title: Sinus rhomboidalis-equivalent portion with exogenous OTX2_2

description: Library name: OT2

source_name: Sinus rhomboidalis-equivalent

value: Sinus rhomboidalis-equivalent


title: rep2_rad14_30min_UV

status: Public on Apr 26 2025

type: SRA

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

country: USA

institute: Washington State University

description: Replicate 2

library_source: genomic

data_processing:
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A1-A6 barcodes, and the barcode sequences were trimmed, as well as the 3' nucleotide of the sequencing read, using a custom perl script
Fastq files were aligned to the Saccharomyces cerevisiae genome (saccer3) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to dipyrimidine sequences (i.e., TT, TC, CT, CC), corresponding to CPD lesions were retained in BED file using custom perl script.
BED files were converted to WIG file using COUNT function of IGVTools
Assembly: saccer3
Supplementary files format and content: WIG files containing counts of DNA CPD lesion reads filtered for only dipyrimidine mapping sequences. A sequencing read count was assigned to both positions in the dipyrimidine sequence
Library strategy: CPD-seq

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast cultures were grown in YPD (yeast extract, peptone, dextrose) to OD600=~0.8 in a 30 degree shaking incubator.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with 250 μl of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA), 250 μl of PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and 150 μl of acid-washed glass beads, and vortexed vigorously twice, 2 min each time. After adding 200 μl of TE (10mM Tris-HCl, pH 7.5, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 1 ml of ethanol to precipitate DNA. DNA pellet was dissolved in 200 μl of TE and incubated with 2 μl of RNase A (ThermoFisher Scientific) at 37˚C for 1 hr to remove RNA. DNA was subsequently purified with PCI extraction, ethanol precipitated, and disolved in sterile deionized H2O.
CPD-seq procedure is adopted from the published emRiboSeq method (Nature Protocols 2015 10, 1433–1444). Briefly, DNA fragments were first ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by terminal transferase and dideoxy-ATP.  CPD lesions were  cleaved with T4 endonuclease V and apurinic/apyrimidinic (AP) endonuclease, APE 1, to generage new 3'-OHs. DNA was then ligated to adaptor  A. Up to 6 different barcoded A adaptors (A1: AAGAGGAT; A2: TTCGTGAT; A3: CCTGAGAT; A4: ATCGCGAT; A5: TACGGAT; A6: GAACTGAT) were used to generate libraries for different experiments. DNA was purified with Streptavidin beads and amplified for up to 6 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing.

treatment_protocol: Cells were collected and resuspended in sterile deionized H2O and irradiated with 125 J/m2 UVC. After UV irradiation, 1/3 of cells were pelleted and taken as the '0min' timepoint. The remaining 2/3 of cells were resuspended in 2% glucose and placed in a petri dish under UVA light for 30 and 60 minutes. After UVA incubation, cells were spun down and kept at -80˚C until genomic DNA isolation.

tag: cell line

value: Yeast cells

tag: genotype

tag: treatment

value: UV irradiated 125 J/m2

tag: repair time_with_uva_light

value: 30 min


title: organoid_Ctrl

city: Los Angeles

first: Frank

last: Pajonk

state: CA

address: 10833 Le Conte Ave

institute: UC Los Angeles

description:
Library name: organoid_Ctrl
10x Genomics

library_source: transcriptomic single cell

data_processing:
FASTQ files were aligned to a custom reference containing the human genome (GRCh38) and processed using the PIPseeker software, version 3.3.3 (Fluent Biosciences). Raw matrices were in processed in Seurat version 5 20. Cells with less than 500 genes were filtered out and cells with high mitochondrial gene count (>5%) were removed.
Assembly: human genome (hg38)
Supplementary files format and content: FASTQ and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: patient-derived cell line

growth_protocol: hips23-derived mature brain organoids (day 120) were culcured in SASAI M4 media, which includes DMEM/F- 12 with Glutamax, 1X N-2 supplement, 1X B27 Supplement (w/Vit.A/Insulin), 1X Lipid Concentrate, 1X Penicillin/streptomycin, 10% Fetal Bovine Serum (GIBCO), 5 μg/mL Heparin (Sigma H3149), and 1% Growth factor reduced Matrigel.

extract_protocol:
At 72 hours and 2 weeks following the final radiation dose, organoids were collected and dissociated into single-cell suspensions using the Papain Dissociation Kit (#LK003150, VWR) according to the manufacturer’s instructions. Cell counts were determined using a cell counter, and the resulting suspensions were processed for sequencing using the PIPseq T2 kit.
Sequencing libraries were prepared according to PIPseq T2 instructions, with 12 cycles for cDNA amplification and 8 cycles for library amplification, depending on the DNA amount. The libraries were quantified using a Qubit 4 Fluorometer and a TapeStation 4200 and sequenced as per manufacturer recommendation on a NovaSeq X Plus – 25B 2 x150bp.

treatment_protocol: Organoids were irradiated at room temperature using an experimental X-ray irradiator (Gulmay Medical Inc. Atlanta, GA) at a dose rate of 5.519 Gy/min. Control samples were sham-irradiated. The X-ray beam was operated at 300 kV and hardened using a 4 mm Be, a 3 mm Al, and a 1.5 mm Cu filter and calibrated using NIST-traceable dosimetry. Corresponding controls were sham irradiated. In this experiment, the organoids were exposed to fractionated irradiation, receiving 2 Gy per day for five consecutive days (total of 5 fractions)

tag: tissue

value: IPSC

value: ipsc23 derived brain organoid

value: control


title: rep2_rad14_0min_UV

description: Replicate 2

value: 0 min


title: Sinus rhomboidalis-equivalent portion with exogenous OTX2_1

city: Takatsuki

first: Hisato

last: Kondoh

state: Osaka

address: 1-1 Murasaki-cho

country: Japan

institute: Biohistory Research Hall

description: Library name: OT1

library_source: transcriptomic

data_processing:
The gene transcripts were assembled with StringTie, and the gene expression profile was represented by FPKM and TPM for a sample.
Assembly: GCF_016700215.2 bGalGal1.pat.whiteleghornlayer.GRCg7w as the reference with annotation by NCBI Gallus gallus Annotation Release 106.
Supplementary files format and content: Expression_Profile.GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w_with_MusOtx2_EGFP_genomic.gene.txt
Supplementary files format and content: Expression_Profile.GCF_016700215.2_bGalGal1.pat.whiteleghornlayer.GRCg7w_with_MusOtx2_EGFP_genomic.transcript.txt

organism: Gallus gallus

growth_protocol: Fertile chicken eggs were incubated at 38 °C to st. 4/5. Embryos on the vitelline membrane with a filter ring support were excised, electroporated, and cultured to st. 10/11.

extract_protocol:
Total RNAs isolated from tissues of four pooled embryos at st. 10-st.11 using Trizol reagents constituted a sample
Libraries for mRNA sequence reads were prepared using TruSeq Etrant mRNA LT Sample Prep Kit.

treatment_protocol: The DNAs of Otx2 expression vector pCAGGS-mOtx2 carrying mouse Otx2 cDNA sequence (Iwafuchi-Doi et al., 2012) at 0.25 µg and pCAGGS-EGFP at 0.2 µg in 1 µl of 10 mM Tris/HCl 1 mM EDTA at pH 7.5 were injected in the space between the epiblasts and the vitelline membrane and electroporated by the standard procedure.

tag: developmental stage

value: WT


title: TIGR4 THY 5 h 3

city: Cambridge

first: Katharina

last: Ribbeck

state: MA

address: 32 Vassar St

department: Biological Engineering

institute: Massachusetts Institute of Technology

data_processing:
Sequencing reads were mapped to the TIGR4 genome with the Burrows-Wheeler aligner
Read counts were quantified via the featureCounts package
Differential gene expression was quantified via the DESeq2 package in the R Bioconductor package
P-values were adjusted for multiple hypothesis testing using the Benjamini-Hochberg method
Assembly: NC_003028.3
Supplementary files format and content: Comma-separated value file includes raw counts for each gene in each sample

organism: Streptococcus pneumoniae TIGR4

extract_protocol:
RNA was extracted using the MasterPure complete DNA and RNA purification kit (Biosearch Technologies) and DNA was removed using the Turbo DNA-free kit (Invitrogen).
80 ng of RNA was used as input and the NEBNext Ultra II RNA library prep kit for Illumina with rRNA depletion was used for RNA library construction for RNA-seq.

value: No treatment


title: HK-390 cells RT + MXC-017 treated

description:
Library name: HK_390-MXC017_RT_MXC017
10x Genomics

growth_protocol: Patient-derived HK-390 gliomaspheres were cultured in serum-free conditions in ultra-low adhesion plates in DMEM/F12, supplemented with SM1 Neuronal Supplement, EGF, bFGF and heparin.

extract_protocol:
At day 5, the gliomaspheres in the suspension culture were collected and dissociated with TrypLE (no phenol red), and the adherent differentiated cells were washed with HBSS and de-attached with Trypsin/EDTA. The cells were then pooled and filtered through a 40-µm strainer and counted with a hemacytometer. The samples were pelleted by centrifugation at 300 g for 5 minutes at 4°C, resuspended in the provided Cell Resuspension Buffer (Fluent Bioscience, Watertown, MA), and 50,000 cells were targeted for capture and processed for single-cell transcriptomics using the PIPseqTM T2 3’ Single Cell RNA Kit v4.0 Plus (Fluent Biosciences).
Sequencing libraries were prepared according to PIPseq T2 instructions, with 12 cycles for cDNA amplification and 8 cycles for library amplification, depending on the DNA amount. The libraries were quantified using a Qubit 4 Fluorometer and a TapeStation 4200 and sequenced as per manufacturer recommendation on a NovaSeq X Plus – 25B 2 x150bp, with 3.25 billion reads in total for 8 samples.

treatment_protocol: HK-390 gliomaspheres were plated onto the Poly-D-Lysine/Laminin coated 6-well plate and treated with MXC-017 at a concentration of 10 µM, one hour before receiving a single dose of 4 Gy the next day. Five days post-irradiation, the cells were collected for sequencing.

value: Glioblastoma


title: rep1_60min_UV_rad14

description: Replicate 1

value: 60 min


title: TIGR4 THY 5 h 2


title: rep1_30min_UV_rad14

description: Replicate 1


title: HK-390 cells MXC-017 treated

description:
Library name: HK_390-MXC017_MXC017
10x Genomics


title: Midbrain-hindbrain portion with exogenous OTX2_1

description: Library name: OH1

source_name: Midbrain-hindbrain

value: Midbrain-hindbrain


title: rep1_0min_UV_rad14

description: Replicate 1


title: TIGR4 THY 5 h 1


title: HK-390 cells irradiated

description:
Library name: HK_390-MXC017_RT
10x Genomics


title: phNPC, mutSTARR, rep4

status: Public on Apr 25 2025

city: Mount Vernon

first: Sophia

last: Gaynor-Gillett

state: IA

address: 600 1st St. W

department: Biology

institute: Cornell College

description: phNPC-Mut-merged.output.csv

data_processing:
Libraries were processed using STARRPeaker v1.2. Default parameters were used for STARRPeaker except for the step size to bin genome (used 500bp window with 50bp step size).
Aligned to GRCh38 reference genome using BWA-MEM v0.7.17.
Merged filtered alignments from 16 sub-reactions to create a single BAM output file for STARRPeaker.
Assembly: GRCh38
Supplementary files format and content: *.bw bigWig signal track
Supplementary files format and content: *.bed BED format peaks
Library strategy: STARR-seq

molecule: polyA RNA

source_name: Brain, cerebral cortex

extract_protocol:
RNA was isolated using the Qiagen Rneasy Mini Kit. mRNA was isolated from total RNA using the Dynabeads mRNA DIRECT Purification Kit (Invitrogen).
mRNA was converted into cDNA using the SuperScript III First-Strand Synthesis SuperMix Kit (Invitrogen). Final cDNA samples were split into 16 separate reactions and amplified using 16 unique Illumina indexing primers and Q5 Hot Start High-Fidelity 2X Master Mix (NEB). Reactions were pooled into a single sample and cleaned using AMPure beads (Beckman Coulter). Library was sequenced on one lane of an Illumina MiSeq.

value: Brain, cerebral cortex

value: phNPC

tag: cell type

value: Primary human neural progenitors

value: MutSTARR-seq


title: phNPC, mutSTARR, rep2

description: phNPC-Mut-merged.output.csv


title: phNPC, mutSTARR, rep1

description: phNPC-Mut-merged.output.csv


title: Midbrain-hindbrain portion with exogenous OTX2_2

description: Library name: OH2


title: HK-390 cells 0 Gy Control

description:
Library name: HK_390-MXC017_0Gy
10x Genomics


title: phNPC, mutSTARR, rep3

description: phNPC-Mut-merged.output.csv


title: phNPC, Panel 2, input

description: The input library serves as the comparison group for peak calling during STARR-seq analysis.

value: Panel 2 Capture STARR-seq


title: phNPC, Panel 2, rep2


title: phNPC, Panel 1, rep2

value: Panel 1 Capture STARR-seq


title: phNPC, Panel 1, rep1


title: phNPC, Panel 1, input


title: phNPC, Panel 2, rep1


title: IDH1R132H immortalized human astrocytes, siRUNX2, replicate 3

city: Heidelberg

first: Sevin

last: Turcan

address: Im Neuenheimer Feld 420

country: Germany

institute: University Hospital Heidelberg

description: Library name: siRUNX2 3

data_processing:
BAM files were produced with the following configurations: RNA paired bulk,  Reference genome: 1KGRef_PhiX, Alignment program: STAR Version 2.5.3a, Merging/duplication marking program: Sambamba Version 0.6.5
Assembly: hg38

source_name: astrocytes

extract_protocol:
For RNA-Seq, samples were seeded in triplicates and harvested 48 days after the last treatment with Doxycycline and CHIR99021, Repsox or YO-01027 as described above. For RNA-Seq with siControl/siRUNX2 samples were harvested after 72h. RNA was isolated with the Rneasy Mini Kit (Qiagen).
UltraLowRNAv4, NEBNext Multiplex Oligos for Illumina UDI. RNA-Seq TruSeq Stranded for sicontrol/siRUNX2.

value: astrocytes

value: immortalized IDH1R132H astrocytes

value: astrocyte


title: IDH1R132H immortalized human astrocytes, siRUNX2, replicate 2

description: Library name: siRUNX2 2


title: IDH1R132H immortalized human astrocytes, siRUNX2, replicate 1

description: Library name: siRUNX2 1


title: phNPC, mutSTARR, input

description: phNPC-Mut-merged.output.csv


title: IDH1R132H immortalized human astrocytes, sicontrol, replicate 3

description: Library name: sicontrol 3


title: IDH1R132H immortalized human astrocytes, sicontrol, replicate 2

description: Library name: sicontrol 2


title: PURB-CLIP

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: PURB-CLIP

library_source: other

data_processing:
CLIP-Seq reads were trimmed using Cutadapt, removing adaptors and reads <10 nt. Trimmed reads were mapped to the human reference genome (hg19) using STAR software, keeping only correctly mapped paired-end reads and removing multi-mapped reads with SAMtools (MAPQ < 40).
Human gene annotation ("gencode.v28lift37.gtf") was downloaded from GENCODE database.
The "featureCounts" tool was used to count reads per gene with parameters "fraction = T" and normalized with total reads per sample to obtain FPKM values.
Assembly: Human reference genome (hg19)
Supplementary files format and content: txt file includes count and FPKM values for each gene

molecule: other

source_name: Lung

growth_protocol: H1299 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were then lysed in CLIP lysis buffer [50 mM Tris-HCl (pH 7.4); 100 mM NaCl; 1% NP-40; 0.1% SDS; 0.5% sodium deoxycholate; 100 U/ml RNase inhibitor SUPERase•in™ (add fresh each time); Protease inhibitors (Sigma P1860, add fresh each time)] on ice for 20min. Lysates were then sonicated, digested with turbo DNase (Invitrogen, AM2238), and centrifuged at 4°C at 22,000 g for 20min. The cleared supernatant was collected, protein concentration was determined, the lysates were normalized, and some of which were saved as input. After adding BSA and yeast tRNA (Invitrogen, AM7119) pre-saturated streptavidin into the lysates and incubate for 2h at 4°C. For CLIP using antibody, the indicated antibody (2 μg) was added into lysates and incubated overnight at 4°C, followed by adding of 20 μl of protein A/G agarose beads (pre-saturated with BSA and yeast tRNA) for 2h at 4°C. Beads were washed once with CLIP lysis buffer, and three time with high-salt wash buffer [50 mM Tris-HCl (pH 7.4); 1 M NaCl; 1 mM EDTA; 1% NP-40; 0.1% SDS; 0.5% sodium deoxycholate]. These washes were done with rotation at 4°C for 5 mins each. The proteins were then eluted with biotin solution (2 mg/ml) or elution buffer [1% SDS; 100 mM NaHCO3]. Some eluate was saved for IP efficiency test. The rest of the eluate, together with the pre-saved input lysate, was subject to a second turbo DNase digestion, followed by proteinase K digestion in PK urea buffer [100 mM Tris-HCl (pH 7.4); 50 mM NaCl; 10 mM EDTA; 7 M urea]. Trizol (Invitrogen) was added to the sample, and RNA was extracted following the protocol of TRIzol reagent.
RNA was subjected to library preparation using a kit (Swift Biosciences, R1024)

treatment_protocol: Cells in culture dish were UV (254nm) radiated at 400mJ/cm2 before harvesting.

value: Lung

value: Cancer cells


title: G19-2

city: Hohhot

first: Kai

last: Cao

address: Inner Mongolia Agricultural University

department: agricultural college

country: China

institute: Inner Mongolia Agricultural University

description:
Library name: sample2
G19-2_FPKM

data_processing:
After sequencing data, the bioinformatics analysis process provided by BMKCloud ( www.biocloud.net ) was used for data analysis. Clean Data was obtained by filtering the offline data, and sequence alignment was performed with the designated reference genome. After obtaining Mapped Data, library quality assessment, structural level analysis, differential expression analysis, gene function annotation and functional enrichment were performed. In addition, in-depth data mining analysis can also be carried out through the B & M cloud platform BMKCloud ( www.biocloud.net ) to achieve a series of personalized interactive operations of transcriptome, such as gene retrieval mapping, unique and common gene analysis, construction of protein interaction network, gene set enrichment analysis ( GSEA ), differential gene co-expression analysis and gene co-expression network construction ( WGCNA ).
Assembly: GCF_002127325.2
Supplementary files format and content: tab-delimited txt files include FPKM values for each Sample

organism: Helianthus annuus

source_name: Leaf flat type

extract_protocol:
( 1 ) NanoDrop 2000 spectrophotometer : detection of RNA purity and concentration ;( 2 ) Agient2100 / LabChip GX detection : Accurate detection of RNA integrity.
( 1 ) Eukaryotic mRNA was enriched by magnetic beads with Oligo ( dT ) ;  ( 2 ) Fragmentation Buffer was added to randomly interrupt mRNA ;  ( 3 ) The first and second cDNA strands were synthesized using mRNA as template, and cDNA was purified.  ( 4 ) The purified double-stranded cDNA was subjected to terminal repair, A tail and ligation of the sequencing adapter, and then the fragment size was selected with AMPure XP beads ;  ( 5 ) Finally, the cDNA library was obtained by PCR enrichment.

value: Leaf flat type

value: petiole


title: IDH1R132H immortalized human astrocytes, sicontrol, replicate 1

description: Library name: sicontrol 1


title: IDH1R132H immortalized human astrocytes, YO-01027, replicate 3

description: Library name: YO-01027 3


title: IDH1R132H immortalized human astrocytes, YO-01027, replicate 1

description: Library name: YO-01027 1


title: IDH1R132H immortalized human astrocytes, YO-01027, replicate 2

description: Library name: YO-01027 2


title: IDH1R132H immortalized human astrocytes, Repsox, replicate 2

description: Library name: Repsox 2


title: IDH1R132H immortalized human astrocytes, Repsox, replicate 3

description: Library name: Repsox 3


title: IDH1R132H immortalized human astrocytes, CHIR99021, replicate 3

description: Library name: CHIR99021 3


title: IDH1R132H immortalized human astrocytes, Repsox, replicate 1

description: Library name: Repsox 1


title: IDH1R132H immortalized human astrocytes, CHIR99021, replicate 1

description: Library name: CHIR99021 1


title: IDH1R132H immortalized human astrocytes, CHIR99021, replicate 2

description: Library name: CHIR99021 2


title: IDH1R132H immortalized human astrocytes, control, replicate 2

description: Library name: control 2


title: IDH1R132H immortalized human astrocytes, control, replicate 1

description: Library name: control 1


title: HepG2 cells, TBTCl, rep 1

city: Raleigh

first: Michael

last: Cowley

state: NC

address: 850 Main Campus Dr

department: Biological Sciences

institute: North Carolina State University

description:
Library name: Sample 25
25_L001.txt

data_processing:
Raw reads were processed for quality control, adapter trimming, and data filtering using ‘fastp’ (Chen 2023). 12 poor-quality bases were trimmed from the 5’-end, and the remaining reads were aligned to the mouse or human reference genome (GRCmm39 version 112 and GRCh38 version 112, respectively) from the Ensembl database using ‘STAR’ aligner (Dobin et al. 2013). Genes with uniquely mapped reads were counted using the ‘htseq-count’ function from the HTSeq python package (Anders et al. 2014). The count matrix was imported to the R statistical computing software for further analysis (R Core Team 2023). Genes with fewer than 10 counts in most replicates were removed, and the remaining count data were normalized for depth and distortion. Data dispersion was estimated using the ‘DESeq2’ package and differentially expressed genes (DEGs) were identified after applying multiple testing corrections using the Benjamini-Hochberg procedure with a false discovery rate of q<0.05 (Love et al. 2014; Benjamini and Hochberg 1995). For visualization and overlap of the DEGs and the IGN, Venn diagrams and volcano plots were generated using the ‘BioVenn’ and ‘ggplot2’ R packages, respectively (Hulsen 2021a; Hulsen 2021b; Wickham 2016).
Assembly: Mouse Genome Assembly - GRCmm39 version 112; Human Genome Assembly - GRCh38 version 112. Genomes were downloaded from the Ensembl database.
Supplementary files format and content: "All_counts.csv" file contains raw gene counts for each sample obtained from HTSeq.

growth_protocol: HepG2 cells (ATCC, HB-8065) were grown in high-glucose DMEM (Gibco, 21063045) containing 10% fetal bovine serum (FBS) (Genesee Scientific, 25-514) and 100 U/mL penicillin, 100 µg/mL streptomycin (HyClone, SV30010). Cells were maintained at 37°C in a humidified atmosphere of 5% CO2. HepG2 cells did not exceed 17 passages.

extract_protocol:
Total RNA was extracted from HepG2 cells using the NucleoSpin RNA kit (Macherey-Nagel, 740955) according to the manufacturer’s. 2 μg of total RNA was submitted to the North Carolina State University Genomic Sciences Laboratory (Raleigh, NC, USA) for library construction and sequencing.
Total RNA was assessed for quality using an Agilent 2100 Bioanalyzer with an RNA 6000 Nano Chip (Agilent Technologies, USA). Purification of messenger RNA (mRNA) was performed using the oligo-dT beads provided in the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, USA). Complementary DNA (cDNA) libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) using the manufacturer-specified protocol. Briefly, the mRNA was chemically fragmented and primed with random oligos for first strand cDNA synthesis. Second strand cDNA synthesis was then carried out with dUTPs to preserve strand orientation information. The double-stranded cDNA was purified, end repaired and “a-tailed” for adaptor ligation. Following ligation, samples were selected with a final library size (adapters included) of 350-550 bp using sequential AMPure XP bead isolation (Beckman Coulter, USA). Library enrichment was performed and specific indexes for each sample were added during the protocol-specified PCR amplification. The amplified library fragments were purified and checked for quality and final concentration using an Agilent 2200 Tapestation with a High Sensitivity DNA chip (Agilent Technologies, USA) and a Qubit fluorometer (ThermoFisher, USA). The final quantified libraries were pooled in equimolar amounts for clustering and sequencing on an Illumina NovaSeq 6000 DNA sequencer, utilizing a 150x2 bp paired end sequencing reagent kit (Illumina, USA). The software package Real Time Analysis (RTA) was used to generate raw base call files (bcl), which were then de-multiplexed by sample into fastq files.

treatment_protocol: HepG2 cells were seeded at 20,000 cells per well in 96-well plates for cytotoxicity assays and 600,000 cells per well in 6-well plates for mRNA extraction. Four independent experiments were performed, each with technical triplicates. Cells were serum-starved for 24 hours before toxicant exposure. After 24 hours, the cells were exposed to the following: (1) Water, (2) DMSO, (3) BPA, (4) CdCl2, (5) PFOS, (6) TBTCl, or (7) TCDD. Cells were exposed for 24 hours and collected for downstream analyses. Concentrations were selected based on previously reported cytotoxicity data in the literature as follows: 50 µM, 75 µM, 150 µM, and 300 µM BPA; 0.1 µM, 0.5 µM, 1 µM, and 5 µM CdCl2; 5 µM, 10 µM, 50 µM, and 100 µM PFOS; 0.01 µM, 0.1 µM, 1 µM, and 10 µM TBTCl; and 0.5 nM, 1 nM, 5 nM, 10 nM, 50 nM, 100 nM, 500 nM, and 1000 nM TCDD (Magnifico et al. 2022; Štampar et al. 2023; Urani et al. 2014; Rosenmai et al. 2018; Eriksen et al. 2010; Hoth et al. 2005; Zeng et al. 2018; Silkworth et al. 2005; Tian et al. 2018; Phark et al. 2016). DMSO content did not exceed 0.1% of the total cell culture media volume.

value: hepatocyte

value: TBTCl


title: HepG2 cells, TBTCl, rep 4

description:
Library name: Sample 28
28_L001.txt


title: HepG2 cells, TBTCl, rep 3

description:
Library name: Sample 27
27_L001.txt


title: HepG2 cells, BPA, rep 3

description:
Library name: Sample 23
23_L001.txt

value: BPA


title: HepG2 cells, BPA, rep 4

description:
Library name: Sample 24
24_L001.txt


title: HepG2 cells, BPA, rep 2

description:
Library name: Sample 22
22_L001.txt


title: HepG2 cells, control DMSO, rep 4

description:
Library name: Sample 12
12_L001.txt

value: DMSO


title: 16751.fastq.gz,52,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_12w,10090

city: Maaloev

first: Jenny

last: Norlin

state: Denmark

address: Novo Nordisk Park 1

department: Translational Leads Department

country: Denmark

institute: Novo Nordisk

description: Library name: 16751.fastq.gz

data_processing:
Read counts were quantified by salmon v1.2.0, read quality of the data was evaluated using FastQC 0.11.9 and Picard, and the inter- and intra-group variability was evaluated using principal component analysis and hierarchical clustering. Differential gene expression was assessed by the R-package DESeq2.
Assembly: GRCm38 from Ensable data base, using STAR v2.7.3a
Supplementary files format and content: tsv-format, read counts

organism: Mus musculus

source_name: liver

extract_protocol:
20 ± 10 mg were taken from the left lateral lobe. RNA was purified using NucleoSpin kit (MACHEREY-NAGEL). Purified RNA (10 ng – 1 µg) from each sample was used to generate a cDNA library using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. The cDNA library was then sequenced on a NextSeq 500 using NextSeq 500/550 High Output Kit V2 (Illumina).
The cDNA library was sequenced on a NextSeq 500 using NextSeq 500/550 High Output Kit V2 (Illumina).

value: liver

tag: strain

tag: Sex

value: male


title: 16747.fastq.gz,96,GUS2021_558_NN,Liver,CDAA_Baseline_group_6_w,10090

description: Library name: 16747.fastq.gz


title: 16868.fastq.gz,27,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_18w,10090

description: Library name: 16868.fastq.gz


title: 17036.fastq.gz,88,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_18w,10090

description: Library name: 17036.fastq.gz


title: 16749.fastq.gz,49,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_12w,10090

description: Library name: 16749.fastq.gz


title: 16753.fastq.gz,54,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_12w,10090

description: Library name: 16753.fastq.gz


title: 16745.fastq.gz,33,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_18w,10090

description: Library name: 16745.fastq.gz


title: 16746.fastq.gz,73,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_18w,10090

description: Library name: 16746.fastq.gz


title: 16748.fastq.gz,37,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_12w,10090

description: Library name: 16748.fastq.gz


title: 17037.fastq.gz,23,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_18w,10090

description: Library name: 17037.fastq.gz


title: 16744.fastq.gz,63,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_12w,10090

description: Library name: 16744.fastq.gz


title: IDH1R132H immortalized human astrocytes, control, replicate 3

description: Library name: control 3


title: PATIENT103

type: RNA

city: Badalona

first: Cristina

last: Gálvez

state: Barcelona

address: Ctra. de Canyet s/n

department: Data Management

country: Spain

institute: IrsiCaixa

hyb_protocol: employs two types of probes: capture probes and reporter probes, hybridization protocol as described my manufacturer

scan_protocol: nCounter instrument

data_processing: Synthetic oligonucleotide pool corresponding to all panel gene targets used for normalization. Data analysis on nCounter software.

label: biotin

source_name: breast cancer

label_protocol: direct hybridization approach for RNA detection and quantification without the need for amplification  Synthetic oligonucleotide pool corresponding to all panel gene targets used for normalization

extract_protocol: Six 10um-thick sections from FFPE archival tumor biopsies were prepared for the extraction of total RNA from tumor cell-rich areas, which were identified by a experienced pathologist

tag: biopsy origin

value: primary

tag: treatment line

tag: status

value: dead

tag: treatment duration (months)

tag: efficay group

value: bad


title: PATIENT101.2

value: metastasis

value: good


title: 16742.fastq.gz,86,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_18w,10090

description: Library name: 16742.fastq.gz


title: HepG2 cells, TBTCl, rep 2

description:
Library name: Sample 26
26_L001.txt


title: 16743.fastq.gz,17,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_12w,10090

description: Library name: 16743.fastq.gz


title: HepG2 cells, control DMSO, rep 3

description:
Library name: Sample 11
11_L001.txt


title: HepG2 cells, BPA, rep 1

description:
Library name: Sample 21
21_L001.txt


title: PATIENT100

value: alive


title: 16752.fastq.gz,38,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_12w,10090

description: Library name: 16752.fastq.gz


title: PATIENT99


title: HepG2 cells, control DMSO, rep 2

description:
Library name: Sample 10
10_L001.txt


title: 16741.fastq.gz,25,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_18w,10090

description: Library name: 16741.fastq.gz


title: 16739.fastq.gz,89,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_18w,10090

description: Library name: 16739.fastq.gz


title: 16740.fastq.gz,4,GUS2021_558_NN,Liver,Chow_18w,10090

description: Library name: 16740.fastq.gz


title: HepG2 cells, control DMSO, rep 1

description:
Library name: Sample 9
09_L001.txt


title: 16738.fastq.gz,35,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_18w,10090

description: Library name: 16738.fastq.gz


title: PATIENT101


title: PATIENT98.2


title: 16737.fastq.gz,62,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_12w,10090

description: Library name: 16737.fastq.gz


title: 16735.fastq.gz,36,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_12w,10090

description: Library name: 16735.fastq.gz


title: HepG2 cells, CdCl2 rep 2

description:
Library name: Sample 6
06_L001.txt


title: HepG2 cells, CdCl2 rep 3

description:
Library name: Sample 7
07_L001.txt


title: HepG2 cells, CdCl2 rep 4

description:
Library name: Sample 8
08_L001.txt


title: 16728.fastq.gz,81,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_18w,10090

description: Library name: 16728.fastq.gz


title: 16732.fastq.gz,46,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_12w,10090

description: Library name: 16732.fastq.gz


title: 16731.fastq.gz,56,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_12w,10090

description: Library name: 16731.fastq.gz


title: HepG2 cells, control H2O rep 4

description:
Library name: Sample 4
04_L001.txt


title: PATIENT98


title: 16729.fastq.gz,31,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_18w,10090

description: Library name: 16729.fastq.gz


title: 16736.fastq.gz,75,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_18w,10090

description: Library name: 16736.fastq.gz


title: PATIENT96


title: 16733.fastq.gz,102,GUS2021_558_NN,Liver,CDAA_Baseline_group_6_w,10090

description: Library name: 16733.fastq.gz


title: PATIENT95


title: PATIENT90


title: 16726.fastq.gz,97,GUS2021_558_NN,Liver,CDAA_Baseline_group_6_w,10090

description: Library name: 16726.fastq.gz


title: HepG2 cells, control H2O rep 3

description:
Library name: Sample 3
03_L001.txt


title: 16725.fastq.gz,29,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_18w,10090

description: Library name: 16725.fastq.gz


title: 16724.fastq.gz,94,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_18w,10090

description: Library name: 16724.fastq.gz


title: 16727.fastq.gz,71,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_18w,10090

description: Library name: 16727.fastq.gz


title: HepG2 cells, control H2O rep 2

description:
Library name: Sample 2
02_L001.txt


title: PATIENT94


title: PATIENT89


title: 16722.fastq.gz,32,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_18w,10090

description: Library name: 16722.fastq.gz


title: HepG2 cells, CdCl2 rep 1

description:
Library name: Sample 5
05_L001.txt


title: 16730.fastq.gz,2,GUS2021_558_NN,Liver,Chow_18w,10090

description: Library name: 16730.fastq.gz


title: PATIENT87.2

value: stop due to toxicity

value: not evaluable


title: HepG2 cells, control H2O rep 1

description:
Library name: Sample 1
01_L001.txt


title: PATIENT91


title: 16720.fastq.gz,100,GUS2021_558_NN,Liver,CDAA_Baseline_group_6_w,10090

description: Library name: 16720.fastq.gz


title: 16721.fastq.gz,12,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_12w,10090

description: Library name: 16721.fastq.gz


title: DAOY _Static_Rep3

city: Toronto

first: Qi

last: Yang

state: ON

address: 686 Bay St

department: Developmental & Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

description: Library name: Sample 12

data_processing:
Pair-end RNA-seq data of ONS76 and DOAY was aligned to GRCh38 using Hisat2 (v 2.2.1). Quantification of aligned bam at gene level was performed with featureCounts function in R package Rsubread (v 2.18.0).
Assembly: GRCh38
Supplementary files format and content: xlsx of raw count and normalized TPM.

source_name: Medulloblastoma

extract_protocol:
RNA was collected from static control or orbital shaker-treated ONS76 and DAOY cells cultured in aCSF. Total RNA was collected after 18 hours of treatment using RNeasy Plus Mini Kit (Qiagen, #74134). RNA integrity number (RIN) was determined using Agilent Bioanalyzer. All samples had RIN > 9.8.
Library preparation was performed using NEBNext Ultra II Directional polyA mRNA Library Prep Kit. Sequencing was performed on Illumina NovaSeq with 30 million paired end reads per sample at 100 bp read length.

treatment_protocol: For orbital shaking, VWR Mini Shaker (VWR #12620-938) was placed in a tissue culture incubator. MB cells cultured on 6 well plates in aCSF were placed on the orbital shaker and gyrated at 100 rpm for 18 hours.

value: Medulloblastoma

value: DAOY

value: Medulloblastoma cell

value: WT

value: Static


title: 16719.fastq.gz,30,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_18w,10090

description: Library name: 16719.fastq.gz


title: 16718.fastq.gz,18,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_12w,10090

description: Library name: 16718.fastq.gz


title: 16717.fastq.gz,68,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_18w,10090

description: Library name: 16717.fastq.gz


title: DAOY _Static_Rep2

description: Library name: Sample 11


title: PATIENT87


title: PATIENT80


title: DAOY _Static_Rep1

description: Library name: Sample 10


title: 16716.fastq.gz,44,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_12w,10090

description: Library name: 16716.fastq.gz


title: 16714.fastq.gz,67,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_18w,10090

description: Library name: 16714.fastq.gz


title: 16715.fastq.gz,15,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_12w,10090

description: Library name: 16715.fastq.gz


title: DAOY _FSS_Rep3

description: Library name: Sample 9

value: FSS


title: 16712.fastq.gz,43,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_12w,10090

description: Library name: 16712.fastq.gz


title: 16723.fastq.gz,64,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_12w,10090

description: Library name: 16723.fastq.gz


title: DAOY _FSS_Rep2

description: Library name: Sample 8


title: PATIENT79


title: 16711.fastq.gz,34,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_18w,10090

description: Library name: 16711.fastq.gz


title: 16710.fastq.gz,8,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_12w,10090

description: Library name: 16710.fastq.gz


title: PATIENT77


title: PATIENT75.2


title: 16709.fastq.gz,99,GUS2021_558_NN,Liver,CDAA_Baseline_group_6_w,10090

description: Library name: 16709.fastq.gz


title: DAOY _FSS_Rep1

description: Library name: Sample 7


title: 16708.fastq.gz,45,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_12w,10090

description: Library name: 16708.fastq.gz


title: ONS76_Static_Rep3

description: Library name: Sample 6


title: 16707.fastq.gz,92,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_18w,10090

description: Library name: 16707.fastq.gz


title: 16713.fastq.gz,24,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_18w,10090

description: Library name: 16713.fastq.gz


title: PATIENT75


title: PATIENT78


title: ONS76_Static_Rep2

description: Library name: Sample 5


title: 16706.fastq.gz,103,GUS2021_558_NN,Liver,CDAA_Baseline_group_6_w,10090

description: Library name: 16706.fastq.gz


title: 16705.fastq.gz,98,GUS2021_558_NN,Liver,CDAA_Baseline_group_6_w,10090

description: Library name: 16705.fastq.gz


title: 16704.fastq.gz,93,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_18w,10090

description: Library name: 16704.fastq.gz


title: PATIENT74


title: ONS76_Static_Rep1

description: Library name: Sample 4


title: 16702.fastq.gz,74,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_18w,10090

description: Library name: 16702.fastq.gz


title: 16703.fastq.gz,60,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_12w,10090

description: Library name: 16703.fastq.gz


title: 16701.fastq.gz,95,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_18w,10090

description: Library name: 16701.fastq.gz


title: ONS76_FSS_Rep3

description: Library name: Sample 3


title: PATIENT73


title: 16698.fastq.gz,5,GUS2021_558_NN,Liver,Chow_18w,10090

description: Library name: 16698.fastq.gz


title: 16699.fastq.gz,53,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_12w,10090

description: Library name: 16699.fastq.gz


title: ONS76_FSS_Rep2

description: Library name: Sample 2


title: 16697.fastq.gz,76,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_18w,10090

description: Library name: 16697.fastq.gz


title: PATIENT72


title: 16696.fastq.gz,16,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_12w,10090

description: Library name: 16696.fastq.gz


title: 16695.fastq.gz,13,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_12w,10090

description: Library name: 16695.fastq.gz


title: STN49, BRAFi+MEKi, 48 hrs, biol rep 2

city: Palo Alto

first: Claudia K

last: Petritsch

address: 265 Campus Drive

institute: Stanford University

description:
Library name: Sample 15
BMi48B4_1

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

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.

value: Patient-derived glioma cell line

value: Glioma cell line

value: BRAF V600E mutation

value: BRAFi+MEKi


title: PATIENT71.2


title: 16693.fastq.gz,78,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_18w,10090

description: Library name: 16693.fastq.gz

value: liver

value: male


title: STN49, BRAFi+MEKi, 48 hrs, biol rep 1

description:
Library name: Sample 14
BMi48B3_1


title: PATIENT71

value: primary


title: PATIENT74.2

value: metastasis

value: dead

value: good


title: 16692.fastq.gz,1,GUS2021_558_NN,Liver,Chow_18w,10090

description: Library name: 16692.fastq.gz


title: 16691.fastq.gz,69,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_18w,10090

description: Library name: 16691.fastq.gz


title: STN49, DMSO, 48 hrs, biol rep 2

description:
Library name: Sample 13
CTRL48B2_1

value: DMSO


title: PATIENT68

value: bad


title: 16688.fastq.gz,19,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_12w,10090

description: Library name: 16688.fastq.gz


title: STN49, DMSO, 48 hrs, biol rep 1

description:
Library name: Sample 12
CTRL48B1_1


title: PATIENT67


title: 16687.fastq.gz,48,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_12w,10090

description: Library name: 16687.fastq.gz


title: STN49, BRAFi+MEKi, 24 hrs, biol rep 2

description:
Library name: Sample 11
BMi24A4_1


title: ONS76_FSS_Rep1

description: Library name: Sample 1

value: Medulloblastoma


title: PATIENT66


title: 16684.fastq.gz,55,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_12w,10090

description: Library name: 16684.fastq.gz


title: 16683.fastq.gz,21,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_18w,10090

description: Library name: 16683.fastq.gz


title: PATIENT65


title: 16694.fastq.gz,84,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_18w,10090

description: Library name: 16694.fastq.gz


title: STN49, DMSO, 24 hrs, biol rep 2

description:
Library name: Sample 9
CTRL24A2_1


title: 16682.fastq.gz,59,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_12w,10090

description: Library name: 16682.fastq.gz


title: PATIENT63


title: 16681.fastq.gz,14,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_12w,10090

description: Library name: 16681.fastq.gz


title: 16680.fastq.gz,11,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_12w,10090

description: Library name: 16680.fastq.gz


title: 16690.fastq.gz,82,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_18w,10090

description: Library name: 16690.fastq.gz


title: STN49, DMSO, 24 hrs, biol rep 1

description:
Library name: Sample 8
CTRL24A1_1


title: 16678.fastq.gz,3,GUS2021_558_NN,Liver,Chow_18w,10090

description: Library name: 16678.fastq.gz


title: 16679.fastq.gz,72,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_18w,10090

description: Library name: 16679.fastq.gz


title: 16677.fastq.gz,39,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_12w,10090

description: Library name: 16677.fastq.gz


title: 16689.fastq.gz,66,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_18w,10090

description: Library name: 16689.fastq.gz


title: Patient 12, post-BRAFi+MEKi treatment

description:
Library name: Sample 7
NG-16816_CXJ031_FT_lib273239_6036_2_R1_001.fastq.gz

source_name: Brain tumor

value: Brain tumor


title: PATIENT60.2


title: PATIENT60


title: 16676.fastq.gz,58,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_12w,10090

description: Library name: 16676.fastq.gz


title: 16686.fastq.gz,22,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_18w,10090

description: Library name: 16686.fastq.gz


title: PATIENT54


title: Patient 12, pre-BRAFi+MEKi treatment

description:
Library name: Sample 6
NG-18091_CXJ017_FT_lib330417_6389_7_R1_001.fastq.gz

value: No treatment


title: 16675.fastq.gz,80,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_18w,10090

description: Library name: 16675.fastq.gz


title: aGBM5, DMSO, 48hr; BRAFi+MEKi, 24hr, 48hr

description: Library name: Sample 5

value: DMSO or BRAFi+MEKi


title: STN49, BRAFi+MEKi, 24 hrs, biol rep 1

description:
Library name: Sample 10
BMi24A3_1


title: 16672.fastq.gz,47,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_12w,10090

description: Library name: 16672.fastq.gz


title: 16671.fastq.gz,6,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_12w,10090

description: Library name: 16671.fastq.gz


title: S-20-extraocular muscle tissue of secondary inferior oblique overaction

city: Tianjin

first: Yuchuan

last: Wang

address: Gansu Road

institute: Tianjin Eye hospital

data_processing:
The reference genome was Homo_sapiens.GRCh38_release95.genome.fa. The mapping RNA-seq reads were performed using HISAT2 program (v0.1.6-beta). Alignment of the sequencing reads to a reference sequence was performed using Bowtie2 (v2.2.5). StringTie was applied to assemble the mapped reads. Differential expression analysis was performed using DESeq2. Results were corrected for multiple testing using the Benjamini-Hochberg method and reported as an adjusted p-value. A combination of an adjusted P value<0.05 and absolute log2 fold change (FC) value ≥1.5 were used as the threshold to determine the signifcance of DEGs.
Assembly: The reference genome was Homo_sapiens.GRCh38_release95.genome.fa. The mapping RNA-seq reads were performed using HISAT2 program (v0.1.6-beta).
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen),  according to manufacturer recommendations.
cDNA library from RNA samples was prepared according to manufacturer's protocol and sequencing was performed with Illumina NovaSeq6000.


title: 16670.fastq.gz,40,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_12w,10090

description: Library name: 16670.fastq.gz


title: PATIENT49


title: S-14-extraocular muscle tissue of secondary inferior oblique overaction


title: 16668.fastq.gz,57,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_12w,10090

description: Library name: 16668.fastq.gz


title: 16669.fastq.gz,42,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_12w,10090

description: Library name: 16669.fastq.gz


title: PATIENT47


title: PATIENT45


title: PATIENT46


title: 16664.fastq.gz,105,GUS2021_558_NN,Liver,CDAA_Baseline_group_6_w,10090

description: Library name: 16664.fastq.gz


title: 16666.fastq.gz,10,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_12w,10090

description: Library name: 16666.fastq.gz


title: S-1-extraocular muscle tissue of secondary inferior oblique overaction


title: 16665.fastq.gz,50,GUS2021_558_NN,Liver,CDAA_vehicle_QD_6_12w,10090

description: Library name: 16665.fastq.gz


title: S-15-extraocular muscle tissue of secondary inferior oblique overaction


title: 16662.fastq.gz,83,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_18w,10090

description: Library name: 16662.fastq.gz


title: 16674.fastq.gz,20,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_12w,10090

description: Library name: 16674.fastq.gz


title: 16663.fastq.gz,28,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_18w,10090

description: Library name: 16663.fastq.gz


title: S-6-extraocular muscle tissue of secondary inferior oblique overaction


title: 16659.fastq.gz,101,GUS2021_558_NN,Liver,CDAA_Baseline_group_6_w,10090

description: Library name: 16659.fastq.gz


title: 16660.fastq.gz,65,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_12w,10090

description: Library name: 16660.fastq.gz


title: S-8-extraocular muscle tissue of secondary inferior oblique overaction


title: PATIENT53


title: S-7-extraocular muscle tissue of secondary inferior oblique overaction


title: PATIENT44


title: PATIENT38


title: 16658.fastq.gz,104,GUS2021_558_NN,Liver,CDAA_Baseline_group_6_w,10090

description: Library name: 16658.fastq.gz


title: PATIENT39


title: PATIENT37

value: alive


title: 16667.fastq.gz,7,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_12w,10090

description: Library name: 16667.fastq.gz


title: 16656.fastq.gz,9,GUS2021_558_NN,Liver,Chow_reversal_vehicle_QD_6_12w,10090

description: Library name: 16656.fastq.gz


title: 16657.fastq.gz,87,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_18w,10090

description: Library name: 16657.fastq.gz


title: S-11-extraocular muscle tissue of secondary inferior oblique overaction


title: S-13-extraocular muscle tissue of secondary inferior oblique overaction


title: P-18-extraocular muscle tissue of primary inferior oblique overaction


title: 16661.fastq.gz,91,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_18w,10090

description: Library name: 16661.fastq.gz


title: P-19-extraocular muscle tissue of primary inferior oblique overaction


title: P-21-extraocular muscle tissue of primary inferior oblique overaction


title: PATIENT30


title: PATIENT26


title: P-2-extraocular muscle tissue of primary inferior oblique overaction


title: PATIENT31


title: P-22-extraocular muscle tissue of primary inferior oblique overaction


title: P-3-extraocular muscle tissue of primary inferior oblique overaction


title: PATIENT24

value: stop due to toxicity

value: not evaluable


title: P-9-extraocular muscle tissue of primary inferior oblique overaction


title: PATIENT23


title: J.Lck Y192F+optimized PTPN22 S449A stimulated, FB

first: Richard

last: Ainsworth

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

data_processing:
mRNA and ADT UMI counts were quantified using Cell Ranger v6.1.2.
Assembly: GRCh38-2020-A
Supplementary files format and content: CellRanger output files: barcodes.tsv, features.tsv, matrix.mtx
Library strategy: CITE-seq

molecule: protein

source_name: Peripheral blood

growth_protocol: J.Lck WT or J.Lck Y192F cell lines were cultured in complete RPMI 1640 medium with selection antibiotics, 10% fetal bovine serum (FBS) and supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 2.5 mg/mL D-glucose, 10 mM HEPES, 100 units/mL penicillin, and 100 μg/mL streptomycin under 5% CO2 at 37 °C

extract_protocol:
RNA samples were extracted by using RNeasy Micro kit (Qiagen)
Library was prepared at UCLA TCGB center

treatment_protocol: Cells were electroporated with optimized PTPN22 WT or S449A plasmids and stimulated with or without antibodies against human CD3/CD28 for 12h. mEGFP+ cells  were sorted out and directly subjected to CITE-seq buy using the Chromium Next GEM Single Cell 3' Kits (10x).

value: Peripheral blood

value: T lymphoblast

tag: library type

value: ADT

tag: adt (antibody-derived_tags)

value: TotalSeq™-B0146 anti-human CD69 Antibody

value: LCKY192F+PTPN22 S449A

value: CD3/CD28 stimulated


title: 16655.fastq.gz,41,GUS2021_558_NN,Liver,Sema_10_nmol_per_kg_QD_6_12w,10090

description: Library name: 16655.fastq.gz

value: liver

value: male


title: PATIENT22

value: primary

value: good


title: J.Lck WT+optimized PTPN22 S449A stimulated, FB

value: LCKWT+PTPN22 S449A


title: S-12-extraocular muscle tissue of secondary inferior oblique overaction


title: J.Lck WT+optimized PTPN22 WT stimulated, FB

value: LCKWT+PTPN22 WT


title: J.Lck Y192F+optimized PTPN22 WT stimulated, FB

value: LCKY192F+PTPN22 WT


title: P-10-extraocular muscle tissue of primary inferior oblique overaction


title: P-17-extraocular muscle tissue of primary inferior oblique overaction


title: PATIENT36

value: dead


title: PATIENT36.2

value: metastasis


title: PATIENT17

value: alive


title: PATIENT19

value: bad


title: PATIENT16


title: PATIENT15


title: J.Lck WT+optimized PTPN22 WT Control, FB

description: FB_Lib_J.WT Control

value: Peripheral blood


title: 15´21 CAR-NK, replicate 3, RNAseq

city: Wuhan

first: Xindi

state: Hubei

address: No.1277 Jiefang Avenue

department: Institute of Hematology

institute: Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Quality control: 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. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample.

source_name: NK-92 cell line

growth_protocol: Untransduced or CAR-engineered NK cells were cultured in complete MEMα (Gibco) supplemented with 12.5% fetal bovine serum, 12.5% equine serum (NEWZERUM), 200 U/ml human recombinant IL-2 (PeproTech), 0.2 mM inositol (TargetMol), 0.1 mM β-mercaptoethanol (Shanghai Zhongqiao Xinzhou), 0.02 mM folic acid (TargetMol), and 1% penicillin/streptomycin (Sigma-Aldrich).

extract_protocol:
RNA was extracted using the RNA extraction kit (CWBio).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic  beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370-420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer.

value: NK-92 cell line

value: natural killer cells

value: 15x21 CAR transduced


title: J.Lck Y192F+optimized PTPN22 WT stimulated, 3'GEX

value: T lymphoblast

value: mRNA


title: J.Lck Y192F+optimized PTPN22 S449A stimulated, 3'GEX

value: LCKY192F+PTPN22 S449A

value: CD3/CD28 stimulated


title: 15´21 CAR-NK, replicate 2, RNAseq


title: 15´21 CAR-NK, replicate 1, RNAseq


title: J.Lck WT+optimized PTPN22 S449A stimulated, 3'GEX


title: P-16-extraocular muscle tissue of primary inferior oblique overaction


title: PATIENT12


title: J.Lck WT+optimized PTPN22 WT Control, 3'GEX

description: 3GEX_Lib_J.WT Control


title: 15 CAR-NK, replicate 2, RNAseq

value: 15 CAR transduced


title: PATIENT10

value: primary


title: J.Lck WT+optimized PTPN22 WT stimulated, 3'GEX


title: 15 CAR-NK, replicate 3, RNAseq


title: tcpq, submergence, rep3

city: Hangzhou

first: Yiyi

last: Guo

state: China

address: Zijingang Campus, Zhejiang Uni

institute: Zhejiang University

data_processing:
After quality control by fastp (version0.23.1; -g -q 5 -u 50 -n 15 -l 150 --min_trim_length 10 --overlap_diff_limit 1 --overlap_diff_percent_limit 10), clean data were mapped to the reference genome of Arabidopsis (TAIR10.56) using STAR software (version 2.7.9a).
Assembly: TAIR10.56
Supplementary files format and content: txt or xls file include read count for each samples

organism: Arabidopsis thaliana

source_name: whole seedlings

extract_protocol:
Germinating seeds or six-day-old seedlings with or without submergence treatment were harvested and ground into a powder in liquid nitrogen. Total RNA was extracted using a Plant RNA Kit (Omega, R6827).
Messenger RNA was purified from total RNA using poly-T oligo attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. After library quality control, quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: whole seedlings

value: tcpq

tag: age

value: tcpq Crispr lines

value: Submergence


title: 15 CAR-NK, replicate 1, RNAseq

tag: cell line


title: PATIENT6

value: dead

value: good


title: tcpq, submergence, rep2

tag: genotype


title: PATIENT3

value: bad


title: PATIENT14

value: stop due to toxicity


title: CAR-NK, replicate 2, RNAseq

value: NK-92 cell line

value: CAR transduced


title: CAR-NK, replicate 1, RNAseq

value: natural killer cells


title: tcpq, submergence, rep1

tag: treatment


title: PATIENT2


city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

description: Library name: ChIPRx_merged_Input_MYCNER_shUSP11_siUSP7

data_processing:
ChIP-Rx samples were mapped separately to the human hg19 and to the murine mm10 genome using Bowtie2 (v2.3.5.1) using the preset parameter “very-sensitive-local”.
ChIP samples were normalized to the number of mapped reads in the smallest samples. Human ChIP-seq samples were either normalized relative to the spiked-in mouse reads (ChIP- Rx), or to the same number of human reads (read-normalized samples). The normalized bam files were sorted using SAMtools v1.9 and converted to bedgraphs using bedtools genomecov (v2.30.0).
Integrated Genome Browser was used to visualize density files. Metagene and density plots were generated with ngs.plot.r v2.63-7 82 or DeepTools v3.5.1 83 using a bin size of 10 bp.
Assembly: GRCh37
Supplementary files format and content: bedgraph files

source_name: Bone Marrow

growth_protocol: Cells were grown in RPMI supplemented with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
For each ChIP-Rx experiment, 3 to 5*10^7 cells per immunoprecipitation were harvested, proteins were crosslinked to chromatin for 5 min at RT with formaldehyde (final concentration 1%). The reaction was quenched by addition of 125 mM Glycine for 5 min at RT. Cell pellets were resuspended in PIPES lysis buffer containing protease and phosphatase inhibitors (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% v/v NP-40) and ChIP-Rx experiments were spiked with murine NHO2A or NIH3T3 cells (ratio 1:10). Nuclei were incubated for 20 min on ice, pelleted by centrifuging, then resuspended in RIPA lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 0.1% v/v SDS, 1% v/v Triton X-100, 0.1% w/v sodium deoxycholate) and incubated for 10 min at 4°C. Chromatin was fragmented using the Covaris M220 Focused Ultrasonicator (Peak Power = 75.0, Cycles/Burst = 200, Duty Factor = 10.0, Duration = 3,000 s per ml cell lysate for IMR-5 cells). Antibodies were coupled to Dynabeads (Thermo Fisher Scientific), then cleared lysates were incubated with the antibody/bead mix at 4 °C. Samples were washed three times each with washing buffer I (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% v/v Triton X- 100, 0.1% v/v SDS), washing buffer II (20 mM Tris-HCl pH 8.1, 500 mM NaCl, 2 mM EDTA, 1% v/v Triton X-100, 0.1% v/v SDS), washing buffer III (10 mM Tris pH 8.1, 250 mM LiCl, 1 mM EDTA, 1% v/v NP-40, 1% w/v sodium deoxycholate) and twice with TE buffer. The elution of the chromatin was performed by incubating the beads with elution buffer (100 mM NaHCO3, 1% v/v SDS in TE buffer) for 15 min at RT on a rotating wheel and repeated for a total of two elution steps. Input and immunoprecipitation samples were de-crosslinked by digestion with RNase A for 1 h at 37°C and followed by incubation overnight at 65°C with shaking, and digestion with proteinase K for 2 h at 45°C. The isolation of the DNA was performed by phenol- chloroform extraction, purified with ethanol precipitation and subsequently quantified with the Quant-iT PicoGreen dsDNA assay (Thermo Fisher Scientific) for ChIP-Rx experiments.
DNA libraries of ChIP-Rx samples were prepared by using the NEBNext Ultra II DNA Library Prep Kit for Illumina Sequencing (New England Biolabs).

treatment_protocol: Treatment as indicated with 1µg/µL of doxycycline, and 4 h of 200 nM 4-OHT. 20 nM siRNA were used as indicated.

value: Bone Marrow

value: SH-EP MYCN-ER

value: neuroblastroma

value: 4-hydroxtamoxifen (4-OHT)-activating MYCN transgene; doxycycline (DOX) inducible shRNA targeting USP11


description: Library name: ChIPRx_pSer2_MYCNER_shUSP11_siNTC_EtOH_EtOH

value: EtOH_EtOH (48 h; 4 h); siNTC (48 h; 20 nM)


description: Library name: ChIPRx_pSer2_MYCNER_shUSP11_siNTC_DOX_EtOH

value: DOX_EtOH (48 h; 4 h); siNTC (48 h; 20 nM)


description: Library name: ChIPRx_pSer2_MYCNER_shUSP11_siUSP7_EtOH_EtOH

value: EtOH_EtOH (48 h; 4 h); siUSP7 (48 h; 20 nM)


title: UTD NK, replicate 3, RNAseq

value: WT


title: tcpq, mock, rep2

value: whole seedlings

value: tcpq

value: tcpq Crispr lines

value: mock


title: UTD NK, replicate 2, RNAseq


title: tcpq, mock, rep1


title: CAR-NK, replicate 3, RNAseq


description: Library name: ChIPRx_RNAP2_MYCNER_shUSP11_siUSP7_EtOH_EtOH


title: UTD NK, replicate 1, RNAseq


title: tcp21, submergence, rep3

value: tcp21 Crispr lines

value: Submergence


title: tcp21, submergence, rep2


description: Library name: ChIPRx_RNAP2_MYCNER_shUSP11_siNTC_DOX_EtOH


description: Library name: ChIPRx_RNAP2_MYCNER_shUSP11_siNTC_DOX_OHT

value: DOX_OHT (48 h; 4 h); siNTC (48 h; 20 nM)


title: Plasma, NoRejection, cmh005956-01

city: Madison

first: Benjamin

middle: L

last: Spector

state: WI

address: 600 Highland Ave

department: Pediatrics

institute: University of Wisconsin- Madison

data_processing:
Sequence Reads were demultiplexed into FASTQ files using Illumina’s bcl2Fastq2-2.19.1 software and trimmed for quality (phred33 >= 20) and Illumina adapters using trimgalore v.0.4.2.
Reads were then aligned to the bisulfite-converted GRCh38 reference genome using DRAGEN EP v2.6.3 in paired-end mode using the directional/Lister methylation protocol presets.
Alignments were calculated for both Watson and Crick strands and the highest quality unique alignment was retained.
Duplicated reads were removed using picard v 2.17.8.42
A genome-wide cytosine methylation report was generated by DRAGEN to record counts of methylated and unmethylated cytosines at each cytosine position in the genome.
Assembly: hg38
Supplementary files format and content: tsv files contain the CpG profile across the genome for each sample in tab deliimited format [chr, start, end, fw_meth_reads, fw_total_reads, fw_meth_frac, rev_meth_reads, rev_total_reads, rev_meth_frac]

source_name: Plasma

extract_protocol:
Cell-free DNA was isolated from plasma specimens using the QIAMP CAN Kit per manufacturer's instructions.
In total of 5 ng of DNA was aliquoted from each sample. Unmethylated λDNA was added to each sample at 0.5% w/v. The samples were then concentrated with a SpeedVac to a volume of 20µL. Due to the fragmented nature of cfDNA, further fragmentation of the samples was not required. The samples then underwent bisulfite conversion with an EZ DNA Methylation- Gold kit (Zymo, Cat. No. D5006). The samples were eluted off the spin columns with 15μl of low EDTA TE buffer (Swift, Cat. No. 30024) before library preparation.  Low-input libraries were prepared using an ACCEL-NGS Methyl-Seq Library kit (Swift, Cat. No. 30024) with a Methyl-Seq Set A Indexing Kit (Swift, Cat. No. 36024), following the protocol associated with the kit. Bead cleanup steps were performed with SPRIselect beads (Beckman Coulter, Cat. No. B23318). Six PCR cycles were performed to amplify the samples. Final libraries were quantified with a Qubit dsDNA HS Assay Kit and size was determined using a BioAnalyzer High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626). The libraries were then sequenced on the Illumina NovaSeq6000 System using 150bp paired-end sequencing.

value: Plasma

tag: biopsy rejection_designation

value: No rejection

tag: time from_transplant_(months)

tag: age (years)

tag: white blood_cell_count_(10e-3/ul)

tag: race

value: Caucasian

tag: recipient/donor sex

value: MM


title: Plasma, NoRejection, cmh006055-01

tag: tissue

value: Other


title: tcp21, mock, rep3

tag: strain


description: Library name: ChIPRx_RNAP2_MYCNER_shUSP11_siNTC_EtOH_OHT

value: Bone Marrow

value: SH-EP MYCN-ER

tag: cell type

value: neuroblastroma

value: 4-hydroxtamoxifen (4-OHT)-activating MYCN transgene; doxycycline (DOX) inducible shRNA targeting USP11

value: EtOH_OHT (48 h; 4 h); siNTC (48 h; 20 nM)


title: tcp21, submergence, rep1

value: whole seedlings


title: Plasma, NoRejection, cmh003401-01


description: Library name: ChIPRx_RNAP2_MYCNER_shUSP11_siNTC_EtOH_EtOH

value: EtOH_EtOH (48 h; 4 h); siNTC (48 h; 20 nM)


title: tcpq, mock, rep3

value: tcpq

value: tcpq Crispr lines


title: Plasma, NoRejection, cmh005984-01

value: MF


title: tcp21, mock, rep2

value: tcp21 Crispr lines

value: mock


title: Plasma, BorderlineRejection, cmh005969-04

value: Plasma

value: Borderline rejection


title: tcp21, mock, rep1


title: Plasma, BorderlineRejection, cmh005935-01A

value: Caucasian


title: RNAseq_IMR5_siTCEAL1_rep2

description: Library name: RNAseq_IMR5_siTCEAL1_rep2

data_processing:
Quality control of raw reads was assessed using FastQC.
Reads were aligned to the human reference genome using STAR (v2.7.10a) following ENCODE paired-end RNA- sequencing recommendations (ENCODE rna-seq-pipeline v0.1.0).
Transcript abundance was estimated using RSEM (1.3.3) and subsequently used for differential expression analysis using DESeq2 (v1.38.3) in R. Transcripts with less than 12 counts across all nine samples were removed.
Assembly: GRCh37, GRCh38
Supplementary files format and content: bedgraph files
Supplementary files format and content: raw count table for each condition

source_name: Abdomen

extract_protocol:
RNA was extracted using the Qiawave Kit (Qiagen) according to the manufacturer’s instructions.
RNA concentration and RQN values were determined with a Fragment Analyzer (Agilent) and 500 ng RNA with RQN > 9 was used for library preparation using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following the manufacturer’s manual. Libraries were size selected using SPRIselect Beads (Beckman Coulter) after amplification with 9 PCR cycles. Library quantification and size determination were performed with the Fragment Analyzer (Agilent) using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent). Libraries were subjected to cluster generation and base calling for 100 cycles paired end on the Illumina NextSeq 2000 platform.

treatment_protocol: Treatment as indicated with 1µg/µL of doxycycline. 20 nM of siRNA were used.

value: Abdomen

value: adrenergic neuroblastoma cell line

value: siTCEAL1 (48 h; 20 nM)


title: PATIENT32

tag: biopsy origin

value: primary

tag: treatment line

tag: status

value: dead

tag: treatment duration (months)

value: good


title: RNAseq_IMR5_siTCEAL1_rep3

description: Library name: RNAseq_IMR5_siTCEAL1_rep3


title: col, Submergence , rep3(tcp21,tcpq)

value: Col

tag: age

value: WT

value: Submergence


title: RNAseq_IMR5_siTCEAL1_rep1

description: Library name: RNAseq_IMR5_siTCEAL1_rep1

tag: cell line


title: Plasma, AcuteRejection, cmh005958-01

value: Acute rejection

value: MM


title: col, Submergence , rep2(tcp21,tcpq)

value: whole seedlings

tag: genotype


description: Library name: ChIPRx_RNAP2_MYCNER_shUSP11_siUSP7_EtOH_OHT

value: Bone Marrow

value: SH-EP MYCN-ER

value: neuroblastroma

value: 4-hydroxtamoxifen (4-OHT)-activating MYCN transgene; doxycycline (DOX) inducible shRNA targeting USP11

tag: treatment

value: EtOH_OHT (48 h; 4 h); siUSP7 (48 h; 20 nM)


title: RNAseq_IMR5_siNTC_rep3

description: Library name: RNAseq_IMR5_siNTC_rep3

value: Abdomen

value: siNTC (48 h; 20 nM)


title: Plasma, AcuteRejection, SOT0024-1-4

value: Plasma

tag: biopsy rejection_designation

value: Caucasian

value: FF


title: col, Submergence , rep1(tcp21,tcpq)


title: col, mock, rep3(tcp21,tcpq)

value: mock


title: Plasma, BorderlineRejection, SOT0032-1-1

value: Borderline rejection

tag: time from_transplant_(months)

value: MF


title: RNAseq_IMR5_siNTC_rep2

description: Library name: RNAseq_IMR5_siNTC_rep2

value: adrenergic neuroblastoma cell line


title: RNAseq_IMR5_siNTC_rep1

description: Library name: RNAseq_IMR5_siNTC_rep1


title: col, mock, rep2(tcp21,tcpq)

value: Col

value: WT


title: Plasma, NoRejection, SOT0005-1-3

value: No rejection

tag: age (years)

value: Black


title: Plasma, AcuteRejection, SOT0024-1-1

value: Acute rejection

tag: white blood_cell_count_(10e-3/ul)


title: RNAseq_SHEP_siTCEAL1_rep3

description: Library name: RNAseq_SHEP_siTCEAL1_rep3

value: Bone Marrow

value: SH-EP

value: mesenchymal neuroblastoma cell line

value: siTCEAL1 (48 h; 20 nM)


title: col, mock, rep1(tcp21,tcpq)

value: whole seedlings

value: bak1-3 bkk1-1 T-DNA lines


title: Plasma, AcuteRejection, SOT0021-1-1

value: Plasma

tag: race

value: Caucasian

value: FM


title: RNAseq_SHEP_siTCEAL1_rep2

description: Library name: RNAseq_SHEP_siTCEAL1_rep2


title: RNAseq_SHEP_siTCEAL1_rep1

description: Library name: RNAseq_SHEP_siTCEAL1_rep1


title: bak1-3 bkk1-1, Submergence , rep2

value: bak1-3 bkk1-1

value: Submergence


title: bak1-3 bkk1-1, Submergence , rep3


title: bak1-3 bkk1-1, Submergence , rep1


title: Plasma, NoRejection, SOT0011-1-1

tag: recipient/donor sex

value: MF


title: RNAseq_SHEP_siNTC_rep3

description: Library name: RNAseq_SHEP_siNTC_rep3

tag: tissue

value: siNTC (48 h; 20 nM)


title: Plasma, AcuteRejection, SOT0016-1-1

value: MM


title: Plasma, AcuteRejection, SOT-KM

value: FF


title: RNAseq_SHEP_siNTC_rep2

description: Library name: RNAseq_SHEP_siNTC_rep2


title: RNAseq_SHEP_siNTC_rep1

description: Library name: RNAseq_SHEP_siNTC_rep1


title: Plasma, BorderlineRejection, SOT0002-1-2

value: Borderline rejection


title: RNAseq_MYCNER_shUSP11_siUSP7_Ctrl_rep3

description: Library name: RNAseq_MYCNER_shUSP11_siUSP7_Ctrl_rep3

value: SH-EP MYCN-ER

value: 4-hydroxtamoxifen (4-OHT)-activating MYCN transgene; doxycycline (DOX) inducible shRNA targeting USP11

value: EtOH_EtOH (48 h; 4 h); siUSP7 (48 h; 20 nM)


title: bak1-3 bkk1-1, mock, rep3

tag: strain

value: mock


title: bak1-3 bkk1-1, mock, rep2


title: Plasma, NoRejection, SOT0006-1-1

value: No rejection

value: Black


title: RNAseq_MYCNER_shUSP11_siUSP7_Ctrl_rep2

description: Library name: RNAseq_MYCNER_shUSP11_siUSP7_Ctrl_rep2

value: Bone Marrow

tag: cell type

value: mesenchymal neuroblastoma cell line


title: bak1-3 bkk1-1, mock, rep1

value: whole seedlings

value: bak1-3 bkk1-1 T-DNA lines


title: col, Submergence , rep3(bak1-3 bkk1-1)

value: Col

value: WT


title: Plasma, NoRejection, SOT0005-1-1

value: Plasma


title: RNAseq_MYCNER_shUSP11_siUSP7_Ctrl_rep1

description: Library name: RNAseq_MYCNER_shUSP11_siUSP7_Ctrl_rep1


title: RNAseq_MYCNER_shUSP11_Dox_rep3

description: Library name: RNAseq_MYCNER_shUSP11_Dox_rep3

value: DOX_EtOH (48 h; 4 h); siNTC (48 h; 20 nM)


title: Plasma, AcuteRejection, SOT0002-1-1

value: Acute rejection

value: Caucasian

value: MM


title: col, Submergence , rep2(bak1-3 bkk1-1)

value: Submergence


title: col, Submergence , rep1(bak1-3 bkk1-1)


title: RNAseq_MYCNER_shUSP11_Dox_rep2

description: Library name: RNAseq_MYCNER_shUSP11_Dox_rep2

value: SH-EP MYCN-ER

value: 4-hydroxtamoxifen (4-OHT)-activating MYCN transgene; doxycycline (DOX) inducible shRNA targeting USP11


title: col, mock, rep3(bak1-3 bkk1-1)

value: mock


title: Plasma, NoRejection, SOT0001-1-1

value: No rejection

value: MF


title: RNAseq_MYCNER_shUSP11_Dox_rep1

description: Library name: RNAseq_MYCNER_shUSP11_Dox_rep1

value: Bone Marrow


title: ASD,434,Passage8,20,rep_1

city: Barcelona

first: Xoel

last: Mato Blanco

address: Doctor Aiguader, 88

department: Neurogenomics

institute: Institut Hospital del Mar d'Investigacions Mèdiques

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: 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.

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: fibroblast

value: iPSC

value: Neural Stem Cells

tag: line

tag: Sex

value: Male

tag: fgf2 concentration_(ng/ml)

tag: time (days_in_vitro)_or_passage

tag: disease

value: Idiophatic  ASD

value: N2-B27 + LDN+SB-induced neuronal differentiation of the iPSCs for 8 days (passage 1). From passage 2 NSCs were serially passaged in N2 +FGF2. Cells were exposed  to 0.1 or  20 ng/mL FGF2.


title: ASD,384,Passage8,20,rep_1

description: HiSeq paired-end, 100 bp

tag: cell line


title: RNAseq_MYCNER_shUSP11_Ctrl_rep3

description: Library name: RNAseq_MYCNER_shUSP11_Ctrl_rep3

value: mesenchymal neuroblastoma cell line

tag: genotype

value: EtOH_EtOH (48 h; 4 h); siNTC (48 h; 20 nM)


title: ASD,375,Passage8,20,rep_1

description: HiSeq paired-end, 100 bp

tag: treatment


title: Control,317,Passage8,20,rep_1

description: HiSeq paired-end, 100 bp

source_name: skin fibroblast

value: skin fibroblast

value: Female

value: Unaffected


title: RNAseq_MYCNER_shUSP11_Ctrl_rep1

description: Library name: RNAseq_MYCNER_shUSP11_Ctrl_rep1

value: SH-EP MYCN-ER


title: RNAseq_MYCNER_shUSP11_Ctrl_rep2

description: Library name: RNAseq_MYCNER_shUSP11_Ctrl_rep2

value: 4-hydroxtamoxifen (4-OHT)-activating MYCN transgene; doxycycline (DOX) inducible shRNA targeting USP11


title: Control,311,Passage8,20,rep_1

description: HiSeq paired-end, 100 bp

source_name: meninge fibroblast

value: meninge fibroblast


title: ChIPRx_merged_Input_MYCNwt_HA-TCEAL1

description: ChIP-Rx seq

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)

tag: dox treatment_(shtceal1_active)

tag: inhibitor treatment_(thz1)

tag: inhibitor treatment_(nvp-2)

tag: constitutive mycn_expression

value: na (merged for all conditions)

tag: constitutive ha-tceal1_expression

tag: antibody

value: Input (no antibody)


title: ChIPRx_TFIIS_MYCNwt_HA-TCEAL1_mut3RA

description: ChIP-Rx seq

value: Yes

value: Yes (HA-TCEAL1 mutant)

value: TFIIS


title: ASD,434,Passage8,0.1,rep_1

description: HiSeq paired-end, 100 bp

tag: tissue

value: fibroblast

value: iPSC

value: Neural Stem Cells

value: Male

value: Idiophatic  ASD


title: ChIPRx_TFIIS_MYCNwt_HA-TCEAL1_wt

description: ChIP-Rx seq

tag: cell type

value: Yes (HA-TCEAL1 wild-type)


title: ASD,384,Passage8,0.1,rep_1

description: HiSeq paired-end, 100 bp

tag: line

value: N2-B27 + LDN+SB-induced neuronal differentiation of the iPSCs for 8 days (passage 1). From passage 2 NSCs were serially passaged in N2 +FGF2. Cells were exposed  to 0.1 or  20 ng/mL FGF2.


title: ChIPRx_TFIIS_MYCNwt_Ctrl

description: ChIP-Rx seq

value: No


title: ASD,375,Passage8,0.1,rep_1

description: HiSeq paired-end, 100 bp

tag: Sex


title: Single cell RNA sequencing of SPF mice pbmc

city: Shenzhen

first: Yifei

last: SHENG

state: Guangdong

address: Complex Building, Beishan Industrial Zone, Yantian District

institute: BGI Research

description:
Library name: SPF-PBMC_S1_L001
10x Genomics

data_processing:
Sequenced reads of mouse were aligned to the mm10 mouse transcriptome, then quantify the expression of transcripts in each cell using Cell Ranger v6.0.2.
Assembly: mm10
Supplementary files format and content: This RDS file contains processed single-cell RNA sequencing (scRNA-seq) data comparing immune cell populations from germ-free (GF) and specific-pathogen-free (SPF) mice.

source_name: peripheral blood

extract_protocol:
10x Genomics Single Cell 3’ Library Kit V3
ScRNA-seq was performed using the 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kit v3.1, followed by library construction.

value: peripheral blood

tag: age

value: 10 weeks old

value: male

tag: strain

value: Kunming

value: SPF


title: Single cell RNA sequencing of GF mice pbmc

description:
Library name: GF-PBMC_S1_L001
10x Genomics

value: GF


title: Single cell RNA sequencing of SPF mice bone marrow

description:
Library name: SPF-GS_S1_L001
10x Genomics

source_name: bone marrow

value: bone marrow


title: Control,311,Passage8,0.1,rep_1

description: HiSeq paired-end, 100 bp

value: meninge fibroblast

value: Female

tag: fgf2 concentration_(ng/ml)

tag: time (days_in_vitro)_or_passage

tag: disease

value: Unaffected


title: Single cell RNA sequencing of GF mice bone marrow

description:
Library name: GF-GS_S1_L001
10x Genomics

tag: treatment


title: ChIPRx_TFIIS_MYCNER_shTCEAL1_OHT_Dox

description: ChIP-Rx seq

tag: cell line

value: SHEP

value: Neuroblastoma

tag: oht treatment_(mycn_active)

value: Yes

value: TFIIS


title: ChIPRx_TFIIS_MYCNER_shTCEAL1_OHT

description: ChIP-Rx seq

tag: dox treatment_(shtceal1_active)

tag: inhibitor treatment_(thz1)


title: Control,290,Passage8,0.1,rep_1

description: HiSeq paired-end, 100 bp

value: iPSC

value: Neural Stem Cells

value: Male


title: ChIPRx_merged_Input_MYCNER_shTCEAL1_exp1

description: ChIP-Rx seq

value: na (merged for all conditions)

tag: inhibitor treatment_(nvp-2)

tag: constitutive mycn_expression

value: Input (no antibody)


title: ACF+StiffA, bio rep 3

city: Singapore

first: Jennifer

last: Young

address: 5A Engineering Drive 1, Mechanobiology Insititute, T-Lab Lv 9, National University of Singapore

country: Singapore

institute: National University of S'pore

description: Library name: H6

data_processing:
STAR (2.7.8a), Bioconductor 3.17
Assembly: mm39
Supplementary files format and content: txt

source_name: cardiac

extract_protocol:
RNA was extracted using TRIZOL method and 20 ng of RNA was used for cDNA synthesis and amplification using NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina®
NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® was used according to supplier's protocols.

value: cardiac

value: N/A (primary cells)

value: primary cardiac fibroblasts


title: col, mock, rep1(bak1-3 bkk1-1)

value: whole seedlings

value: Col

tag: genotype

value: WT

value: mock


title: ACF+StiffA, bio rep 2

description: Library name: H5

tag: tissue


title: ASD,434,Passage4,20,rep_1

description: HiSeq paired-end, 100 bp

value: fibroblast

tag: cell type

value: Idiophatic  ASD

value: N2-B27 + LDN+SB-induced neuronal differentiation of the iPSCs for 8 days (passage 1). From passage 2 NSCs were serially passaged in N2 +FGF2. Cells were exposed  to 0.1 or  20 ng/mL FGF2.


title: col, mock, rep2(bak1-3 bkk1-1)


title: Control,290,Passage8,20,rep_1

description: HiSeq paired-end, 100 bp

value: meninge fibroblast

tag: line

value: Unaffected


title: ACF+StiffA, bio rep 1

description: Library name: H4


title: ChIPRx_pSer2_MYCNER_shTCEAL1_OHT_Dox

description: ChIP-Rx seq

value: SHEP

value: Neuroblastoma

value: Yes

tag: constitutive ha-tceal1_expression

tag: antibody

value: pSer2 RNAP2


title: ChIPRx_pSer2_MYCNER_shTCEAL1_OHT

description: ChIP-Rx seq

value: No


title: YCF+StiffA, bio rep 2

description: Library name: H2

value: cardiac


title: YCF+StiffA, bio rep 3

description: Library name: H3

value: N/A (primary cells)


title: ChIPRx_RNAP2_MYCNER_shTCEAL1_Dox

description: ChIP-Rx seq

value: total RNAP2


title: ASD,384,Passage4,20,rep_1

description: HiSeq paired-end, 100 bp

value: iPSC

value: Neural Stem Cells

tag: Sex

value: Male


title: Control,317,Passage4,20,rep_1

description: HiSeq paired-end, 100 bp

value: skin fibroblast

value: Female

tag: fgf2 concentration_(ng/ml)


title: ASD,375,Passage4,20,rep_1

description: HiSeq paired-end, 100 bp

value: fibroblast

tag: time (days_in_vitro)_or_passage

value: Idiophatic  ASD


title: Control,317,Passage8,0.1,rep_1

description: HiSeq paired-end, 100 bp

tag: disease

value: N2-B27 + LDN+SB-induced neuronal differentiation of the iPSCs for 8 days (passage 1). From passage 2 NSCs were serially passaged in N2 +FGF2. Cells were exposed  to 0.1 or  20 ng/mL FGF2.


title: YCF+StiffA, bio rep 1

description: Library name: H1

value: primary cardiac fibroblasts


title: Control,311,Passage4,20,rep_1

description: HiSeq paired-end, 100 bp

value: meninge fibroblast

value: Unaffected

tag: treatment


title: ChIPRx_merged_Input_MYCNER_shTCEAL1_exp2

description: ChIP-Rx seq

tag: cell line

value: SHEP

value: Neuroblastoma

value: na (merged for all conditions)

value: Input (no antibody)


title: ChIPRx_RNAP2_MYCNER_shTCEAL1_OHT

description: ChIP-Rx seq

tag: oht treatment_(mycn_active)

value: Yes

value: No


title: ACF+SoftA, bio rep 3

description: Library name: G6

value: cardiac

value: N/A (primary cells)


title: Control,290,Passage4,20,rep_1

description: HiSeq paired-end, 100 bp

value: iPSC

value: Neural Stem Cells

value: Male


title: ChIPRx_RNAP2_MYCNER_shTCEAL1_Ctrl

description: ChIP-Rx seq

tag: dox treatment_(shtceal1_active)

value: total RNAP2


title: ASD,434,Passage4,0.1,rep_1

description: HiSeq paired-end, 100 bp

value: fibroblast

value: Idiophatic  ASD


title: ChIPseq_merged_Input_MYCNER_HA-TCEAL1

description: ChIP seq

tag: inhibitor treatment_(thz1)


title: ASD,384,Passage4,0.1,rep_1

description: HiSeq paired-end, 100 bp

value: N2-B27 + LDN+SB-induced neuronal differentiation of the iPSCs for 8 days (passage 1). From passage 2 NSCs were serially passaged in N2 +FGF2. Cells were exposed  to 0.1 or  20 ng/mL FGF2.


title: ACF+SoftA, bio rep 2

description: Library name: G5

value: primary cardiac fibroblasts


title: ACF+SoftA, bio rep 1

description: Library name: G4


title: ASD,375,Passage4,0.1,rep_1

description: HiSeq paired-end, 100 bp


title: ChIPRx_RNAP2_MYCNER_shTCEAL1_OHT_Dox

description: ChIP-Rx seq

tag: inhibitor treatment_(nvp-2)


title: Control,317,Passage4,0.1,rep_1

description: HiSeq paired-end, 100 bp

value: skin fibroblast

value: Female

value: Unaffected


title: ChIPseq_HA-tag_MYCNER_HA-TCEAL1_OHT_NVP2

description: ChIP seq

value: SHEP

value: Neuroblastoma

tag: constitutive mycn_expression

value: anti-HA


title: YCF+SoftA, bio rep 3

description: Library name: G3


title: YCF+SoftA, bio rep 2

description: Library name: G2


title: Control,311,Passage4,0.1,rep_1

description: HiSeq paired-end, 100 bp

value: meninge fibroblast


title: ChIPseq_HA-tag_MYCNER_Ctrl_OHT

description: ChIP seq

value: Yes

value: No


title: ChIPseq_HA-tag_MYCNER_HA-TCEAL1_OHT_THZ1

description: ChIP seq


title: YCF+SoftA, bio rep 1

description: Library name: G1

value: cardiac

value: N/A (primary cells)


title: ChIPseq_HA-tag_MYCNER_HA-TCEAL1_OHT

description: ChIP seq


title: Control,290,Passage4,0.1,rep_1

description: HiSeq paired-end, 100 bp

value: iPSC

value: Neural Stem Cells

value: Male


title: ACF+StiffY, bio rep 2

description: Library name: F5


title: ACF+StiffY, bio rep 1

description: Library name: F4


title: ASD,434,Passage2,20,rep_1

description: HiSeq paired-end, 100 bp

value: fibroblast

value: Idiophatic  ASD


title: RNAseq_MYCNER_shTCEAL1_OHT_Dox_rep2

description: polyA-RNAseq


title: RNAseq_MYCNER_shTCEAL1_OHT_Dox_rep3

description: polyA-RNAseq


title: ChIPseq_RNAP2_MYCNER_HA-TCEAL1_OHT

description: ChIP seq

value: total RNAP2


title: ASD,384,Passage2,20,rep_1

description: HiSeq paired-end, 100 bp

value: N2-B27 + LDN+SB-induced neuronal differentiation of the iPSCs for 8 days (passage 1). From passage 2 NSCs were serially passaged in N2 +FGF2. Cells were exposed  to 0.1 or  20 ng/mL FGF2.


title: ASD,375,Passage2,20,rep_1

description: HiSeq paired-end, 100 bp


title: RNAseq_MYCNER_shTCEAL1_OHT_Dox_rep1

description: polyA-RNAseq


title: ZmWUS1, DAP-seq

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:
alignment using bowtie2 Filtering using samtools Calling peaks using GEM
Assembly: B73 v5
Supplementary files format and content: Bw file - Chromosome(column 1), Start position (column 2), End position (column 3)
Library strategy: DAP-seq

organism: Zea mays

source_name: Leaves

extract_protocol:
genomic DNA was extracted from the leaves of 14 day-old B73 seedlings using a phenol:cholorform:Iso amyl alcohol procedure.
5ug of extracted DNA was sheared in a Covaris S2 sonicator to 200bp fragments. The fragmented DNA was then end repaired using the END-IT DNA repair kit (Lucigen) per the manufacturer’s recommendations and cleaned using a QiaQuick PCR clean-up method (Qiagen). Eluted DNA was then A-tailed using Klenow exo- (NEB) for 30min at RT. Samples were cleaned using a QiaQuick PCR-clean-up method. Eluted DNA was ligated to truncated Illumina Y-adapters overnight at 16 degrees C using T4 DNA ligase (NEB). Samples were heat inactivated for 10 min at 70 degrees C followed by a 1:1 bead clean-up using AmpureXP beads (Beckman-Coulter). Libraries were quantified using the Qubit HS kit. 1ug of this library was then incubated with in vitro expressed HALO-WUS1 protein bound to 10ul of MagneHALO beads (TNT rabbit reticulocyte expression system and MagneHALO beads, Promega) generated from 1ug of pIX-HALO-WUS1 plasmid. Unbound DNA was washed away using six washes of phosphate buffered saline (PBS), and bound DNA was eluted from the beads using 30ul of 10mM Tris (EB) and heating to 98 degrees C for 10 min. DNA was barcoded and enriched with 19 cycles and Illumina primers prior to sequencing on a NextSeq500 with 75bp Single End reads.

value: Leaves

tag: genotype


title: Control,317,Passage2,20,rep_1

description: HiSeq paired-end, 100 bp

tag: tissue

value: skin fibroblast

value: Female

value: Unaffected


title: YCF+StiffY, bio rep 3

description: Library name: F3

tag: cell type

value: primary cardiac fibroblasts


title: YCF+StiffY, bio rep 2

description: Library name: F2


title: RNAseq_MYCNER_shTCEAL1_Dox_rep3

description: polyA-RNAseq

value: SHEP

value: Neuroblastoma


title: Healthy control skin 6

city: Seoul

first: Hye Li

last: Kim

address: 50-1, Yonsei-ro

country: South Korea

institute: Yonsei university

description: Library name: HC6

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: Healthy control skin 5

description: Library name: HC5


title: ACF+StiffY, bio rep 3

description: Library name: F6

value: cardiac


title: RNAseq_MYCNER_shTCEAL1_Dox_rep2

description: polyA-RNAseq

value: No

value: Yes


title: ASD,434,Passage2,20,rep_2

description: HiSeq paired-end, 100 bp

value: iPSC

value: Neural Stem Cells

tag: line


title: Control,311,Passage2,20,rep_1

description: HiSeq paired-end, 100 bp

value: meninge fibroblast


title: RNAseq_MYCNER_shTCEAL1_Dox_rep1

description: polyA-RNAseq


title: ACF+SoftY, bio rep 3

description: Library name: E6

value: N/A (primary cells)


title: YCF+StiffY, bio rep 1

description: Library name: F1


title: Healthy control skin 3

description: Library name: HC3


title: Healthy control skin 4

description: Library name: HC4


title: Control,290,Passage2,20,rep_1

description: HiSeq paired-end, 100 bp

value: Male


title: ACF+SoftY, bio rep 2

description: Library name: E5


title: RNAseq_MYCNER_shTCEAL1_OHT_rep3

description: polyA-RNAseq


title: ASD,434,Passage2,0.1,rep_1

description: HiSeq paired-end, 100 bp

value: fibroblast

value: Idiophatic  ASD

value: N2-B27 + LDN+SB-induced neuronal differentiation of the iPSCs for 8 days (passage 1). From passage 2 NSCs were serially passaged in N2 +FGF2. Cells were exposed  to 0.1 or  20 ng/mL FGF2.


title: RNAseq_MYCNER_shTCEAL1_OHT_rep2

description: polyA-RNAseq


title: ASD,384,Passage2,0.1,rep_1

description: HiSeq paired-end, 100 bp


title: ACF+SoftY, bio rep 1

description: Library name: E4


title: Healthy control skin 1

description: Library name: HC1


title: Healthy control skin 2

description: Library name: HC2


title: YCF+SoftY, bio rep 2

description: Library name: E3


title: RNAseq_MYCNER_shTCEAL1_OHT_rep1

description: polyA-RNAseq


title: ASD,375,Passage2,0.1,rep_1

description: HiSeq paired-end, 100 bp


title: YCF+SoftY, bio rep 1

description: Library name: E1


title: Psoriasis skin 7

description: Library name: PSO7


title: RNAseq_MYCNER_shTCEAL1_Ctrl_rep3

description: polyA-RNAseq


title: Control,317,Passage2,0.1,rep_1

description: HiSeq paired-end, 100 bp

value: skin fibroblast

value: Female


title: Psoriasis skin 6

description: Library name: PSO6


title: fresh ACF, bio rep 3

description: Library name: A6

value: primary cardiac fibroblasts


title: Control,311,Passage2,0.1,rep_1

description: HiSeq paired-end, 100 bp

value: Unaffected


title: RNAseq_MYCNER_shTCEAL1_Ctrl_rep1

description: polyA-RNAseq

value: SHEP

value: Neuroblastoma


title: Control,290,Passage2,0.1,rep_2

description: HiSeq paired-end, 100 bp


title: fresh ACF, bio rep 2

description: Library name: A5

value: cardiac


title: fresh ACF, bio rep 1

description: Library name: A4


title: Control,290,Passage2,0.1,rep_1

description: HiSeq paired-end, 100 bp


title: fresh YCF, bio rep 3

description: Library name: A3


title: Psoriasis skin 3

description: Library name: PSO3

value: skin


title: Slide7_Bif3_Replicate4

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

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 2

description: Library name: PSO2


title: ASD,434,DIV 38,rep_1

description: HiSeq paired-end, 100 bp

value: iPSC

value: No FGF2

value: DIV 38

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


title: fresh YCF, bio rep 2

description: Library name: A2

value: N/A (primary cells)


title: Slide6_Bif3_Replicate4

description: Illumina


title: ASD,384,DIV 38,rep_1

description: HiSeq paired-end, 100 bp

value: fibroblast

value: Neural Stem Cells

value: Male


title: fresh YCF, bio rep 1

description: Library name: A1


title: Psoriasis skin 1

description: Library name: PSO1


title: ASD,375,DIV 38,rep_1

description: HiSeq paired-end, 100 bp

value: Idiophatic  ASD


title: Slide4_Bif3_Replicate2

description: Illumina