title: Lung, day-25-p.i.+ glutamine, rep 3 [C1-9_infection_D25_+_glutamine]

description:
C1-9_infection_D25_+_glutamine
V1_25vsC1_25_STAR_DESeq2.csv
C1_25vsV1_25_STAR_DESeq2.csv

value: day-25-p.i.+ glutamine-3


title: HeLa, siCtrl_DMSO_20J_rep2

status: Public on Feb 10 2026

type: SRA

city: Miami

first: Carolina

middle: Paula

last: Banuelos

state: Florida

address: 1580 NW 10th Ave

department: Medicine

country: USA

institute: University of Miami

description: Library name: siCtrl_DMSO_20J_rep2

library_source: genomic

data_processing:
For strand-bias analysis, paired-end ChIPseq fastq files were aligned to the human genome hg19 using BWA-MEM v 0.7.17-r1188. The aligned files were converted to BAM files and sorted using Samtools v1.9. Duplicates reads were removed with Picard v3.00. Reads from each DNA strand (plus and minus) and split using Samtools. bamCoverage v3.3.1 using RPKM option was used to generate normalized ChIP-seq peak profiles for each sample. The resulting BigWig output files were visualized in the UCSC Genome Browser (https://genome.ucsc.edu). The Strand Specificity Index (SSI) was calculated based on the numbers of forward and reverse mapped reads, using the formula presented in Supplemental Figure 4E. Positive and negative SSI values indicate bidirectional gene orientation. Genes with fewer than 1 RPM were excluded from the analysis. The results were visualized with plotProfile from deepTools v 3.5.3. The lowest value among the profiles for each sample was used for graph normalization. In DRB-ChIP, samples were filtered with the IgG reads using bigwigCompare from deepTools v 3.5.3.
Assembly: hg19
Supplementary files format and content: Bigwig files with RPKM normalization with the reads of plus or minus DNA strand

molecule: genomic DNA

organism: Homo sapiens

source_name: HeLa

growth_protocol: DMEM (Gibco, #11965-092) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific, #10437-028), 1X GlutaMAX (Gibco, #35050-061), 1X MEM non-essential amino acids (Corning 25-025-Cl) and 1X Antibiotic Antimycotic solution (Corning, #30-004-Cl), 5% CO2, and 21% O2.

extract_protocol:
Cells were cross-linked with ChIP Cross-link Gold (Diagenode, #C01019027) following manufacturer instructions. After incubation at room temperature for 30 min, the cells were fixed with a 1% formaldehyde solution (Thermo Fisher Scientific, #28908) for 10 min at room temperature. To stop the fixation, 125 mM glycine was added and incubated for 5 min. The cells were then washed twice with PBS and harvested on ice using cell scrapers. The harvested cells were resuspended in ChIP lysis buffer supplemented with protease inhibitors (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.25% SDS) and sonicated on a Bioruptor Pico for 4 rounds of 10 cycles each at 4 °C with a short vortex between rounds to generate DNA fragments <500 bp. The sonicated cells were centrifuged, and the supernatants were transferred to new tubes and diluted with one volume of IP Dilution buffer (1% Triton X-100, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM Tris-HCl pH 8.0, proteases and phosphatases inhibitors). For the immunoprecipitation step, 1 mg of pre-cleared protein extracts were incubated with 10 g of antibodies, along with 1 g of Spike-in antibody (Active Motif, #61686) and 50 ng of Spike-in chromatin from Drosophila (Active Motif, #53083) overnight at 4 °C with gentle rotation. For the negative control, Normal Rabbit IgG (Cell Signaling, #2729S) was employed. The next day, 50 l of Protein A/G PLUS-Agarose beads (Santa Cruz, #sc-2003) were added to each IP reaction and incubated for 2 h at 4 °C with rotation. The beads were washed twice with IP Dilution buffer supplemented with 0.1% SDS (final), 3 times with ChIP wash buffer (IP Dilution buffer plus 0.5 M NaCl, 0.1% SDS, and 1% [w/v] Sodium Deoxycholate), and once with TE buffer (10mM Tris-HCl, 1mM EDTA) containing 50 mM NaCl. Elution of immunocomplexes from beads was performed with Elution Buffer (50 mM Tris-HCl, pH 8; 10 mM EDTA, 1% SDS) and incubation at 65 °C for 15 min. Then, the supernatants were reverse crosslinked at 65 °C for 3 h, treated sequentially with RNAse A (Sigma-Aldrich, #R5503) at 37 °C for 2 h, and then treated with Proteinase K (New England Biolabs, #P8107S) at 55 °C for 2 h. DNA purification was performed with the QIAquick PCR Purification Kit (Qiagen, #28106).
Purified DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs, #7370) following the manufacturer’s instructions.

tag: cell line

value: HeLa

tag: cell type

value: Human epithelial cell line derived from cervical cancer

tag: genotype

value: WT

tag: treatment

tag: chip antibody

value: RPB1 NTD (D8L4Y) Rabbit mAb (Cell Signaling, #14958)


title: HeLa, siCtrl_DMSO_20J_rep1

description: Library name: siCtrl_DMSO_20J_rep1


title: WO, HeLa WT, A485, Control, RPB1, ChIP, biol rep2

description:
ChIP sample
WO_S13_A485_Ctrl_rep2

data_processing:
Single (or paired-end) read ChIP-seq fastq files were processed using the ENCODE-DCC/chip-seq-pipeline2 pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) with default parameters and aligned to the hg19 genome. Peak calling was performed with MACS2 v2.2.4, and the peaks compared with each INPUT samples were used for subsequent analysis. DeepTools v3.3.1 was used to generate the ChIP-seq peak profiles for each sample. Bigwig output files were visualized in the UCSC genome browser (https://genome.ucsc.edu).
For strand-bias analysis, paired-end ChIPseq fastq files were aligned to the human genome hg19 using BWA-MEM v 0.7.17-r1188. The aligned files were converted to BAM files and sorted using Samtools v1.9. Duplicates reads were removed with Picard v3.00. Reads from each DNA strand (plus and minus) were split using Samtools. bamCoverage v3.3.1 using RPKM option was used to generate normalized ChIP-seq peak profiles for each sample.
For RNAPII mapping to CPD dimers, the same files utilized in the strand bias analysis were normalized to RPCG (1x genome coverage) using Deeptools v3.3.1. Dimer sites and flanking regions, extending 400 bases from both ends, were extracted from genes longer than 20 kb on chromosome 1 of the hg19 genome sequence in the positive strand of DNA. Read coverage for each sample were calculated using computeMatrix from Deeptools.
Assembly: hg19
Supplementary files format and content: bigWig (Except for INPUT samples)

growth_protocol: DMEM (Gibco, #11965-092) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific, #10437-028), GlutaMAX (Gibco, #35050-061) and antibiotics (Penicillin-Streptomycin, Gibco, #15140-122).

extract_protocol:
Cells were cross-linked with ChIP Cross-link Gold (Diagenode, #C01019027). After incubation at room temperature for 30 min, the cells were fixed with a 1% formaldehyde solution (Thermo Fisher Scientific, #28908) for 10 min at room temperature. To stop the fixation, glycine was added to a final concentration of 125 mM and incubated for 5 min. The cells were then washed twice with PBS and harvested on ice using cell scrapers. The harvested cells were resuspended in ChIP lysis buffer supplemented with protease inhibitors (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.25% SDS) and sonicated on a Bioruptor Pico for 4 rounds of 10 cycles each at 4 °C with a short vortex between rounds to generate DNA fragments <500 bp.
Purified DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs, #7370) following the manufacturer’s instructions.

value: human cervical cancer cell line (ATCC, #CCL-2)

value: A485- Control

value: Rabbit monoclonal anti-Rbp1 NTD [clone D8L4Y], Cell Signaling Technology, #14958


title: HeLa, siCtrl_DMSO_0J_rep1

description: Library name: siCtrl_DMSO_0J_rep1


title: HeLa, siCtrl_DMSO_0J_rep2

description: Library name: siCtrl_DMSO_0J_rep2


title: Lung, day-25-p.i.+ glutamine, rep 2 [C1-8_infection_D25_+_glutamine]

city: Newark

first: Ryan

last: Dikdan

state: NJ

address: 225 Warren St

department: Dept. of Medicine

institute: NJMS

description:
C1-8_infection_D25_+_glutamine
V1_25vsC1_25_STAR_DESeq2.csv
C1_25vsV1_25_STAR_DESeq2.csv

library_source: transcriptomic

data_processing:
The resultant fastq files from transcriptomic sequencing were initially analyzed with Fastqc
The fastq files were then processed using fastp to trim adapters and filter based on quality
The processed fastq files were then aligned with the GENCODE GRCm39 primary assembly mouse genome using the STAR aligner. The GENCODE M31 gene annotations were used for gene counts.
Custom scripts in R were used to load the resulting gene counts from STAR into R. Transcripts per million (TPM) were calculated using a custom script along with genecode files and the samples’ raw counts were analyzed using DESeq2 and fGSEA for Differential Gene Expression (DGE) analysis and Gene Set Enrichment Analysis, respectively.
Assembly: GENCODE GRCm39 primary assembly
Supplementary files format and content: TPM and gene counts for each sample and differential gene expression data generated by DESeq2 across certain conditions are provided in csv files (as indicated in the corresponding sample description field)

molecule: polyA RNA

organism: Mus musculus

source_name: lung

extract_protocol:
RNA was extracted from frozen lungs using RNAzol® RT Column Kit (Molecular research Center, Cincinnati, OH) following the manufacturer’s instruction
The library construction was performed using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA) and RNA sequencing by a NovaSeq S4 V1.5 (Illumina, California, USA).

treatment_protocol: Infected C57BL/6 mice were randomly assigned to two groups: (1) phosphate-buffered saline (PBS) or (2) glutamine supplementation. Glutamine was administered orally via gavage at a dosage of 500 mg/kg/day throughout the duration of the experiments. On days 12, 25, and 55 post-infection, both infected mice and uninfected control mice were sacrificed, and the lung tissues were collected and rapidly frozen in liquid nitrogen for subsequent RNA extraction and RNA-seq analysis.

tag: tissue

value: lung

value: day-25-p.i.+ glutamine-2


title: WO, HeLa WT, A485, 20j2h, RPB1, ChIP, biol rep1

description:
ChIP sample
WO_S11_A485_20j2h_rep1


title: WO, HeLa WT, A485, 20j1h, RPB1, ChIP, biol rep2

description:
ChIP sample
WO_S14_A485_20j1h_rep2


title: HeLa, siCtrl_A485_20J_rep2

description: Library name: siCtrl_A485_20J_rep2


title: HeLa, siCtrl_A485_0J_rep2

description: Library name: siCtrl_A485_0J_rep2


title: WO, HeLa WT, A485, 20j1h, RPB1, ChIP, biol rep1

description:
ChIP sample
WO_S10_A485_20j1h_rep1


title: HeLa, siCSB_DMSO_20J_rep2

description: Library name: siCSB_DMSO_20J_rep2


title: Lung, day-25-p.i., rep 3 [V1-8_infection_D25_+H2O]

description:
V1-8_infection_D25_+H2O
V1_55vsV1_25_STAR_DESeq2.csv
V1_25vsV1_55_STAR_DESeq2.csv
V1_25vsC1_25_STAR_DESeq2.csv
UvsV1_25_STAR_DESeq2.csv
C1_25vsV1_25_STAR_DESeq2.csv


title: HeLa, siCtrl_A485_0J_rep1

description: Library name: siCtrl_A485_0J_rep1


title: Lung, day-25-p.i., rep 2 [V1-7_infection_D25_+H2O]

description:
V1-7_infection_D25_+H2O
V1_55vsV1_25_STAR_DESeq2.csv
V1_25vsV1_55_STAR_DESeq2.csv
V1_25vsC1_25_STAR_DESeq2.csv
UvsV1_25_STAR_DESeq2.csv
C1_25vsV1_25_STAR_DESeq2.csv


title: Lung, day-25-p.i.+ glutamine, rep 1 [C1-6_infection_D25_+_glutamine]

description:
C1-6_infection_D25_+_glutamine
V1_25vsC1_25_STAR_DESeq2.csv
C1_25vsV1_25_STAR_DESeq2.csv

value: day-25-p.i.+ glutamine-1


title: HeLa, siCSB_DMSO_20J_rep1

description: Library name: siCSB_DMSO_20J_rep1


title: WO, HeLa WT, A485, Control, RPB1, ChIP, biol rep1

description:
ChIP sample
WO_S9_A485_Ctrl_rep1


title: HeLa, siCSB_DMSO_0J_rep2

description: Library name: siCSB_DMSO_0J_rep2


title: WO, HeLa WT, DMSO, 20j3h, RPB1, ChIP, biol rep2

description:
ChIP sample
WO_S8_DMSO_20j3h_rep2

value: DMSO- UV (20 J/m2) 3h


title: NHF1_NoUV_UVDE-HS-seq_rep2

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

description:
Library name: NHF1_NoUV_UVDE-HS-seq_rep2
Replicate 2

data_processing:
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A adapter barcodes, and the barcode sequences and the final base in the sequencing read were trimmed, using a custom perl script.
Fastq files were aligned to the human genome (hg19) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools. The resulting BAM files were uploaded as the raw sequencing data for each experiment.
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to dipyrimidine (dipy; i.e., TT, TC, CT, CC) for 6-4PP or thymine-adenine (TA) sequences were retained in BED files using custom perl script
BED files were converted to WIG file using COUNT function of IGVTools or custom perl scripts
Assembly: hg19
Supplementary files format and content: WIG files containing counts of 6-4PP damage reads filtered for only dipyrimidine mapping sequences (dipy files). TA files contain counts of damage reads associated with likely TA photoproducts (TA files)

source_name: NHF1 cells

growth_protocol: Telomerase-immortalized normal human fibroblast (NHF1) cells were grown in 10 cm plates to confluence in Dulbecco's  modified Eagle's medium (DMEM) containing 10% fetal bovine serum (FBS) at 37 C and 5% CO2.

extract_protocol:
NHF1 genomic DNA was isolated with GenElute Mammalian Genomic DNA Miniprep kits (G1N70, Sigma), following the manufacturer’s manual. Cells used for naked DNA samples were cultured and DNA isolated as previously described, excluding the UV exposure. Following genomic DNA isolation, samples were pipetted onto a microscope cover slip in 10µL aliquots, and exposed to 400J/m^2 UVC. Library preparation then continued as described, resuming at sonication.
UVDE-HS-seq procedure is adopted from the recently published emRiboSeq method (Nature Protocols 2015 10, 1433-1444) and our own UVDE-seq publication in yeast (Laughery et al, Cell Reports 2020,33, 108401). Briefly, sonicated DNA fragments were ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by  terminal transferase and dideoxy-GTP.  CPD lesions were repaired with CPD photolyase in the presence of uracil DNA glycosylase inhibitor (UGI), afterwhich 6-4PP and TA-PP lesions were cleaved with UVDE. DNA was then ligated to different barcoded A adaptors to generate libraries for different time points. DNA was purified with Streptavidin beads and amplified for ~8 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing.

treatment_protocol: Once confluent, media was removed and 2mL PBS was pipetted onto cells and cells were exposed to 500J/m^2 UVC light. Cells were then treated with trypsin to digest cell adhesions,neutralized with DMEM+10% FBS, and transferred to a 15mL conical tube and pelleted at 400xg for 4 minutes.

value: NHF1 cells

value: No UV

tag: repair time

value: 0 min


title: Lung, day-25-p.i., rep 1 [V1-6_infection_D25_+H2O]

description:
V1-6_infection_D25_+H2O
V1_55vsV1_25_STAR_DESeq2.csv
V1_25vsV1_55_STAR_DESeq2.csv
V1_25vsC1_25_STAR_DESeq2.csv
UvsV1_25_STAR_DESeq2.csv
C1_25vsV1_25_STAR_DESeq2.csv


title: NHF1_NoUV_UVDE-HS-seq_rep1

description:
Library name: NHF1_NoUV_UVDE-HS-seq_rep1
Replicate 1


title: WO, HeLa WT, A485, 20j3h, RPB1, ChIP, biol rep1

description:
ChIP sample
WO_S12_A485_20j3h_rep1


title: HeLa, siCSB_A485_20J_rep1

description: Library name: siCSB_A485_20J_rep1


title: HeLa, siCSB_A485_20J_rep2

description: Library name: siCSB_A485_20J_rep2


title: Lung, day12-p.i., rep 4 [V1-5_infection_D12_+H2O]

description:
V1-5_infection_D12_+H2O
UvsV1_12_STAR_DESeq2.csv


title: WO, HeLa WT, DMSO, 20j2h, RPB1, ChIP, biol rep2

description:
ChIP sample
WO_S7_DMSO_20j2h_rep2

value: DMSO- UV (20 J/m2) 2h


title: WO, HeLa WT, DMSO, 20j1h, RPB1, ChIP, biol rep2

description:
ChIP sample
WO_S6_DMSO_20j1h_rep2

value: DMSO- UV (20 J/m2) 1h


title: Lung, day-25-p.i., rep 4 [V1-9_infection_D25_+H2O]

description:
V1-9_infection_D25_+H2O
V1_55vsV1_25_STAR_DESeq2.csv
V1_25vsV1_55_STAR_DESeq2.csv
V1_25vsC1_25_STAR_DESeq2.csv
UvsV1_25_STAR_DESeq2.csv
C1_25vsV1_25_STAR_DESeq2.csv


title: HeLa, siCUL4A_A485_20J_rep2

description: Library name: siCUL4A_A485_20J_rep2


title: HeLa, siCSB_DMSO_0J_rep1

description: Library name: siCSB_DMSO_0J_rep1


title: Lung, day12-p.i., rep 3 [V1-4_infection_D12_+H2O]

description:
V1-4_infection_D12_+H2O
UvsV1_12_STAR_DESeq2.csv


title: HeLa, siCSB_A485_0J_rep2

description: Library name: siCSB_A485_0J_rep2


title: NHF1_naked_400JUVC_UVDE-HS-seq_rep2

description:
Library name: NHF1_naked_400JUVC_UVDE-HS-seq_rep2
Replicate 2

source_name: Genomic DNA derived from NHF1 cells

value: Genomic DNA derived from NHF1 cells

value: UV irradiated 400 J/m2


title: HeLa, siCSB_A485_0J_rep1

description: Library name: siCSB_A485_0J_rep1

value: HeLa

value: Human epithelial cell line derived from cervical cancer


title: WO, HeLa WT, DMSO, 20j3h, RPB1, ChIP, biol rep1

description:
ChIP sample
WO_S4_DMSO_20j3h_rep1

value: WT


title: Lung, day12-p.i., rep 1 [V1-2_infection_D12_+H2O]

description:
V1-2_infection_D12_+H2O
UvsV1_12_STAR_DESeq2.csv


title: HeLa, siCSA_DMSO_20J_rep2

description: Library name: siCSA_DMSO_20J_rep2

value: RPB1 NTD (D8L4Y) Rabbit mAb (Cell Signaling, #14958)


title: Lung, day12-p.i., rep 2 [V1-3_infection_D12_+H2O]

description:
V1-3_infection_D12_+H2O
UvsV1_12_STAR_DESeq2.csv


title: NHF1_naked_400JUVC_UVDE-HS-seq_rep1

description:
Library name: NHF1_naked_400JUVC_UVDE-HS-seq_rep1
Replicate 1


title: WO, HeLa WT, DMSO, Control, RPB1, ChIP, biol rep2

description:
ChIP sample
WO_S5_DMSO_Ctrl_rep2

value: human cervical cancer cell line (ATCC, #CCL-2)

value: DMSO- Control


title: WO, HeLa WT, DMSO, 20j1h, RPB1, ChIP, biol rep1

description:
ChIP sample
WO_S2_DMSO_20j1h_rep1

value: Rabbit monoclonal anti-Rbp1 NTD [clone D8L4Y], Cell Signaling Technology, #14958


title: NHF1_cell_500JUVC_UVDE-HS-seq_rep1

description:
Library name: NHF1_cell_500JUVC_UVDE-HS-seq_rep1
Replicate 1

value: UV irradiated 500 J/m2


title: NHF1_cell_500JUVC_UVDE-HS-seq_rep2

description:
Library name: NHF1_cell_500JUVC_UVDE-HS-seq_rep2
Replicate 2


title: Lung, noninfection, rep 4 [U4_noninfection_time_0]

description:
U4_noninfection_time_0
UvsV1_55_STAR_DESeq2.csv
UvsV1_25_STAR_DESeq2.csv
UvsV1_12_STAR_DESeq2.csv

value: lung


title: HeLa, siCSA_DMSO_0J_rep2

description: Library name: siCSA_DMSO_0J_rep2


title: WO, HeLa WT, DMSO, 20j2h, RPB1, ChIP, biol rep1

description:
ChIP sample
WO_S3_DMSO_20j2h_rep1


title: HeLa, siCSA_DMSO_20J_rep1

description: Library name: siCSA_DMSO_20J_rep1


title: Lung, noninfection, rep 3 [U3_noninfection_time_0]

description:
U3_noninfection_time_0
UvsV1_55_STAR_DESeq2.csv
UvsV1_25_STAR_DESeq2.csv
UvsV1_12_STAR_DESeq2.csv


title: 833K_T_2_GCAGAATT-ACCGGCCA_L00M_R1_001

city: Urbana

first: Mehwish

middle: Wahid

last: Khan

state: Illinois

address: 2001 S Lincoln Ave

department: Department of Comparative BioSciences

institute: University of Illinois Urbana-Champaign

description:
Library name: sample 29
Matched control sample GSM3720343

data_processing:
FASTQ files were aligned to human genome assembly NCBI GRCh38 using STAR aligner .
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Differentially expressed genes (>=|1.3|-fold and <=1% false discovery rate) were identified
Assembly: human genome assembly NCBI GRCh38
Supplementary files format and content: The excel work books includeTMM normalized log counts per million (log CPM) values for each Sample.

molecule: total RNA

source_name: testis

growth_protocol: Cells were treated with 0.5 µM Cisplatin for 6hrs. After 6 hours the media was left in fresh media and RNA was left for 24 hours.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
The libraries were sequenced on a HiSeq 4000 using HiSeq 4000 sequencing kit version 1. according to the manufacturer’s instructions.

value: testis

value: human testicular germ cell tumor cisplatin sensitive

value: Cisplatin


title: HeLa, siCSA_DMSO_0J_rep1

description: Library name: siCSA_DMSO_0J_rep1


title: WO, HeLa WT, DMSO, Control, RPB1, ChIP, biol rep1

description:
ChIP sample
WO_S1_DMSO_Crtl_rep1


title: Lung, noninfection, rep 1 [U1_noninfection_time_0]

description:
U1_noninfection_time_0
UvsV1_55_STAR_DESeq2.csv
UvsV1_25_STAR_DESeq2.csv
UvsV1_12_STAR_DESeq2.csv


title: 833K_T_1_AACGTTCC-GGAGTACT_L00M_R1_001

description:
Library name: sample 28
Matched control sample GSM3720342


title: HeLa, siCSA_A485_20J_rep2

description: Library name: siCSA_A485_20J_rep2


title: Lung, noninfection, rep 2 [U2_noninfection_time_0]

description:
U2_noninfection_time_0
UvsV1_55_STAR_DESeq2.csv
UvsV1_25_STAR_DESeq2.csv
UvsV1_12_STAR_DESeq2.csv


title: DRB, HeLa WT, IgG, ChIP, biol rep2

description:
ChIP sample
DRB_S14_IgG_rep2

value: P300 knockout

value: Control

value: Normal Rabbit IgG, Cell Signaling Technology, #2729


title: NPC cells, BIHi043-A, control, vehicle [0.1% DMSO] treated für 24 hours, replicate 3

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

country: Germany

institute: Charite

description:
Library name: XN001_DMSO_24C
Column_name in FPKM_joined.tab: FPKM_XN001_DMSO_24C

data_processing:
FASTQ files were aligned to the human genome (GeneCode GRCh38.p14_47) using STAR v2.7.11a with the following settings: --runThreadN 36 --outReadsUnmapped Fastx --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --seedSearchStartLmax 75 --outFilterMatchNmin 250 --alignSoftClipAtReferenceEnds No --outSAMattrIHstart 0 --alignEndsType EndToEnd --twopassMode Basic. The resulting *.bam file was sorted and indexed using samtools v1.17.
The sorted *.bam file was passed to StringTie v2.2.1 with the following settings: -u -p 36. The resulting *.gtf files were merged using stringtie merge and normalized read counts (TPM and FPKM) were generated using stringtie ballgown. The read counts of all experimental samples were then concatenated into a single table: output.tpm.csv and output.fpkm.csv.
Assembly: GeneCode GRCh38.p14_47
Supplementary files format and content: Stringtie ballgown output files: *.cov.refs.ballgown.gtf => contains details of the transcripts that StringTie assembles from RNA-Seq data in the GTF format; *.gene_abund.ballgown.tab => contains gene abundance counts as normalized FPKM and TPM values as a CSV table; *.out.ballgown.gtf => This is a file listing all the transcripts in the reference annotation that are fully covered, end to end, by reads. The output format is a GTF file as described above. Each line of the GTF is corresponds to a gene or transcript in the reference annotation.
Supplementary files format and content: FPKM_joined.tab, FPKM_joined.csv, TPM_joined.tab, TPM_joined.csv => fused tables with all the samples of the experiment in CSV and EXCEL format provided as TPM and FPK values.

source_name: NPC generated from iPSC

growth_protocol: Neuronal Progenitor Cells (NPCs) were generated from iPSCs from controls and of patients with MT-ATP6 mutations using a protocol described by Zink et al., 2021 (https://doii.org/10.21769/BioProtoc.3939). NPCs were then maintained on Geltrex- or Matrigel-coated 6-well plates at 37°C and 5% CO2 with media changes every other day according to the published protocol from Reinhardt et al., 2013 (https://doi.org/10.1371/journal.pone.0059252) and Zink et al., 2021. NPCs were maintained in 21 mM glucose-containing media consisting of the following components: 0.5x Neurobasal [Thermo Fisher Scientific, Waltham, MA, USA, Gibco #21103049], 0.5x DMEM/F12 [Thermo Fisher Scientific, Gibco #31330038], 0.5x N2 [Thermo Fisher Scientific, Gibco #17502-048], 0.5x B27 without vitamin A [Thermo Fisher Scientific, Gibco #12587010], 1x MycoZap Plus-CL [Lonza, Basel, Switzerland, #VZA-2012] with the addition of 0.5 µM PMA [Merck Millipore, Burlington, MA, USA, #483367], 3 µM CHIR 99021 [Cayman Chemical, Ann Arbor, MI, USA, #13122], and 150 µM ascorbic acid [Sigma-Aldrich, St. Louis, MO, USA, #A92902].

extract_protocol:
RNA was purified using the NucleoSpin RNA Plus kit (Macherey-Nagel, Düren, Germany, #740984) and eluted in 30 µL RNase-free H2O. The RNA concentration was measured using the NanoDrop 2000 photometer and aliquots of 1-2 µg RNA were snap-frozen in liquid nitrogen and stored at -80°C.
The construction of the eukaryotic strand-specific transcriptome library was performed according to the „DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing“ protocol of the  Beijing Genetics Institute (BGI). Briefly, 500 ng total RNA was enriched for polyA-carrying molecules using oligo-dT beads. The RNA was then fragmented and the first cDNA strand was synthesized using random primers. Second strand cDNA was synthesized using dUTP instead of dTTP and the synthesized cDNA was subjected to end repair and 3' adenylation. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments, which were then amplified by PCR. After quality control, the library was circularized and amplified to produce DNA nanoballs (DNBs).
The DNB library was then paired-end sequenced on the DNBSEQ-500 platform (DNBSEQ Technology, BGI, Beijing, China) with a read length of 150 bp. After removing of the sequencing adapters, the resulting FASTQ files were finally filtered for the desired length of 150 bp and for quality scores of Phred+33.

treatment_protocol: NPCs were seeded at a density of 500,000 cells/well in neural progenitor medium (sm+) on Geltrex-coated or Matrigel-coated 6-well plates and incubated at 37°C and 5% CO2 with medium change every other day. After reaching 70% confluence, the medium was supplemented with 0.1% DMSO (vehicle) or 10 µM Sildenafil (Selleckchem, Cologne, Germany, #S4684) dissolved in 0.1% DMSO and incubated at 37°C and 5% CO2 for 16 hours (in triplicates). At the end of the incubation period, the medium was aspirated and the cells were washed twice with Dulbecco's Phosphate-Buffered Saline (DPBS). Cells were then rapidly scraped in 1 mL DPBS. The cell suspension was collected in a 1.5 mL Eppendorf tube and centrifuged at 8,000 x g for 5 minutes at 4°C. The supernatant was aspirated and the cell pellet was flash-frozen in liquid nitrogen and stored at -80°C.

value: NPC generated from iPSC

value: Neuronal precursor cells (NPCs)

value: wildtype

value: Control 0.1% DMSO only

tag: biological replicate


title: HeLa, siCSA_A485_20J_rep1

description: Library name: siCSA_A485_20J_rep1

value: HeLa

value: Human epithelial cell line derived from cervical cancer

value: WT


title: DRB, HeLa WT, IgG, ChIP, biol rep1

description:
ChIP sample
DRB_S13_IgG_rep1

value: human cervical cancer cell line (ATCC, #CCL-2)


title: DRB, HeLa △P300, RPB1ser2, 40min, UV, ChIP, biol rep2

description:
ChIP sample
DRB_S12_P300ko_40min_20j_rep2

value: Rabbit polyclonal anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2), Abcam, #ab5095


title: 833K_T_3_ATGAGGCC-GTTAATTG_L00M_R1_001

description:
Library name: sample 30
Matched control sample GSM3720344


title: HeLa, siCtrl_A485_20J_rep1

description: Library name: siCtrl_A485_20J_rep1

value: RPB1 NTD (D8L4Y) Rabbit mAb (Cell Signaling, #14958)


title: NPC cells, BIHi043-A, control, vehicle [0.1% DMSO] treated für 24 hours, replicate 2

description:
Library name: XN001_DMSO_24B
Column_name in FPKM_joined.tab: FPKM_XN001_DMSO_24B


title: NPC cells, BIHi043-A, control, vehicle [0.1% DMSO] treated für 24 hours, replicate 1

description:
Library name: XN001_DMSO_24A
Column_name in FPKM_joined.tab: FPKM_XN001_DMSO_24A


title: HeLa, siCSA_A485_0J_rep1

description: Library name: siCSA_A485_0J_rep1


title: DRB, HeLa △P300, RPB1ser2, 40min, Control, ChIP, biol rep2

description:
ChIP sample
DRB_S10_P300ko_40min_Ctrl_rep2


title: 833K_B4_T_3_GATTCTGC-GACGAGAG_L00M_R1_001

description:
Library name: sample 27
Matched control sample GSM3720350

value: human testicular germ cell tumor cisplatin resistant


title: 833K_B4_T_2_AGCCTCAT-AGTAGAGA_L00M_R1_001

description:
Library name: sample 26
Matched control sample GSM3720349

value: testis


title: 833K_B4_T_1_CGTTAGAA-TTCAGGTC_L00M_R1_001

description:
Library name: sample 25
Matched control sample GSM3720348


title: 833K_A2_T_2_CCGTGAAG-CAGTGGAT_L00M_R1_001

description:
Library name: sample 23
Matched control sample GSM3720346


title: DRB, HeLa △P300, RPB1ser2, 40min, Control, ChIP, biol rep1

description:
ChIP sample
DRB_S9_P300ko_40min_Ctrl_rep1


title: NPC cells, BIHi043-A, control, 10 µM Sildenafil  in 0.1% DMSO für 24 hours, replicate 3

description:
Library name: XN001_10uM_SILDENAFIL_24C
Column_name in FPKM_joined.tab: FPKM_XN001_10uM_SILDENAFIL_24C

value: 10 µM Sildenafil in 0.1% DMSO


title: HeLa, IgG_rep2

description: Library name: IgG_rep2

value: siCtrl

value: Normal Rabbit IgG (Cell Signaling Technology, 2729)


title: 833K_A2_T_3_TTACAGGA-TGACAAGC_L00M_R1_001

description:
Library name: sample 24
Matched control sample GSM3720347

value: Cisplatin


title: NPC cells, BIHi043-A, control, 10 µM Sildenafil  in 0.1% DMSO für 24 hours, replicate 2

description:
Library name: XN001_10uM_SILDENAFIL_24B
Column_name in FPKM_joined.tab: FPKM_XN001_10uM_SILDENAFIL_24B


title: DRB, HeLa △P300, RPB1ser2, 0min, ChIP, biol rep2

description:
ChIP sample
DRB_S8_P300ko_0min_rep2

value: P300 knockout

value: Control


title: NPC cells, BIHi043-A, control, 10 µM Sildenafil in 0.1% DMSO für 24 hours, replicate 1

description:
Library name: XN001_10uM_SILDENAFIL_24A
Column_name in FPKM_joined.tab: FPKM_XN001_10uM_SILDENAFIL_24A

value: NPC generated from iPSC

value: Neuronal precursor cells (NPCs)


title: HeLa, IgG_rep1

description: Library name: IgG_rep1


title: NT2B3_T3_ATTCAGAA-GGCTCTGA_L00M_R1_001

description:
Library name: sample 21
Matched control sample GSM3720320


title: HeLa, siCSA_A485_0J_rep2

description: Library name: siCSA_A485_0J_rep2


title: HeLa, DMSO_20J_rep2

description: Library name: DMSO_20J_rep2


title: DRB, HeLa △P300, RPB1ser2, 40min, UV, ChIP, biol rep1

description:
ChIP sample
DRB_S11_P300ko_40min_20j_rep1


title: HeLa, DMSO_FT671_20J_rep2

description: Library name: DMSO_FT671_20J_rep2


title: 833K_A2_T_1_TCCAACGC-TTGGACTT_L00M_R1_001

description:
Library name: sample 22
Matched control sample GSM3720345


title: DRB, HeLa WT, RPB1ser2, 40min, Control, ChIP, biol rep2

description:
ChIP sample
DRB_S4_WT_40min_Ctrl_rep2


title: NPC cells, HHUUKDi009-A, control, 10 µM Sildenafil  in 0.1% DMSO für 24 hours, replicate 3

description:
Library name: TFJB_10uM_SILDENAFIL_24C
Column_name in FPKM_joined.tab: FPKM_TFJB_10uM_SILDENAFIL_24C

value: wildtype


title: DRB, HeLa WT, RPB1ser2, 40min, Control, ChIP, biol rep1

description:
ChIP sample
DRB_S3_WT_40min_Ctrl_rep1

value: HeLa


title: NT2B3_T2_ATTCAGAA-CCTATCCT_L00M_R1_001

description:
Library name: sample 20
Matched control sample GSM3720319


title: HeLa, DMSO_0J_rep1

description: Library name: DMSO_0J_rep1

value: Human epithelial cell line derived from cervical cancer

value: DMSO


title: DRB, HeLa WT, RPB1ser2, 0min, ChIP, biol rep2

description:
ChIP sample
DRB_S2_WT_0min_rep2

value: human cervical cancer cell line (ATCC, #CCL-2)

value: WT


title: NPC cells, HHUUKDi009-A, control, vehicle [0.1% DMSO] treated für 24 hours, replicate 3

description:
Library name: TFJB_DMSO_24C
Column_name in FPKM_joined.tab: FPKM_TFJB_DMSO_24C

value: Control 0.1% DMSO only


title: NT2A4_T1_TCCGGAGA-GTACTGAC_L00M_R1_001

description:
Library name: sample 16
Matched control sample GSM3720315

value: human testicular germ cell tumor cisplatin resistant


title: HeLa, DMSO_FT671_20J_rep1

description: Library name: DMSO_FT671_20J_rep1

value: RPB1 NTD (D8L4Y) Rabbit mAb (Cell Signaling, #14958)


title: DRB, HeLa △P300, RPB1ser2, 0min, ChIP, biol rep1

description:
ChIP sample
DRB_S7_P300ko_0min_rep1

value: Rabbit polyclonal anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2), Abcam, #ab5095


title: HeLa, A485_FT671_20J_rep2

description: Library name: A485_FT671_20J_rep2


title: DRB, HeLa WT, RPB1ser2, 0min, ChIP, biol rep1

description:
ChIP sample
DRB_S1_WT_0min_rep1


title: NT2A4_T3_CGCTCATT-ATAGAGGC_L00M_R1_001

description:
Library name: sample 18
Matched control sample GSM3720317

value: testis


title: HeLa, DMSO_0J_rep2

description: Library name: DMSO_0J_rep2


title: NPC cells, CRMi003-A, control, vehicle [0.1% DMSO] treated für 24 hours, replicate 3

description:
Library name: NCRM1_DMSO_24C
Column_name in FPKM_joined.tab: FPKM_NCRM1_DMSO_24C


title: DRB, HeLa WT, RPB1ser2, 40min, UV, ChIP, biol rep1

description:
ChIP sample
DRB_S5_WT_40min_20j_rep1


title: NPC cells, HHUUKDi009-A, control, vehicle [0.1% DMSO] treated für 24 hours, replicate 2

description:
Library name: TFJB_DMSO_24B
Column_name in FPKM_joined.tab: FPKM_TFJB_DMSO_24B


title: NT2B3_T1_ATTCAGAA-ATAGAGGC_L00M_R1_001

description:
Library name: sample 19
Matched control sample GSM3720318


title: NPC cells, HHUUKDi009-A, control, vehicle [0.1% DMSO] treated für 24 hours, replicate 1

description:
Library name: TFJB_DMSO_24A
Column_name in FPKM_joined.tab: FPKM_TFJB_DMSO_24A


title: NT21_21_1t_T2_CGCTCATT-CAGGACGT_L00M_R1_001

description:
Library name: sample 14
Matched control sample GSM3720310

value: human testicular germ cell tumor cisplatin sensitive


title: NT21_21_1t_T1_CGCTCATT-TAATCTTA_L00M_R1_001

description:
Library name: sample 13
Matched control sample GSM3720309

value: Cisplatin


title: DRB, HeLa WT, RPB1ser2, 40min, UV, ChIP, biol rep2

description:
ChIP sample
DRB_S6_WT_40min_20j_rep2


title: NPC cells, CRMi003-A, control, vehicle [0.1% DMSO] treated für 24 hours, replicate 1

description:
Library name: NCRM1_DMSO_24A
Column_name in FPKM_joined.tab: FPKM_NCRM1_DMSO_24A


title: NPC cells, HHUUKDi009-A, control, 10 µM Sildenafil  in 0.1% DMSO für 24 hours, replicate 2

description:
Library name: TFJB_10uM_SILDENAFIL_24B
Column_name in FPKM_joined.tab: FPKM_TFJB_10uM_SILDENAFIL_24B

value: 10 µM Sildenafil in 0.1% DMSO


title: NPC cells, HHUUKDi009-A, control, 10 µM Sildenafil in 0.1% DMSO für 24 hours, replicate 1

description:
Library name: TFJB_10uM_SILDENAFIL_24A
Column_name in FPKM_joined.tab: FPKM_TFJB_10uM_SILDENAFIL_24A


title: NT2A4_T2_CGCTCATT-TATAGCCT_L00M_R1_001

description:
Library name: sample 17
Matched control sample GSM3720316


title: HeLa, DMSO_20J_rep1

description: Library name: DMSO_20J_rep1


title: HeLa WT, RPB1ser2, ChIP, biol rep2

description:
ChIP sample
9_WT_RPB1ser2_rep2

value: Control


title: HeLa △P300, RPB1ser2, UV, ChIP, biol rep1

description:
ChIP sample
8_P300_KO_UV_RPB1ser2_rep1

value: P300 knockout


title: HeLa, A485_20J_rep2

description: Library name: A485_20J_rep2


title: HeLa △P300, RPB1ser2, UV, ChIP, biol rep2

description:
ChIP sample
12_P300_KO_UV_RPB1ser2_rep2


title: NPC cells, CRMi003-A, control, vehicle [0.1% DMSO] treated für 24 hours, replicate 2

description:
Library name: NCRM1_DMSO_24B
Column_name in FPKM_joined.tab: FPKM_NCRM1_DMSO_24B

value: NPC generated from iPSC

value: Neuronal precursor cells (NPCs)


title: HeLa, A485_FT671_20J_rep1

description: Library name: A485_FT671_20J_rep1

value: HeLa


title: HeLa △P300, RPB1ser2, ChIP, biol rep2

description:
ChIP sample
11_P300_KO_RPB1ser2_rep2


title: HeLa, A485_0J_rep1

description: Library name: A485_0J_rep1

value: Human epithelial cell line derived from cervical cancer


title: NT21_21_1t_T3_CGCTCATT-GTACTGAC_L00M_R1_001

description:
Library name: sample 15
Matched control sample GSM3720311


title: 2102EP_T_1_CGGACAAC-TCCGGATT_L00M_R1_001

description:
Library name: sample 10
Matched control sample GSM3720330


title: HeLa, A485_20J_rep1

description: Library name: A485_20J_rep1


title: NPC cells, CRMi003-A, control, 10 µM Sildenafil  in 0.1% DMSO für 24 hours, replicate 3

description:
Library name: NCRM1_10uM_SILDENAFIL_24C
Column_name in FPKM_joined.tab: FPKM_NCRM1_10uM_SILDENAFIL_24C

value: wildtype


title: HeLa WT, RPB1ser2, UV, ChIP, biol rep2

description:
ChIP sample
10_WT_UV_RPB1ser2_rep2

value: human cervical cancer cell line (ATCC, #CCL-2)


title: HeLa, siCtrl_WT_Pre_wash_rep2

description: Library name: siCtrl_WT_Pre_wash_rep2

value: WT

value: siCtrl


title: 2102EP_T_2_ATATGGAT-CTGTATTA_L00M_R1_001

description:
Library name: sample 11
Matched control sample GSM3720331


title: 2102EP_C1_T_2_GATCTATC-ATGAGGCT_L00M_R1_001

description:
Library name: sample 8
Matched control sample GSM3720340

value: human testicular germ cell tumor cisplatin resistant


title: HeLa WT, RPB1ser2, UV, ChIP, biol rep1

description:
ChIP sample
6_WT_UV_RPB1ser2_rep1


title: HeLa, siCtrl_WT_Pre_wash_rep1

description: Library name: siCtrl_WT_Pre_wash_rep1

value: RPB1 NTD (D8L4Y) Rabbit mAb (Cell Signaling, #14958)


title: NPC cells, CRMi003-A, control, 10 µM Sildenafil  in 0.1% DMSO für 24 hours, replicate 2

description:
Library name: NCRM1_10uM_SILDENAFIL_24B
Column_name in FPKM_joined.tab: FPKM_NCRM1_10uM_SILDENAFIL_24B


title: HeLa, siCtrl_WT_20J_40min_rep2

description: Library name: siCtrl_WT_20J_40min_rep2


title: NPC cells, CRMi003-A, control, 10 µM Sildenafil in 0.1% DMSO für 24 hours, replicate 1

description:
Library name: NCRM1_10uM_SILDENAFIL_24A
Column_name in FPKM_joined.tab: FPKM_NCRM1_10uM_SILDENAFIL_24A


title: HeLa, A485_0J_rep2

description: Library name: A485_0J_rep2


title: HeLa △P300, RPB1ser2, ChIP, biol rep1

description:
ChIP sample
7_P300_KO_RPB1ser2_rep1

value: Rabbit polyclonal anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2), Abcam, #ab5095


title: NPC cells, MDCi009-A, MILS patient, vehicle [0.1% DMSO] treated für 24 hours, replicate 3

description:
Library name: C11_DMSO_24C
Column_name in FPKM_joined.tab: FPKM_C11_DMSO_24C

value: m.8993T>G (heteroplasmy 96.2%)

value: Control 0.1% DMSO only


title: 2102EP_C1_T_1_CATAATAC-TTCTAACG_L00M_R1_001

description:
Library name: sample 7
Matched control sample GSM3720339

value: testis

value: Cisplatin


title: 2102EP_C1_T_3_AGCTCGCT-GCAGAATC_L00M_R1_001

description:
Library name: sample 9
Matched control sample GSM3720341


title: NPC cells, MDCi009-A, MILS patient, vehicle [0.1% DMSO] treated für 24 hours, replicate 1

description:
Library name: C11_DMSO_24A
Column_name in FPKM_joined.tab: FPKM_C11_DMSO_24A


title: NPC cells, MDCi009-A, MILS patient, vehicle [0.1% DMSO] treated für 24 hours, replicate 2

description:
Library name: C11_DMSO_24B
Column_name in FPKM_joined.tab: FPKM_C11_DMSO_24B


title: 2102EP_B3_T_2_CAACAATG-CTTCACGG_L00M_R1_001

description:
Library name: sample 5
Matched control sample GSM3720337


title: HeLa WT, RPB1ser2, ChIP, biol rep1

description:
ChIP sample
5_WT_RPB1ser2_rep1

value: Control


title: HeLa △P300, RPB1, UV, ChIP, biol rep2

description:
ChIP sample
4_P300_KO_UV_RPB1_rep2

value: P300 knockout

value: Rabbit monoclonal anti-Rbp1 NTD [clone D8L4Y], Cell Signaling Technology, #14958


title: HeLa △P300, RPB1, ChIP, biol rep2

description:
ChIP sample
3_P300_KO_RPB1_rep2


title: HeLa, siCtrl_WT_0J_40min_rep2

description: Library name: siCtrl_WT_0J_40min_rep2


title: HeLa, siCtrl_WT_20J_40min_rep1

description: Library name: siCtrl_WT_20J_40min_rep1


title: 2102EP_B3_T_3_TGGTGGCA-TCCTGTAA_L00M_R1_001

description:
Library name: sample 6
Matched control sample GSM3720338


title: NPC cells, MDCi009-A, MILS patient, 10 µM Sildenafil  in 0.1% DMSO für 24 hours, replicate 3

description:
Library name: C11_10uM_SILDENAFIL_24C
Column_name in FPKM_joined.tab: FPKM_C11_10uM_SILDENAFIL_24C

value: NPC generated from iPSC

value: Neuronal precursor cells (NPCs)

value: 10 µM Sildenafil in 0.1% DMSO


title: NPC cells, MDCi009-A, MILS patient, 10 µM Sildenafil in 0.1% DMSO für 24 hours, replicate 1

description:
Library name: C11_10uM_SILDENAFIL_24A
Column_name in FPKM_joined.tab: FPKM_C11_10uM_SILDENAFIL_24A


title: 2102EP_B3_T_1_GGTGAACC-GCGTTGGA_L00M_R1_001

description:
Library name: sample 4
Matched control sample GSM3720336


title: HeLa WT, RPB1, UV, ChIP, biol rep2

description:
ChIP sample
2_WT_UV_RPB1_rep2

value: HeLa


title: HeLa, siCtrl_WT_0J_40min_rep1

description: Library name: siCtrl_WT_0J_40min_rep1

value: Human epithelial cell line derived from cervical cancer


title: HeLa, siCtrl_p300KO_Pre_wash_rep2

description: Library name: siCtrl_p300KO_Pre_wash_rep2


title: NPC cells, MDCi008-A, MILS patient, vehicle [0.1% DMSO] treated für 24 hours, replicate 3

description:
Library name: B12_DMSO_24C
Column_name in FPKM_joined.tab: FPKM_B12_DMSO_24C

value: m.8993T>C (heteroplasmy 97.9%)


title: 2102EP_T_3_GCGCAAGC-TCACGCCG_L00M_R1_001

description:
Library name: sample 12
Matched control sample GSM3720332

value: human testicular germ cell tumor cisplatin sensitive


title: 2102EP_A1_T_2_GTTCCAAT-AATTCTGC_L00M_R1_001

description:
Library name: sample 2
Matched control sample GSM3720334

value: human testicular germ cell tumor cisplatin resistant


title: HeLa, siCtrl_p300KO_Prewash_rep1

description: Library name: siCtrl_p300KO_Prewash_rep1

value: siCtrl

value: RPB1 NTD (D8L4Y) Rabbit mAb (Cell Signaling, #14958)


title: HeLa, siCtrl_p300KO_20J_40min_rep2

description: Library name: siCtrl_p300KO_20J_40min_rep2


title: 2102EP_A1_T_3_ACCTTGGC-GGCCTCAT_L00M_R1_001

description:
Library name: sample 3
Matched control sample GSM3720335


title: NPC cells, MDCi009-A, MILS patient, 10 µM Sildenafil  in 0.1% DMSO für 24 hours, replicate 2

description:
Library name: C11_10uM_SILDENAFIL_24B
Column_name in FPKM_joined.tab: FPKM_C11_10uM_SILDENAFIL_24B

value: m.8993T>G (heteroplasmy 96.2%)


title: HeLa △P300, RPB1, UV, ChIP, biol rep1

description:
ChIP sample
6_P300_KO_UV_RPB1_rep1

value: human cervical cancer cell line (ATCC, #CCL-2)


title: NPC cells, MDCi008-A, MILS patient, vehicle [0.1% DMSO] treated für 24 hours, replicate 2

description:
Library name: B12_DMSO_24B
Column_name in FPKM_joined.tab: FPKM_B12_DMSO_24B

value: Control 0.1% DMSO only


title: 2102EP_A1_T_1_GCAATGCA-GGAACGTT_L00M_R1_001

description:
Library name: sample 1
Matched control sample GSM3720333

value: testis

value: Cisplatin


title: HeLa WT, RPB1, ChIP, biol rep2

description:
ChIP sample
1_WT_RPB1_rep2

value: WT

value: Control


title: HeLa △P300, RPB1, ChIP, biol rep1

description:
ChIP sample
5_P300_KO_RPB1_rep1

value: P300 knockout

value: Rabbit monoclonal anti-Rbp1 NTD [clone D8L4Y], Cell Signaling Technology, #14958


title: NPC cells, MDCi008-A, MILS patient, vehicle [0.1% DMSO] treated für 24 hours, replicate 1

description:
Library name: B12_DMSO_24A
Column_name in FPKM_joined.tab: FPKM_B12_DMSO_24A

value: NPC generated from iPSC

value: Neuronal precursor cells (NPCs)


title: 3xFLAG ADR-1 iCLIP Rep 3 (iCLIP)

city: Bloomington

first: Boyoon

last: Yang

address: 1001 E 3rd St

institute: Indiana University

description: Library name: ADR-1 CLIP Rep 3

data_processing:
Fastq raw sequencing files were assessed for quality and filtered to remove adapters by fastp (v0.21.0). Barcodes were subsequently removed and reads deduplicated. Paired reads were merged with Ngmerge (v0.03). Processed reads were mapped to the ce11 C. elegans genome using STAR (v2.7.10b). Only reads that mapped uniquely (NH=1) were kept for further analysis.  The STAR results were then introduced into the CLIPPER software pipeline, which can handle two replicates at a time along with their paired input controls. As three replicates were available in this study, CLIPPER was run on every permutation of the replicate pairs (replicate 1 vs replicate 2, replicate 2 vs replicate 3, and replicate 3 vs replicate 1), and the non-reproducible read clusters were removed using an irreproducible discovery rate (IDR) approach. Then, the chromosomal coordinates of the shared reproducible read clusters between two replicates were unified for all possible pair-wise comparisons and then input into CLIPPER to determine the significance of the read clusters in each biological replicate based on the enrichment of the CLIP reads compared to the input reads. Enriched read clusters were annotated to their gene features using the C. elegans genome annotation WS275. Read clusters annotated to two or more overlapping genes were removed.
Assembly: WBcel235
Supplementary files format and content: dataset_ADR-1 CLIP_Rep 1-3.csv

organism: Caenorhabditis elegans

source_name: Whole organism

growth_protocol: Unsynchronized mixed stage populations of 3xFLAG ADR-1 worms were grown on nematode growth media (NGM) plates seeded with Escherichia coli OP50 at 20°C.

extract_protocol:
To obtain cell lysates, frozen worms were ground with a mortar and pestle on dry ice. The lysates (5 mg) were treated with 150 U of RNase I (Ambion) at 37 ̊C for 10 minutes with constant shaking at 1200 rpm prior to immunoprecipitation. Upon RNase I digestion, 2% of the 5 mg worm lysate was taken as inputs and the rest of the lysate was incubated with 100 µl of anti-FLAG magnetic beads (Sigma) with a final concentration of 1:5 dilution of wash buffer (20 mM Tris-HCl (pH 7.5), 10 mM MgCl2, 5 mM NaCl, 0.2% Tween-20) for 1 hour. Then, IP samples were washed once with high-salt wash buffer (50 mM Tris-HCl (pH 7.5), 1 M NaCl, 1 mM EDTA, 0.1% SDS, 1% NP-40) and washed twice with wash buffer. T4 PNK Minus reaction was performed on bead using T4 PNK Minus (NEB) at 37 ̊C for 20 minutes with constant shaking at 1200 rpm, followed by 1x wash with high-salt wash buffer and 3x wash with wash buffer. dsRNA ligation reaction was performed with T4 RNA Ligase (high-concentration, NEB) at RT for 2 hours, and IP samples were washed 3x with high-salt wash buffer and 3x with wash buffer. Then, IP samples were subjected to Fast AP (Thermo Scientific) reaction at 37 ̊C for 10 minutes with constant shaking at 1200 rpm and PNK reaction with T4 PNK (NEB) at 37 ̊C for 20 minutes with constant shaking at 1200 rpm without removing the FastAP reaction mixture. Then, IP samples were washed 1x with high-salt wash buffer and 3x with wash buffer. 3’ RNA adapter (CLASHInvRiL19) was ligated on bead using T4 RNA ligase (high-concentration, NEB) at RT for 75 minutes on a rotator. IP samples were washed 1x with wash buffer, 1x with high-salt wash buffer, and 2x with wash buffer. All input and IP samples were denatured using 4xNuPAGE™ sample buffer (Invitrogen) at 65°C for 10 minutes and resolved in NuPAGE™ 4-12% Bis-Tris gel (Invitrogen) at 150 V for 75 minutes, followed by transfer to nitrocellulose membrane at 30 V for overnight. After confirming the position of ADR-1 proteins by western blot using FLAG antibody (Sigma), regions above the ADR-1 proteins (up to ~250 kDa) were excised for proteinase K (NEB) treatment at 37°C for 40 minutes with constant shaking at 1200 rpm. Then, RNA was isolated from proteinase K treatment reaction using Zymo RNA clean & concentrator kit (Zymo Research). Upon RNA isolation, input samples were also treated with FastAP (Thermo Scientific) for 10 minutes and T4 PNK (NEB) for 20 minutes, both at 37°C with constant shaking at 1200 rpm, followed by clean up using Zymo RNA clean & concentrator kit (Zymo Research).
3’ RNA adapter (CLASHInvRiL19, listed in Table S1) was ligated to input samples after incubation at 65 ̊C for 2 minutes using T4 RNA ligase (high-concentration, NEB) at RT for 60 minutes with flicking every 15 minutes. Input samples were cleaned up using MyONE Silane beads (Invitrogen). Reverse transcription was performed for both IP and input samples after incubation at 65 ̊C for 2 minutes using an RT primer (InvAR17) and then at 55 ̊C for 20 minutes using Superscript IV (Invitrogen). The reaction was cleaned up using ExoSAP-IT (Applied Biosystems) and MyONE Silane beads (Invitrogen). Then, 5’ DNA adapter (Invrand10_3Tr3) was ligated after incubation at 70 ̊C for 2 minutes and then at RT for overnight using T4 RNA ligase (high-concentration, NEB) and 5’ deadenylase (NEB). Samples were cleaned up using MyONE Silane beads (Invitrogen) and PCR amplified for 8 cycles (Input) and 14-18 cycles (IP) using Q5 High-Fidelity PCR master mix (NEB) and PCR forward and reverse primers with barcodes. Libraries were purified using Ampure XP beads (Beckman Coulter) and quantified using the D1000 high sensitivity screen tape system (Agilent, La Jolla, CA) before pooling. Pooled library was sequenced on NextSeq2000 (Illumina, San Diego, CA) at center of bioinformatics and genomics (CGB) at Indiana University, Bloomington using paired-end sequencing (2X101 bp).

treatment_protocol: Mixed stage animals grown on the NGM plates were washed three times with 1x M9 buffer (22.0 mM KH2PO4, 42.3 mM Na2HPO4, 85.6 mM NaCl, 1 mM MgSO4) and resuspended in 50 ml of 1x M9 buffer and rocked on a rotator for 20 min to remove gut bacteria. The animals were spread on unseeded NGM plates and UV-crosslinked using the Spectrolinker XL-1000 (Spectronics, New Cassel, NY) with energy setting at 3 J/cm2. Then, animals were resuspended in 1 ml of extract buffer (50 mM HEPES (pH 7.4), 70 mM K-Acetate, 5 mM Mg-Acetate, 0.05% NP-40, and 10% glycerol, one cOmplete™ Protease inhibitor tablet (Roche)) and stored at -80 ̊C as frozen pellets.

value: Whole organism


title: HeLa △P300, IgG, ChIP, biol rep1

description:
ChIP sample
4_P300_KO_IgG_rep1

value: HeLa

value: Normal Rabbit IgG, Cell Signaling Technology, #2729


title: HeLa, siCtrl_p300KO_20J_40min_rep1

description: Library name: siCtrl_p300KO_20J_40min_rep1

value: Human epithelial cell line derived from cervical cancer


title: NPC cells, MDCi008-A, MILS patient, 10 µM Sildenafil  in 0.1% DMSO für 24 hours, replicate 3

description:
Library name: B12_10uM_SILDENAFIL_24C
Column_name in FPKM_joined.tab: FPKM_B12_10uM_SILDENAFIL_24C

value: m.8993T>C (heteroplasmy 97.9%)

value: 10 µM Sildenafil in 0.1% DMSO


title: HeLa WT, RPB1, UV, ChIP, biol rep1

description:
ChIP sample
3_WT_UV_RPB1_rep1


title: NPC cells, MDCi008-A, MILS patient, 10 µM Sildenafil  in 0.1% DMSO für 24 hours, replicate 2

description:
Library name: B12_10uM_SILDENAFIL_24B
Column_name in FPKM_joined.tab: FPKM_B12_10uM_SILDENAFIL_24B


title: HeLa, siCtrl_p300KO_0J_40min_rep2

description: Library name: siCtrl_p300KO_0J_40min_rep2

value: siCtrl

value: RPB1 NTD (D8L4Y) Rabbit mAb (Cell Signaling, #14958)


title: HeLa, siCtrl_p300KO_0J_40min_rep1

description: Library name: siCtrl_p300KO_0J_40min_rep1


title: 3xFLAG ADR-1 iCLIP Rep 2 (iCLIP)

description: Library name: ADR-1 CLIP Rep 2


title: 3xFLAG ADR-1 iCLIP Rep 1 (iCLIP)

description: Library name: ADR-1 CLIP Rep 1


title: 3xFLAG ADR-1 iCLIP Rep 3 (Input)

description: Library name: ADR-1 Input Rep 3


title: HeLa, siCtrl_IgG_rep2

description: Library name: siCtrl_IgG_rep2

value: Normal Rabbit IgG (Cell Signaling Technology, 2729)


title: HeLa WT, IgG, ChIP, biol rep1

description:
ChIP sample
1_WT_IgG_rep1

value: human cervical cancer cell line (ATCC, #CCL-2)


title: HeLa, siCtrl_IgG_rep1

description: Library name: siCtrl_IgG_rep1


title: Wild-type zebrafish embryos 24hpf (100) Sample 3

city: London

first: Matthew

middle: Paul

last: Bostock

address: New Hunt's House, Guy's Campus

department: CDN

country: United Kingdom

institute: King's College London

description: Library name: C3

data_processing:
Raw sequencing reads were aligned to GRCz11 using HISAT2 (v2.2.1) with default parameters.
Transcriptom Assembly was perfomed using StringTie (v3.0.0) and sample specific assemblies were generated.
Cryptic Last exons were identifed as unannotated alternative last exons.
Whippet was used to quantify splicing differences across samples.
Assembly: danrer10
Supplementary files format and content: TpMs and psi values are reported for each CLE in xlsx format for each sample

organism: Danio rerio

source_name: Whole Embryo

growth_protocol: Zebrafish embryos were raised at 28.5oC in system fish water.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). Samples A-B were raised to 24hpf, 48hpf, and 72hpf and 100ng of each timepoint was pooled after mRNA extraction. Samples A-C total RNA was sent to Novagene for QC and library preparation.
RNA integrity was checked using Agilent 5400 -  all samples were above RIN 8.0.

treatment_protocol: Samples A-B were injected with 200pg TRAP mRNA at the first cell stage and whole embryos were used for total RNA extraction. Samples C were 24hpf untreated whole embryos.

value: Whole Embryo

tag: batch


title: NPC cells, MDCi008-A, MILS patient, 10 µM Sildenafil in 0.1% DMSO für 24 hours, replicate 1

description:
Library name: B12_10uM_SILDENAFIL_24A
Column_name in FPKM_joined.tab: FPKM_B12_10uM_SILDENAFIL_24A


title: NPC cells, HHUi002-A, MILS patient, vehicle [0.1% DMSO] treated für 24 hours, replicate 3

description:
Library name: A3_DMSO_24C
Column_name in FPKM_joined.tab: FPKM_A3_DMSO_24C

value: Control 0.1% DMSO only


title: HeLa WT, RPB1, ChIP, biol rep1

description:
ChIP sample
2_WT_RPB1_rep1

value: WT

value: Control


title: NPC cells, HHUi002-A, MILS patient, vehicle [0.1% DMSO] treated für 24 hours, replicate 2

description:
Library name: A3_DMSO_24B
Column_name in FPKM_joined.tab: FPKM_A3_DMSO_24B


title: 3xFLAG ADR-1 iCLIP Rep 2 (Input)

description: Library name: ADR-1 Input Rep 2


title: Wild-type zebrafish embryos 24hpf (100) Sample 1

description: Library name: C1


title: NPC cells, HHUi002-A, MILS patient, vehicle [0.1% DMSO] treated für 24 hours, replicate 1

description:
Library name: A3_DMSO_24A
Column_name in FPKM_joined.tab: FPKM_A3_DMSO_24A


title: HeLa, siCSB_WT_Pre_wash_rep2

description: Library name: siCSB_WT_Pre_wash_rep2

value: siCSB


title: HeLa, siCSB_WT_Pre_wash_rep1

description: Library name: siCSB_WT_Pre_wash_rep1


title: HeLa, siCSB_WT_20J_40min_rep2

description: Library name: siCSB_WT_20J_40min_rep2


title: Wild-type zebrafish embryos 24hpf (100) Sample 2

description: Library name: C2


title: Coculture_St_T3_C

city: Seattle

first: David

last: Wiener

state: Washington

department: School of Oceanography

institute: University of Washington

description:
Library name: Coculture_St_T3_C
Column name in AMsummary & TPsummary.csv:  Coculture_St_T3_C

data_processing:
Sequence reads were trimmed using Trimmomatic 0.39, run in paired-end mode with the adaptor and other Illumina-specific sequences (ILLUMINACLIP) set to TruSeq3-PE.fa:2:30:10:1, leading and trailing quality thresholds of 25, a sliding window trimming approach (SLIDINGWINDOW) of 4:15, an average quality level (AVGQUAL) of 20, and a minimum length (MINLEN) of 60.
Paired-end reads were aligned with STAR v2.7.10b to the T. pseudonana genome (Thaps3, FilteredModels2) plus an additional “chromosome” containing an updated version of the ribosomal sequences or to a combined T. pseudonana -A. macleodii Te101.  Default parameters were used, with the maximum intron length limited to 500 nucleotides (‘–alignIntronMax 500’).
Reads per chromosome were calculated using the samtools idxstats command
Assigned to gene models using featureCounts
Assembly: T. pseudonana genome (Thaps3, FilteredModels2) & A. macleodii Te101 genome
Supplementary files format and content: AMsummary.csv and TPsummary.csv contain gene counts per gene model for each organism (A. macleodii and T. pseudonana).
Supplementary files format and content: ReadsPerChr.csv contains the number of reads aligned per chromosome for each treatment (Total RNA, PolyA selection, and Ribodepletion).

organism:
Alteromonas macleodii
Thalassiosira pseudonana

growth_protocol: T. pseudonana CCMP 1335 strain was maintained as a semicontinuous batch culture in 30ml L1+Si medium (NCMA) at 20°C with a 16:8h light cycle, under ~160µmol photons m−2 s−1. Before the experiments, diatom cells were acclimated to exponential growth after a minimum of three 1:10 dilutions and diluted in L1+Si medium to reach the designated growth phases before coculture. Growth was monitored by relative fluorescence units (RFU) using a fluorometer. In the exponential phase, cultures doubled in cell number approximately over 24 Hrs. Stationary phase cultures were defined as those sampled 7 days after the last doubling event when the culture reached ~800,000 cells/ml. Mid-exponential/Exponential cultures were defined as having undergone two doubling events before reaching stationary (~200,000 cells/ml). Early exponential phase cultures were defined as five doubling events before reaching stationary (~25,000 cells/ml).

extract_protocol:
Total RNA was extracted from 0.2 µm polycarbonate membrane filters using the Zymo Direct-zol RNA MiniPrep Plus kit for all samples.
For T. pseudonana transcriptome ribodepletion calibration, three samples obtained from exponentially growing cells were prepared: Total RNA, poly(A) selected with oligo dT-beads (Dynabeads mRNA DIRECT Kit, Life Technologies), and ribodepleted using a tailored Thalassiosira pseudonana riboPOOL following the manufacturer’s instructions. For Duo-RNA-seq, samples were prepared in triplicate for each time point and ribodepleted using the T.pseudonana riboPOOL combined with the Pan-Bacteria riboPOOL, with beads mixed in a 1:1 ratio. At this point, libraries were submitted for preparation, and sequencing to the Northwest Genomics Center (University of Washington) using a NextSeq (Illumina) platform.

treatment_protocol: For the coculture experiments, glycerol stocks of A. macleodii EP were streaked on marine agar plates (marine broth (MB) with 1.5% w/v agar) and grown at 25°C for 48 hours. Single colonies were grown overnight in Marine Broth with shaking at 25°C until an OD600 of ~0.5 was reached, measured using a NanoDrop One Microvolume UV-Vis Spectrophotometer. Cultures were then diluted 1:10 and allowed to double twice (~3:30 hours) before removing the media and washing twice with L1+Si. Finally, A. macleodii cells were added to the diatom culture to a ~40000 cells/ml concentration. All experiments were performed in L1+Si medium.

tag: time

value: Coculture (Alteromonas macleodii)


title: Coculture_St_T3_B

description:
Library name: Coculture_St_T3_B
Column name in AMsummary & TPsummary.csv:  Coculture_St_T3_B


title: 3xFLAG ADR-1 iCLIP Rep 1 (Input)

description: Library name: ADR-1 Input Rep 1


title: TRAP mRNA injected zebrafish embryos pooled 24hpf, 48hpf, and 72hpf - TRAP-pull-down_3

description: Library name: B3


title: NPC cells, HHUi002-A, MILS patient, 10 µM Sildenafil  in 0.1% DMSO für 24 hours, replicate 2

description:
Library name: A3_10uM_SILDENAFIL_24B
Column_name in FPKM_joined.tab: FPKM_A3_10uM_SILDENAFIL_24B

value: NPC generated from iPSC

value: Neuronal precursor cells (NPCs)


title: HeLa, siCSB_WT_20J_40min_rep1

description: Library name: siCSB_WT_20J_40min_rep1

value: HeLa


title: NPC cells, HHUi002-A, MILS patient, 10 µM Sildenafil in 0.1% DMSO für 24 hours, replicate 1

description:
Library name: A3_10uM_SILDENAFIL_24A
Column_name in FPKM_joined.tab: FPKM_A3_10uM_SILDENAFIL_24A


title: TRAP mRNA injected zebrafish embryos pooled 24hpf, 48hpf, and 72hpf - TRAP-pull-down_2

description: Library name: B2


title: NPC cells, HHUi002-A, MILS patient, 10 µM Sildenafil  in 0.1% DMSO für 24 hours, replicate 3

description:
Library name: A3_10uM_SILDENAFIL_24C
Column_name in FPKM_joined.tab: FPKM_A3_10uM_SILDENAFIL_24C


title: NPC cells, BIHi269-B, control, vehicle [0.1% DMSO] treated für 24 hours, replicate 3

description:
Library name: 269B_DMSO_24C
Column_name in FPKM_joined.tab: FPKM_269B_DMSO_24C

value: wildtype


title: Coculture_St_T2_B

description:
Library name: Coculture_St_T2_B
Column name in AMsummary & TPsummary.csv:  Coculture_St_T2_B


title: HeLa, siCSB_WT_0J_40min_rep1

description: Library name: siCSB_WT_0J_40min_rep1

value: Human epithelial cell line derived from cervical cancer


title: HeLa, siCSB_WT_0J_40min_rep2

description: Library name: siCSB_WT_0J_40min_rep2


title: TRAP mRNA injected zebrafish embryos pooled 24hpf, 48hpf, and 72hpf - TRAP-pull-down_1

description: Library name: B1


title: Coculture_St_T2_A

description:
Library name: Coculture_St_T2_A
Column name in AMsummary & TPsummary.csv:  Coculture_St_T2_A


title: Coculture_St_T2_C

description:
Library name: Coculture_St_T2_C
Column name in AMsummary & TPsummary.csv:  Coculture_St_T2_C


title: NPC cells, BIHi269-B, control, vehicle [0.1% DMSO] treated für 24 hours, replicate 2

description:
Library name: 269B_DMSO_24B
Column_name in FPKM_joined.tab: FPKM_269B_DMSO_24B


title: HeLa, siCSB_p300KO_Pre_wash_rep2

description: Library name: siCSB_p300KO_Pre_wash_rep2


title: TRAP mRNA injected zebrafish embryos pooled 24hpf, 48hpf, and 72hpf - Flow-through_3

description: Library name: A3


title: Coculture_St_T1_C

description:
Library name: Coculture_St_T1_C
Column name in AMsummary & TPsummary.csv:  Coculture_St_T1_C


title: TRAP mRNA injected zebrafish embryos pooled 24hpf, 48hpf, and 72hpf - Flow-through_2

description: Library name: A2


title: NPC cells, BIHi269-B, control, vehicle [0.1% DMSO] treated für 24 hours, replicate 1

description:
Library name: 269B_DMSO_24A
Column_name in FPKM_joined.tab: FPKM_269B_DMSO_24A


title: HeLa, siCSB_p300KO_Pre_wash_rep1

description: Library name: siCSB_p300KO_Pre_wash_rep1


title: Coculture_St_T1_B

description:
Library name: Coculture_St_T1_B
Column name in AMsummary & TPsummary.csv:  Coculture_St_T1_B


title: NPC cells, BIHi269-B, control, 10 µM Sildenafil  in 0.1% DMSO für 24 hours, replicate 3

description:
Library name: 269B_10uM_SILDENAFIL_24C
Column_name in FPKM_joined.tab: FPKM_269B_10uM_SILDENAFIL_24C


title: HeLa, siCSB_p300KO_20J_40min_rep2

description: Library name: siCSB_p300KO_20J_40min_rep2


title: TotalRNA

description:
Library name: TotalRNA
Column name in ReadsPerChr.csv:  TotalRNA

organism: Thalassiosira pseudonana

value: Total RNA


title: TRAP mRNA injected zebrafish embryos pooled 24hpf, 48hpf, and 72hpf - Flow-through_1

description: Library name: A1


title: Coculture_St_T1_A

description:
Library name: Coculture_St_T1_A
Column name in AMsummary & TPsummary.csv:  Coculture_St_T1_A


title: PolyA

description:
Library name: PolyA
Column name in ReadsPerChr.csv:  PolyASelected

value: Poly(A) selection


title: HeLa, siCSB_p300KO_0J_40min_rep2

description: Library name: siCSB_p300KO_0J_40min_rep2


title: Coculture_Exp_T3_B

description:
Library name: Coculture_Exp_T3_B
Column name in AMsummary & TPsummary.csv:  Coculture_Exp_T3_B


title: HeLa, siCSB_p300KO_0J_40min_rep1

description: Library name: siCSB_p300KO_0J_40min_rep1


title: Coculture_Exp_T3_C

description:
Library name: Coculture_Exp_T3_C
Column name in AMsummary & TPsummary.csv:  Coculture_Exp_T3_C


title: Coculture_Exp_T2_C

description:
Library name: Coculture_Exp_T2_C
Column name in AMsummary & TPsummary.csv:  Coculture_Exp_T2_C


title: HeLa, siCSB_p300KO_20J_40min_rep1

description: Library name: siCSB_p300KO_20J_40min_rep1


title: RiboD

description:
Library name: RiboD
Column name in ReadsPerChr.csv:  RiboDepleted

value: Ribodepletion


title: NPC cells, BIHi269-B, control, 10 µM Sildenafil  in 0.1% DMSO für 24 hours, replicate 2

description:
Library name: 269B_10uM_SILDENAFIL_24B
Column_name in FPKM_joined.tab: FPKM_269B_10uM_SILDENAFIL_24B

value: 10 µM Sildenafil in 0.1% DMSO


title: HeLa, siCSB_IgG_rep2

description: Library name: siCSB_IgG_rep2

value: Normal Rabbit IgG (Cell Signaling Technology, 2729)


title: Coculture_Exp_T2_B

description:
Library name: Coculture_Exp_T2_B
Column name in AMsummary & TPsummary.csv:  Coculture_Exp_T2_B


first: Leif

last: Ludwig

address: Hannoversche Str. 28

institute: Berlin Institute for Medical Systems Biology

description:
Library name: HEK293 POLG-D274A knock-in cell Galactose vs Glucose, HTO, channel 2
Tn5-derived chromatin accessibity profile, HTO library: Reads1 contains UMI, Reads2 contains cell barcode, Read3 file contains Hashtag antibodies derived Tag reads

library_source: other

data_processing:
Raw fastq files/sequencing reads were aligned to the mtDNA blacklist modified hg38 reference genome using CellRanger-ATAC count (v2.1.0) to generate possorted_bam.bam, fragments.tsv.gz and filtered_peak_bc_matrix.h5
The cell hashtag tag abundances were quantified using ASAP_to_kite.py (https://github.com/caleblareau/asap_to_kite), followed by the kallisto, bustools, and kite pipeline.
Assembly: hg38
Supplementary files format and content: CellRanger output files: singlecell.csv, fragments.tsv.gz, fragments.tsv.gz.tbi and filtered_peak_bc_matrix.h5
Supplementary files format and content: kb-kite output files: featurecounts.barcodes.txt, featurecounts.genes.txt, and featurecounts.mtx
Library strategy: CITE-seq

molecule: protein

growth_protocol: Control and KI36 HEK293 cell lines were cultured in basal medium Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% [v/v] FBS Standard, 50 µg/L Uridine, and 1 U/ml Pen-Strep. KIA2 HEK293 cell lines were supplemented additionally with 50 µg/ml Hygromycin B, and 15 µg/ml Blasticidin S Hydrochloride without the induction of mitoEagI.

extract_protocol:
Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) according to the manufacturers instructions with the Chromium Controller and Chromium Next GEM Single Cell ATAC Reagent Kits v1.1  (PN-1000176) or v2 (PN-1000390) with minor modification and sample multiplexing with TotalSeq hashtag antibodies.
ASAP-seq libraries were generated as previously described (PMID: 34083792)

treatment_protocol: Control and POLGD274A  knock-in clone 36 HEK293 cell lines were cuturled in glucose-free DMEM supplemented with 1 mM sodium pyruvate and with either 10 mM glucose (3 days) or 10 mM galactose (1 day or 3 days).

value: mixed sample (WT, POLG-D274A)

value: Glucose for 3 days, Glactose for 1 and 3 days

tag: library type

value: HTO

tag: hto

value: TotalSeq-B0251 anti-human Hashtag 1 Antibody (CTRL_Glucose), TotalSeq-B0252 anti-human Hashtag 2 Antibody (CTRL_Galactose_1), TotalSeq-B0253 anti-human Hashtag 3 Antibody (CTRL_Galactose_3), TotalSeq-B0254 anti-human Hashtag 4 Antibody (KI36_Glucose), TotalSeq-B0255 anti-human Hashtag 5 Antibody (KI36_Galactose_1), TotalSeq-B0256 anti-human Hashtag 6 Antibody (KI36_Galactose_3),


description:
Library name: HEK293 POLG-D274A knock-in cell Galactose vs Glucose, HTO, channel 1
Tn5-derived chromatin accessibity profile, HTO library: Reads1 contains UMI, Reads2 contains cell barcode, Read3 file contains Hashtag antibodies derived Tag reads

value: ATAC


title: NPC cells, BIHi269-B, control, 10 µM Sildenafil in 0.1% DMSO für 24 hours, replicate 1

description:
Library name: 269B_10uM_SILDENAFIL_24A
Column_name in FPKM_joined.tab: FPKM_269B_10uM_SILDENAFIL_24A


title: Coculture_Exp_T2_A

description:
Library name: Coculture_Exp_T2_A
Column name in AMsummary & TPsummary.csv:  Coculture_Exp_T2_A


title: NPC cells, BIHi267-B, MILS patient, vehicle [0.1% DMSO] treated für 24 hours, replicate 1

description:
Library name: 267B_DMSO_24A
Column_name in FPKM_joined.tab: FPKM_267B_DMSO_24A

value: m.9176T>G (heteroplasmy 98.0%)

value: Control 0.1% DMSO only


title: NPC cells, BIHi267-B, MILS patient, 10 µM Sildenafil  in 0.1% DMSO für 24 hours, replicate 3

description:
Library name: 267B_10uM_SILDENAFIL_24C
Column_name in FPKM_joined.tab: FPKM_267B_10uM_SILDENAFIL_24C

value: NPC generated from iPSC


title: NPC cells, BIHi267-B, MILS patient, vehicle [0.1% DMSO] treated für 24 hours, replicate 3

description:
Library name: 267B_DMSO_24C
Column_name in FPKM_joined.tab: FPKM_267B_DMSO_24C

value: Neuronal precursor cells (NPCs)


description:
Library name: HEK293 POLG-D274A knock-in cell Galactose vs Glucose, scATAC, channel 1
Tn5-derived chromatin accessibity profile, ATAC: Read1 and Read3 files contains  ATAC sequence, Reads2 contains cell barcode

library_source: genomic single cell

data_processing:
Raw fastq files/sequencing reads were aligned to the mtDNA blacklist modified hg38 reference genome using CellRanger-ATAC count (v2.1.0) to generate possorted_bam.bam, fragments.tsv.gz and filtered_peak_bc_matrix.h5
The cell hashtag tag abundances were quantified using ASAP_to_kite.py (https://github.com/caleblareau/asap_to_kite), followed by the kallisto, bustools, and kite pipeline.
Assembly: hg38
Supplementary files format and content: CellRanger output files: singlecell.csv, fragments.tsv.gz, fragments.tsv.gz.tbi and filtered_peak_bc_matrix.h5
Supplementary files format and content: kb-kite output files: featurecounts.barcodes.txt, featurecounts.genes.txt, and featurecounts.mtx


title: HeLa, siCSB_IgG_rep1

description: Library name: siCSB_IgG_rep1

value: HeLa

value: WT

value: siCSB


title: Coculture_Exp_T1_B

description:
Library name: Coculture_Exp_T1_B
Column name in AMsummary & TPsummary.csv:  Coculture_Exp_T1_B

value: Coculture (Alteromonas macleodii)


title: NPC cells, BIHi267-B, MILS patient, vehicle [0.1% DMSO] treated für 24 hours, replicate 2

description:
Library name: 267B_DMSO_24B
Column_name in FPKM_joined.tab: FPKM_267B_DMSO_24B


title: SMG1i, RNA-seq, unlabeled

city: Bethesda

first: J. Robert

last: Hogg

state: MD

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

institute: National Heart, Lung, and Blood Institute

description:
Library name: Sample 8
TL-seq from HEK-293 cells treated with 1µM SMG1i, no 4-thiouridine labeling

data_processing:
TL-seq: All processing was performed with fastq2EZbakR (https://github.com/isaacvock/fastq2EZbakR). In fastq2EZbakR, reads were trimmed with fastp and aligned to hg38 with STAR (default parameters and --outFilterType BySJout --twopassMode Basic --outSJfilterCountTotalMin 10 3 3 3 --alignEndsType EndToEnd --outSJfilterCountUniqueMin 10 3 3 3 --outFilterMismatchNmax 20 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4). Uniquely mapped reads were assigned to features with featureCounts, and mutations in those reads were counted with a custom script. Browser tracks were made using STAR. Tracks were converted to binary format using IGVtools (toTDF).
Iso-seq: Unaligned BAM files were converted into FASTQ format using the bam2fastq tool (https://github.com/jts/bam2fastq). FASTQ files were aligned to hg38 using minimap2 with the splice-aware option (Li, 2018), producing SAM files [minimap2 -ax splice -ub hg38.fa ccs.fastq.gz > ccs.sam]. The resulting SAM files were then converted to sorted BAM files using samtools [samtools view -bS ccs.sam | samtools sort -o .ccs_sorted.bam] (Li et al., 2009).
Assembly: hg38
Supplementary files format and content: TL-seq: bedgraph files where reads are separated by the number of T-to-C mutations (0-5+) and strandedness (min/pos).

growth_protocol: DMEM, 5% FBS, 1% L-glutamine, 1% penicillin-streptomycin

extract_protocol:
Total RNA was extracted using Trizol Reagent and TimeLapse chemistry was performed as described (Schofield et al., 2018).
TL-seq: rRNA depletion was performed by oligo hybridization and digestion with thermostable RNase H (Baldwin et al, 2021). 100 ng of ribodepleted RNA was used as input for the NEBNext Ultra II Directional Library Prep Kit.
Iso-seq: 2 µg total RNA was used as input for the Clontech SMARTer PCR cDNA Synthesis kit, followed by PCR amplification. SMRTbell libraries were generated using the SMRTbell Template Prep Kit.

treatment_protocol: Treatment with 1 µM SMG1i or DMSO for 8 hours; TL-seq: labeling with 100 µM 4-thiouridine for 2 hours

value: human embryonic kidney

value: 1µM SMG1i, unlabeled


title: NPC cells, BIHi267-B, MILS patient, 10 µM Sildenafil  in 0.1% DMSO für 24 hours, replicate 2

description:
Library name: 267B_10uM_SILDENAFIL_24B
Column_name in FPKM_joined.tab: FPKM_267B_10uM_SILDENAFIL_24B

value: 10 µM Sildenafil in 0.1% DMSO


title: NPC cells, BIHi267-B, MILS patient, 10 µM Sildenafil in 0.1% DMSO für 24 hours, replicate 1

description:
Library name: 267B_10uM_SILDENAFIL_24A
Column_name in FPKM_joined.tab: FPKM_267B_10uM_SILDENAFIL_24A


description:
Library name: HEK293 POLG-D274A knock-in cell, scATAC, deeper sequencing
Tn5-derived chromatin accessibity profile, ATAC: Read1 and Read3 files contains  ATAC sequence, Reads2 contains cell barcode


title: SMG1i, TL-seq, rep3

description:
Library name: Sample 7
TL-seq from HEK-293 cells treated with 1µM SMG1i, 100 µM 4-thiouridine labeling

data_processing:
TL-seq: All processing was performed with fastq2EZbakR (https://github.com/isaacvock/fastq2EZbakR). In fastq2EZbakR, reads were trimmed with fastp and aligned to hg38 with STAR (default parameters and --outFilterType BySJout --twopassMode Basic --outSJfilterCountTotalMin 10 3 3 3 --alignEndsType EndToEnd --outSJfilterCountUniqueMin 10 3 3 3 --outFilterMismatchNmax 20 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4). Uniquely mapped reads were assigned to features with featureCounts, and mutations in those reads were counted with a custom script. Browser tracks were made using STAR. Tracks were converted to binary format using IGVtools (toTDF).
Iso-seq: Unaligned BAM files were converted into FASTQ format using the bam2fastq tool (https://github.com/jts/bam2fastq). FASTQ files were aligned to hg38 using minimap2 with the splice-aware option (Li, 2018), producing SAM files [minimap2 -ax splice -ub hg38.fa ccs.fastq.gz > ccs.sam]. The resulting SAM files were then converted to sorted BAM files using samtools [samtools view -bS ccs.sam | samtools sort -o .ccs_sorted.bam] (Li et al., 2009).
Assembly: hg38
Supplementary files format and content: TL-seq: bedgraph files where reads are separated by the number of T-to-C mutations (0-5+) and strandedness (min/pos).
Library strategy: TL-seq

value: 1µM SMG1i, 100 µM 4-thiouridine


title: Coculture_Exp_T1_C

description:
Library name: Coculture_Exp_T1_C
Column name in AMsummary & TPsummary.csv:  Coculture_Exp_T1_C


description:
Library name: HEK293 POLG-D274A knock-in cell Galactose vs Glucose, scATAC, channel 2
Tn5-derived chromatin accessibity profile, ATAC: Read1 and Read3 files contains  ATAC sequence, Reads2 contains cell barcode

value: mixed sample (WT, POLG-D274A)


title: SMG1i, TL-seq, rep2

description:
Library name: Sample 6
TL-seq from HEK-293 cells treated with 1µM SMG1i, 100 µM 4-thiouridine labeling


title: NPC cells, BIHi266-A, control, vehicle [0.1% DMSO] treated für 24 hours, replicate 3

description:
Library name: 266A_DMSO_24C
Column_name in FPKM_joined.tab: FPKM_266A_DMSO_24C

value: wildtype


title: Coculture_Exp_T1_A

description:
Library name: Coculture_Exp_T1_A
Column name in AMsummary & TPsummary.csv:  Coculture_Exp_T1_A


title: Human RNAseq NTC, Rep2

city: Los Angeles

first: Jeong Hyun

last: Ji

state: CA

address: 615 Charles E Young Dr S, Rm 247

institute: University of California, Los Angeles

description: Library name: Human_RNAseq_NTC_Rep2

data_processing:
FastQC (v0.12.0), Trimmomatic (v0.39), and STAR (v2.7.11)
Assembly: hg38
Supplementary files format and content: Comma-separated text file includes raw counts for each sample.

source_name: NK cells

extract_protocol:
RNA was harvested using the Quick-RNA microprep kit (Zymo). 10ng of RNA was used for library preparation.
RNA libraries were constructed using the Illumina RNA Prep with Enrichment kit following manufacturer's instructions.

value: NK cells

value: NTC


title: Human RNAseq NTC, Rep3

description: Library name: Human_RNAseq_NTC_Rep3


title: Human RNAseq NTC, Rep1

description: Library name: Human_RNAseq_NTC_Rep1


title: Cryptocercus punctulatus was dissociated into single nuclei

city: Sydney

first: Fabio

last: Zanini

state: NSW

address: Lowy L2

country: Australia

institute: UNSW Sydney

description:
Library name: CRYPTO_PUN1
10X Genomics 3’ end

library_source: transcriptomic single cell

data_processing:
Reads were aligned against the recently sequenced Cryptocercus meridianus genome using cellranger 9.
Assembly: Cryptocercus meridianus (https://www.biorxiv.org/content/10.1101/2025.01.20.633303v1.full).
Supplementary files format and content: Tab-separated files  and mtx (matrix) files.

organism: Cryptocercus punctulatus

source_name: all

extract_protocol:
One adult specimen of Cryptocercus punctulatus was kept in the Bourguignon lab at Okinawa Institute of Technology, Japan. After slicing with ethanol-cleaned scissors and pestle maceration (~20 strokes) in 1 ml homogenisation buffer (Supplementary Table 4), the slurry was centrifuged for 10 minutes at 1000g and 4 ℃, and resuspended in 1ml PBS 0.5% BSA, then filtered through a 100 μm (Falcon 352360) and 35 μm cell strainers to eliminate large debris and immediately moved to the precalibrated sorter (Sony SH800S). 0.1% DAPI was added and nuclei were sorted within 20 minutes using a gate DAPI+ FSClow. After sorting, nuclei were inspected under an epifluorescence microscope, pelletted and resuspended after removing 700 μl of supernatant, then finally adjusted to 700-1200 nuclei / μl using a hemocytometer.
Libraries were constructed using a 10X Genomics Chromium with 3’ chemistry v3 and dual-index Nextera-equivalent barcodes, and sequenced at a total depth of 621,418,196 reads pairs.

value: all


title: SMG1i, TL-seq, rep1

description:
Library name: Sample 5
TL-seq from HEK-293 cells treated with 1µM SMG1i, 100 µM 4-thiouridine labeling


title: Human RNAseq FLI1 KO, Rep3

description: Library name: Human_RNAseq_FLI1KO_Rep3

value: FLI1 KO


title: NPC cells, BIHi266-A, control, vehicle [0.1% DMSO] treated für 24 hours, replicate 2

description:
Library name: 266A_DMSO_24B
Column_name in FPKM_joined.tab: FPKM_266A_DMSO_24B

value: Control 0.1% DMSO only


title: DMSO, RNA-seq, unlabeled

description:
Library name: Sample 4
TL-seq from HEK-293 cells treated with DMSO, no 4-thiouridine labeling

value: DMSO, unlabeled


title: NPC cells, BIHi266-A, control, vehicle [0.1% DMSO] treated für 24 hours, replicate 1

description:
Library name: 266A_DMSO_24A
Column_name in FPKM_joined.tab: FPKM_266A_DMSO_24A

value: NPC generated from iPSC

value: Neuronal precursor cells (NPCs)


title: DMSO, TL-seq, rep2

description:
Library name: Sample 2
TL-seq from HEK-293 cells treated with DMSO, 100 µM 4-thiouridine labeling

value: DMSO, 100 µM 4-thiouridine


title: DMSO, TL-seq, rep3

description:
Library name: Sample 3
TL-seq from HEK-293 cells treated with DMSO, 100 µM 4-thiouridine labeling


title: NPC cells, BIHi266-A, control, 10 µM Sildenafil  in 0.1% DMSO für 24 hours, replicate 2

description:
Library name: 266A_10uM_SILDENAFIL_24B
Column_name in FPKM_joined.tab: FPKM_266A_10uM_SILDENAFIL_24B


title: Human RNAseq FLI1 KO, Rep1

description: Library name: Human_RNAseq_FLI1KO_Rep1


title: Human RNAseq FLI1 KO, Rep2

description: Library name: Human_RNAseq_FLI1KO_Rep2


title: NPC cells, BIHi266-A, control, 10 µM Sildenafil in 0.1% DMSO für 24 hours, replicate 1

description:
Library name: 266A_10uM_SILDENAFIL_24A
Column_name in FPKM_joined.tab: FPKM_266A_10uM_SILDENAFIL_24A


title: LN229 CONTROL 0 mins_rep2

type: protein

city: Bangalore

first: Jayita

last: Goswami

address: CV Raman road

country: India

institute: Indian Institute of Science

hyb_protocol: Not applicable.

scan_protocol: RPPA slides were scanned and signal intensities were acquired by the MD Anderson Cancer Center RPPA Core Facility using standardized scanning procedures.

data_processing: Raw signal intensities were processed and normalized by the MD Anderson Cancer Center RPPA Core Facility using established RPPA data processing pipelines, including background correction and normalization across samples.

source_name: Glioblastoma cell line

label_protocol: No labeling was performed. RPPA is a label-free antibody-based protein detection assay.

growth_protocol: Cells were cultured in appropriate growth medium under standard conditions (37 °C, 5% CO₂) prior to experimental treatment and protein extraction.

extract_protocol: Protein lysates were prepared by the MD Anderson Cancer Center Reverse Phase Protein Array (RPPA) Core Facility using standard operating procedures.

treatment_protocol: Cells were treated with sCT for 60 mins and cell pellet was harvested for RPPA

value: Untreated


title: LN229 sCT 60 mins_rep1

value: Treated


title: NPC cells, BIHi266-A, control, 10 µM Sildenafil  in 0.1% DMSO für 24 hours, replicate 3

description:
Library name: 266A_10uM_SILDENAFIL_24C
Column_name in FPKM_joined.tab: FPKM_266A_10uM_SILDENAFIL_24C


title: LN229 sCT 60 mins_rep2


title: HS05_late_stage_Total_01

status: Public on Feb 09 2026

city: Sacramento

first: JAEHWAN

last: KIM

address: 10535 Hospital Way

department: Dermatology

institute: University of California, Davis

description:
Library name: HS05_late_stage_Total_01
HS05_late_stage_Total_01

data_processing:
CellRanger version 3.1 (10X Genomics) pipelines were used for demultiplexing base calls into Fastq, filtering, barcode counting and filtering, UMI counting and alignment with reference human genome GRCh38.
The quality control, normalization, linear regression of number of UMIs and scaling were performed using Seurat (v4.0).
Seurat R package (version 4.0, https://satijalab.org/seurat/) was used for the single-cell data integration. We first merged single-cell data of samples with the common sequencer and the identical reagent kit version. To harmonize merged groups into a single dataset without batch effects, correspondences between cells in three merged datasets were identified by the FIndIntegrationAnchors function, and used for data integration with the IntegratedData function in Seurat R package.
Principal component analysis and graph-based clustering analysis were performed with Seurat R package (version 4.0, https://satijalab.org/seurat/). Sixty principal components (PCs) were selected for Uniform Manifold Approximation and Projection (UMAP) for Dimension Reduction. With a resolution of 0.4, cells were clustered by the FindClusters function. Then, differentially expressed genes of each cluster compared to all other cells were found by the FindAllMarkers function. Differentially expressed genes between psoriasis and control within each cluster were found by the FindMarkers function. The average gene expression of psoriasis vs. control cells within a cluster was calculated by the AverageExpression function.
Assembly: GRCh38
Supplementary files format and content: barcode table, gene table and gene expression matrix files generated by Cell Ranger version 3.1.

source_name: Skin

extract_protocol:
Skin biopsy tissues from human skin were incubated in culture medium for harvesting emigrating cells. Harvested skin tissue was immediately placed in 0.2% Dispase II (Sigma-Aldrich) and incubated in a humidified incubator at 37 Celsius and 5% CO2 for 3 hours. Then, epidermis and dermis were separated with forceps and sliced into small pieces with #10 blade scalpels. Epidermis and dermis were separately cultured in RPMI-1640 medium with L-glutamine (Cytiva) supplemented with 10% human albumin serum (Sigma-Aldrich) and without any enzyme or antibiotic agent in a humidified incubator at 37 Celsius and 5% CO2. Nonplastic adherent cells that had emigrated out of epidermis and dermis were harvested after 48 hours. The harvested cells from epidermis and dermis were filtered through a 40-µm cell strainer (Corning) and stored on ice.
The 10x Genomics Chromium Single Cell 3′ Reagents Kit user guide (https://support.10xgenomics.com/single-cell-gene-expression/library-prep) was used to prepare the single cell suspension. The appropriate volume of each sample was diluted to recover 10,000 cells. Subsequently, the single cell suspension, Gel Beads and oils were added to the 10x Genomics single-cell chip. After droplet generation, samples were transferred into PCR tubes and we performed reverse transcription using a ProFlex PCR Thermocycler System (Applied Biosystems). After reverse transcription, cDNA was recovered using a recovery agent, provided by 10x Genomics, followed by silane DynaBead clean-up as outlined in the user guide.

value: Skin

tag: disease

value: Hidradenitis suppurativa

tag: lesional/non-lesiona

value: Lesional

tag: Stage

value: Late-stage


title: Psoriasis30_LS_Total_01

description:
Library name: Psoriasis30_LS_Total_01
Psoriasis30_LS_Total_01

value: Psoriasis

value: Severe


title: HS04_early_stage_B_01

description:
Library name: HS04_early_stage_B_01
HS04_early_stage_B_01

value: Early-stage


title: Psoriasis30_NL_Total_01

description:
Library name: Psoriasis30_NL_Total_01
Psoriasis30_NL_Total_01

value: Non-lesional


title: 24hpf_AP1

first: Johanna

middle: Berenike

last: Kroll

address: Hannoversche Str.28

department: Berlin Institute for medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

description: Library name: Sample 1

data_processing:
Paired end reads were aligned to the transcriptome using STARsolo. The zebrafish transcriptome was based on genome release zv11. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike-ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012)
Assembly: Danio rerio GRCz11
Supplementary files format and content: does not apply

source_name: embryo

growth_protocol: does not apply

extract_protocol:
Sections were either obtained by sectioning along the anterior/posterior axis (AP, sample 1,2) or along the dorsal/ventral axis (DV, sample 3, 4). After cryosectioning, RNA was isolated from sections (two for each direction)  by TRIzol extraction. see: Junker et al., 2014, Cell
RNA was barcoded and amplified using the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012) see: Junker et al., 2014, Cell

treatment_protocol: 24 hpf Embryos were covered with Jung tissue freezing medium (Leica), oriented laterally and the region where the PGCs were located (developing gonad region) was marked by polyacrylamide beads. Next embryos were embedded in tissue freezing medium. Blocks were cryosectioned either along the dorsal-ventral axis or along the anterior-posterior axis. Each section was transferred to pre-cooled Eppendorf tubes on dry ice.

value: embryo

tag: developmental stage

value: 24 hpf


title: 24hpf_DV2

description: Library name: Sample 4


title: TC-81

type: RNA

city: Rostock

first: Teresa M.

last: Cardesa-Salzmann

address: Ernst-Heydemann Strasse, 8

institute: Universitätsmedizin Rostock. Klinik für Kinder- und Jugendmedizin

hyb_protocol: According to Nanostring manufacturer's instructions

data_processing: Rosalind

label: NanoString

source_name: NCLT

extract_protocol: For Burkitt lymphoma cases on average, 4 10 um-thick FFPE sections of tumor tissue were prepared for the extraction of total RNA from tumor cell-rich areas. The miRNAeasy FFPE-kit (Qiagen, Hilden, Germany) was used for miRNA extraction. For Burkitt leukemia bone marrow samples total RNA was extracted using TriPure Isolation Reagent (Roche Diagnostics, Indianapolis, IN, USA) and Direct-zol RNA MiniPrep kit (Zymo Research, California, USA). Total RNA from Raji and DG-75 cell lines (supplier: DSMZ, Braunschweig, Germany) was extracted with the miRNeasy Micro Kit (Qiagen).

tag: histology

value: NCLT


title: LN229 CONTROL 0 mins_rep1


title: 24hpf_AP2

description: Library name: Sample 2


title: TC-76

scan_protocol: According to Nanostring manufacturer's instructions

value: normal lymph node


title: HS04_early_stage_A_02

description:
Library name: HS04_early_stage_A_02
HS04_early_stage_A_02


title: TC-80

label_protocol: According to Nanostring manufacturer's instructions


title: TC-61

source_name: B-Ly

value: Abdominal mass

tag: age at diagnosis (years)

value: B-Ly

tag: Sex

value: M

value: III

tag: cns involvement

tag: relapse

value: N

tag: alive

value: Y

tag: eber

value: EBER-


title: DMSO, TL-seq, rep1

description:
Library name: Sample 1
TL-seq from HEK-293 cells treated with DMSO, 100 µM 4-thiouridine labeling

tag: cell line

tag: cell type

value: human embryonic kidney

tag: treatment

value: DMSO, 100 µM 4-thiouridine


title: TC-77

tag: tissue

value: normal tonsil (pt TC-4)


title: 24hpf_DV1

description: Library name: Sample 3

tag: genotype


title: TC-62


title: TC-60

value: Rhinopharynx

value: IV


title: TC-55

value: Tonsil


title: HS04_early_stage_B_02

description:
Library name: HS04_early_stage_B_02
HS04_early_stage_B_02

value: Skin

value: Hidradenitis suppurativa

value: Lesional

value: Early-stage


title: TC-49

source_name: B-AL

value: bone marrow

value: B-AL

value: no


title: TC-46

value: M


title: TC-44

value: F

value: N


title: TC-45

value: Y


title: TC-41


title: TC-39


title: TC-24

value: Breast

value: B-Ly

value: II

value: EBER+


title: TC-23

value: Soft tissue

value: IV

value: EBER-


title: TC-52

value: Cavum


title: TC-20

value: Intestinal

value: III


title: TC-17

value: Oropharynx


title: TC-21


title: TC-43

value: bone marrow

value: B-AL


title: TC-11

value: M


title: TC-13

value: (at relapse) Lymph node

value: F


title: TC-07

value: Lymph node

value: N

value: Y


title: TC-19

value: B-Ly


title: TC-10


title: TC-03


title: TC-04

value: Tonsil


title: TC-01

value: II


title: TC-12

value: Abdominal mass

value: EBER+


title: TC-05

value: IV

value: EBER-


title: B. fragilis RNA-Seq, phage-treated, replicate 2

first: Dmitry

last: Sutormin

address: 401 Terry Ave N

institute: Institute for Systems Biology

description:
Library name: Bfragilis_phage_rep2
Unstranded RNA-Seq

data_processing:
RNA-Seq data was aligned to the B. fragilis NCTC 9343 reference genome, and gene counts were calculated using STAR (v2.7.10a) with --quantMode GeneCounts option.
Assembly: GCF_000025985.1 (Bacteroides fragilis NCTC 9343)
Supplementary files format and content: Tab-separated gene counts tables, generated by STAR.

organism: Bacteroides fragilis

source_name: NCTC 9343

growth_protocol: 200 uL B. fragilis overnight culture was mixed with 1.75mL CMC Media (Anaerob Systems) and 50 uL of Bf12P1 at MOI of 0.00004. For no-phage conditions, 50 uL of spent B. fragilis CMC media was used instead of the phage. Cultivation was performed anaerobically in a deep-well 2 mL plate at 37C with shaking. At time of collection (t=2.15 h), RNA-Protect (Qiagen) was added in equal volume to each culture in the anaerobic chamber. After addition and RNA-Protect, cultures were removed from the anaerobic chamber and the remaining steps were carried out in the biosafety cabinet.

extract_protocol:
Cells were pelleted at 5,000 x g for 10 min, RNA was extracted using the RNeasy kit (Qiagen) and subsequently treated with DNase I.
Sequencing library was prepared using TruSeq RNA Library Prep Kit (Illumina).

value: NCTC 9343


title: B. fragilis RNA-Seq, no phage, replicate 2

description:
Library name: Bfragilis_NOphage_rep2
Unstranded RNA-Seq


title: TC-02

value: III


title: TC-15

value: Mandible


title: B. fragilis RNA-Seq, phage-treated, replicate 3

description:
Library name: Bfragilis_phage_rep3
Unstranded RNA-Seq


title: B. fragilis RNA-Seq, phage-treated, replicate 1

description:
Library name: Bfragilis_phage_rep1
Unstranded RNA-Seq


title: Compound 32 sample 3

city: Shihezi

first: Yeernaer

last: Hazaisihan

state: Xinjiang

address: Beierlu 121

department: School of Medicine

country: China

institute: Shihezi University

description:
Library name: Sample 9
C_32

data_processing:
Quality control: Raw reads were trimmed using fastp to remove adapters, poly-N sequences, and low-quality bases. Clean reads were assessed for Q20, Q30, and GC content.
Alignment: Clean paired-end reads were aligned to the reference genome (e.g., mm10) using HISAT2 v2.0.5, which leverages gene annotation to improve splice-aware mapping.
Quantification: Gene-level read counts were generated with featureCounts, and expression levels were normalized as FPKM.
Differential expression:With biological replicates: DESeq2 (FDR ≤ 0.05, |log₂FC| ≥ 1).Without replicates: edgeR with scaling normalization (same significance thresholds).
Assembly: hg38
Supplementary files format and content: gene_count.xls

source_name: High-grade serous ovarian cancer

growth_protocol: HEYA8 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS) and antibiotics, maintained in a humidified atmosphere with 5% CO₂ at 37°C.

extract_protocol:
RNA was extracted using the TRIzol reagent.
RNA libraries for RNA-seq were prepared using oligo(dT) magnetic bead-based mRNA enrichment followed by cDNA synthesis with random hexamer primers, according to standard protocols.

treatment_protocol: Sunitinib group: three samples treated with sunitinib for 24 h at 70% confluency; DMSO control group: three samples treated with an equal volume of DMSO for 24 h; Compound 32 group: three samples treated with Compound 32 for 24 h under the same conditions.

value: High-grade serous ovarian cancer

value: WT

value: compound 32

tag: batch

value: Day 1


title: TC-06

value: Lymph node

value: F


title: B. fragilis RNA-Seq, no phage, replicate 1

description:
Library name: Bfragilis_NOphage_rep1
Unstranded RNA-Seq


title: Compound 32 sample 2

description:
Library name: Sample 8
B_32


title: Sunitinib sample 2

description:
Library name: Sample 5
B_1

value: Sunitinib


title: Compound 32 sample 1

description:
Library name: Sample 7
A_32


title: TC-08

value: B-Ly

value: M

value: N

value: Y


title: TC-09

value: Oropharynx

value: II

value: EBER+


title: TC-18

value: Pleura

value: EBER-


title: Sunitinib sample 3

description:
Library name: Sample 6
C_1


title: B. fragilis RNA-Seq, no phage, replicate 3

description:
Library name: Bfragilis_NOphage_rep3
Unstranded RNA-Seq

value: NCTC 9343


title: Sunitinib sample 1

description:
Library name: Sample 4
A_1

value: High-grade serous ovarian cancer


title: DMSO sample 2

description:
Library name: Sample 2
DMSO_2

value: WT

value: DMSO


title: DMSO sample 1

description:
Library name: Sample 1
DMSO_1

value: Day 1


title: 3334392_G401_input_SMARCB1_3_ChIP

city: Memphis

last: Navarro

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description: Library name: 3334392_G401_input_SMARCB1_3_ChIP_HAM

data_processing:
Raw reads were processed using Trim-Galore (v0.6.3, Krueger F. (2012)
Reads were mapped to human-drosophila reference hybrid genome (merged hg19/GRCh37.p13 and dm6 genomes) with bwa aln, followed by bwa samse or sampe (v0.7.17-r1039, PMID: 19451168)
Reads mapping to human reference genome were extracted for further analysis using samtools, duplicated reads were marked with bamsormadup tool from biobambam2 (v2.0.87, DOI: 10.1186/1751-0473-9-13) and Cross-Correlation analysis was conducted with SPP (v1.11, PMID: 19029915)
Uniquely mapped reads were then extracted with samtools, extended with bedtools (v2.24.0, PMID: 20110278) using the fragment size value previously estimated with Cross-Correlation analysis, and then converted to bigwig track files by UCSC tools (v4, PMID: 22908213).
Peaks were called using MACS2 (PMID: 18798982) program with –nomodel -q 0.05 flags (high confidence peaks).
Assembly: merged hg19/GRCh37.p13 and dm6
Supplementary files format and content: bigWig, narrowPeak (except for input sample)

source_name: cell line

growth_protocol: McCoy's Media + 10% FBS

extract_protocol:
Covaris truCHIP Chromatin Shearing Kit
KAPA Library Prep Kit

value: cell line

value: rhabdoid tumor


title: 3334391_G401_input_SMARCB1_2_ChIP

description: Library name: 3334391_G401_input_SMARCB1_2_ChIP_HAM


title: CHLA266_RNAseq_siPHIP_NA_2

description:
Library name: 3399702_CHLA266_RNAseq_siPHIP_NA_2_HAM
20251104 RNAseq after PHIP KD CHLA266
ROBERTS-864304-STRANDED_RSEM_gene_count.txt

data_processing:
trim_galore v0.6.3 remove adapter sequences
alignment with STAR2.7.9a --twopassMode Basic
read counts quantified by RSEMv1.3.3
Assembly: hg19/GRCh37.p13
Supplementary files format and content: tab delimited table of read counts for each sample

growth_protocol: McCoy's Medium + 10% FBS + 10% GlutaMAX

extract_protocol:
ZymoResearch Direct-zol™ RNA MiniPrep Plus Cat # R2070 according to manufacturer's instructions
TruSeq Stranded mRNA Library Prep Kit, Illumina, PN 20020595

treatment_protocol: 48 hour transfection with individual siRNAs

value: ATRT

value: siPHIP


title: DMSO sample 3

description:
Library name: Sample 3
DMSO_3


title: 3128867_G401_PHIPmarc_siCtrl_1_ChIP

description: Library name: 3128867_G401_PHIPmarc_siCtrl_1_ChIP_HAM

value: siCtrl


title: BIN67_RNAseq_siPHIP_NA_3

description:
Library name: 3396602_BIN67_RNAseq_siPHIP_NA_3_HAM
20251020 RNAseq after PHIP KD BIN67
ROBERTS-863692-STRANDED_RSEM_gene_count.txt

value: SCCOHT


title: 3128875_G401_PHIPmarc_siPHIP_3_ChIP

description: Library name: 3128875_G401_PHIPmarc_siPHIP_3_ChIP_HAM


title: 3128877_G401_PHIPinput_siPHIP_1_ChIP

description: Library name: 3128877_G401_PHIPinput_siPHIP_1_ChIP_HAM


title: 3334383_G401_CHD4ab240640_GFP_3_ChIP

description: Library name: 3334383_G401_CHD4ab240640_GFP_3_ChIP_HAM

value: GFP


title: 3128876_G401_PHIPinput_siCtrl_1_ChIP

description: Library name: 3128876_G401_PHIPinput_siCtrl_1_ChIP_HAM


title: 3334387_G401_input_GFP_1_ChIP

description: Library name: 3334387_G401_input_GFP_1_ChIP_HAM


title: 3128868_G401_PHIPmarc_siCtrl_2_ChIP

description: Library name: 3128868_G401_PHIPmarc_siCtrl_2_ChIP_HAM


title: 3334388_G401_input_GFP_2_ChIP

description: Library name: 3334388_G401_input_GFP_2_ChIP_HAM


title: 3128873_G401_PHIPmarc_siPHIP_1_ChIP

description: Library name: 3128873_G401_PHIPmarc_siPHIP_1_ChIP_HAM


title: 3334381_G401_CHD4ab240640_GFP_1_ChIP

description: Library name: 3334381_G401_CHD4ab240640_GFP_1_ChIP_HAM


description: Library name: 3334384_G401_CHD4ab240640_SMARCB1_1_ChIP_HAM


title: 3334390_G401_input_SMARCB1_1_ChIP

description: Library name: 3334390_G401_input_SMARCB1_1_ChIP_HAM


title: CHLA266_RNAseq_siCtrl_NA_1

description:
Library name: 3399698_CHLA266_RNAseq_siCtrl_NA_1_HAM
20251104 RNAseq after PHIP KD CHLA266
ROBERTS-864304-STRANDED_RSEM_gene_count.txt


description: Library name: 3334385_G401_CHD4ab240640_SMARCB1_2_ChIP_HAM


title: BIN67_RNAseq_siPHIP_NA_2

description:
Library name: 3396601_BIN67_RNAseq_siPHIP_NA_2_HAM
20251020 RNAseq after PHIP KD BIN67
ROBERTS-863692-STRANDED_RSEM_gene_count.txt


description: Library name: 3334386_G401_CHD4ab240640_SMARCB1_3_ChIP_HAM


title: CHLA266_RNAseq_siPHIP_NA_3

description:
Library name: 3399703_CHLA266_RNAseq_siPHIP_NA_3_HAM
20251104 RNAseq after PHIP KD CHLA266
ROBERTS-864304-STRANDED_RSEM_gene_count.txt


title: 3334389_G401_input_GFP_3_ChIP

description: Library name: 3334389_G401_input_GFP_3_ChIP_HAM


title: BIN67_RNAseq_siCtrl_NA_3

description:
Library name: 3396599_BIN67_RNAseq_siCtrl_NA_3_HAM
20251020 RNAseq after PHIP KD BIN67
ROBERTS-863692-STRANDED_RSEM_gene_count.txt