-DMSO-CART19 [S18]

growth_protocol: Cell lines were maintained in RPMI-10%FBS

extract_protocol:
GFP+ DLBLC cell lines (OCI-LY18 or SU-DHL-4) were pre-treated with tazemetostat (500 nM) or DMSO for 72 hs and then exposed to CART19 or UTD cells for 48 hs, in the presence of tazemetostat or DMSO. Cell lines were sorted based on viability and GFP+ and used to extract RNA for bulk RNA sequencing.
NEB NEXT Ultra II RNA seq library kit

treatment_protocol: Tazemetostat (EPZ6438; 500 nM or DMSO)


title: RCC10_2

city: Dallas

first: Weibo

last: Luo

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
mRNA-seq Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/ fastq_screen), and trimmed using fastq-mcf (ea-utils/version 1.1.2-806, https://github.com/ExpressionAnalysis/ea-utils). Trimmed fastq files were mapped to hg19 (UCSC version from igenomes) using Tophat. Duplicates were marked using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). Read counts were generated using featureCounts and the differential expression analysis was performed using edgeR with FDR<0.05.
Assembly: hg19
Supplementary files format and content: TPM

source_name: RCC10 cells

growth_protocol: Cells were cultured with DMEM+10% FBS

extract_protocol:
Total RNA was isolated using a RNeasy Mini kit and treated with DNase (Qiagen).
mRNA-seq libraries were prepared with a Kapa mRNA Hyper Prep kit (Roche).

treatment_protocol: Cells were treated with vehicle or SGI1027 for 2 days.

value: RCC10 cells

tag: agent

value: Vehicle


title: SGI1027_2


title: SU-DHL-4-DMSO-CART19 [S16]


title: Exp2, Rywal, roots, inoculated_PS-216_26h_YFP_22

description:
Exp2_raw_counts_allgenes.txt
Exp2_roots_TMMnorm_counts_filtered.txt
Processed data file's Sample column: BS847


title: SU-DHL-4-TAZ-UTD [S21]

value: tazemetostat (500 nM) - UTD


title: mouse_770_cart19 [M_770_C]


title: SU-DHL-4-DMSO-CART19 [S17]