title: liver_day8_Cyclobutrifluram_120ppm_24B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916341_S01_GE1_107_Sep09_2_4


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

status: Public on Dec 31 2025

type: SRA

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

country: Germany

institute: Charite

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

library_source: transcriptomic

data_processing:
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. 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.

molecule: polyA RNA

organism: Homo sapiens

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 [Thermo Fisher Scientific, Gibco, #A1413302]-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 4.5 mM glucose-containing media consisting of the following components: 0.5x Neurobasal without glucose [Thermo Fisher Scientific, Waltham, MA, USA, Gibco, A2477501], 0.5x DMEM/F12 without glucose [Elabscience, EP-CM-L0128], 0.5x N2 [Thermo Fisher Scientific, Gibco, #17502-048], 0.5x B27 without vitamin A [Thermo Fisher Scientific, Gibco #12587010], 2 mM L-Glutamine [Invitrogen, 25030-02425], 1x MycoZap Plus-CL [Lonza, Basel, Switzerland, #VZA-2012] with the addition of 0.5 µM PMA [Miltenyi Biotech, #130-104-465], 3 µM CHIR 99021 [Cayman Chemical, Ann Arbor, MI, USA, #13122], 150 µM ascorbic acid [Sigma-Aldrich, St. Louis, MO, USA, #A92902], 0.115 mM sodium pyruvate [Thermo Fisher Scientific, Gibco, #11360070]  and 4.5 mM glucose [Sigma-Aldrich, #G-5400].

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).

treatment_protocol: NPCs were seeded at a density of 500,000 cells/well in neural progenitor medium containing 4.5 mM glucose 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 1 µM or 10 µM Sildenafil (Selleckchem, Cologne, Germany, #S4684) dissolved in 0.1% DMSO and incubated at 37°C and 5% CO2 for 6 or 24 hours (in triplicates). Control cells were grown without additives (in triplicate). 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.

tag: tissue

value: NPC generated from iPSC

tag: cell line

tag: cell type

value: Neuronal precursor cells (NPCs)

tag: genotype

value: wildtype

tag: treatment

value: 0.1% DMSO for 24 hours

tag: biological replicate


title: genomic DNA from 3h_3

type: genomic

city: Xiangyang

first: Ya-nan

last: Zhu

address: No.136, Jingzhou Road, Xiangcheng District

country: China

institute: Xiangyang Central Hospital

description: changes of genome-wide DNA methylation at 3hrs in placental trophoblast

hyb_protocol: Bisulfite-converted DNA was isothermally amplified and enzymatically fragmented, followed by purification and hybridization with the Infinium MethylationEPIC (850K) BeadChip (Illumina).

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

data_processing: Idat files were imported and then preprocessed with ChAMP (version 2.12.4) package in R to get the raw data. The raw data was normalized with the Beta-Mixture Quantile dilation (BMIQ) algorithm.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: placenta

label_protocol: Standard Illumina Protocol

growth_protocol: Standard Illumina Protocol

extract_protocol: Total DNA was extracted from primary cultured placental cytotroblasts and syncytiotrophoblasts using a Qiagen DNA kit (Qiagen, Germany)

value: cytotrophoblasts


title: Brain, adult (3 months), H3K4me3, rep3

city: La Jolla

first: Aditya

last: Parmar

state: California

address: 9500 Gilman Dr.

department: Pathology

country: USA

institute: University of California San Diego

description: Library name: Adult, brain, H3K4me3, replicate 3

library_source: genomic

data_processing:
Raw FASTQ reads were trimmed using Trimmomatic v0.39.
Trimmed reads were aligned to the mm10 genome with Bowtie2 v2.3.4.1.
BAM files were sorted and unmapped reads were removed with SAMtools v1.14
BigWig files were generated using bamCoverage (DeepTools v3.5.0) with 50 bp bins
A blacklist of alignment artifact regions was removed prior to normalization
BigWigs were normalized based on 99th percentile peak height, using scaling factors to correct for differences in sequencing depth.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Run

organism: Mus musculus

source_name: brain

extract_protocol:
For native CUT&RUN nuclei were extracted using conventional methods.
CUT&RUN libraries were prepared using the NEB Ultra™ II DNA Library Prep Kit for Illumina. Reactions were performed at half scale using between 10 ng and 30 ng of DNA  starting material. The amount of inut was kept consistent across a given histone modification.  Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were size selected at 200-500 bp in length using SPRIselect beads from Beckman Coulter. Libraries were validated using tapestation.

value: brain

tag: developmental timepoint

value: adult (3 months)

tag: antibody


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

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


title: NPC cells, HHUi002-A, MILS patient, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 1

description:
Library name: TDA3_10um_DRUG_06A
Column_name in FPKM_joined.tab: FPKM_TDA3_10um_DRUG_06A

value: m.9185T>C Mutation (homoplasmy)


title: liver_day8_Cyclobutrifluram_120ppm_26B

type: RNA

city: Bracknell

first: Liam

last: Doonan

state: Berkshire

address: Jealott's Hill International Research Centre

country: United Kingdom

institute: Syngenta

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916344_S01_GE1_107_Sep09_2_2

hyb_protocol: Purified cRNA was fragmented (Agilent gene expression hybridisation kit, 5188-5242) and hybridised to Agilent mouse whole genome expression microarrays (G4852/G4853).

scan_protocol: The arrays were washed in Agilent Gene Expression Wash Buffer 1 and Agilent Gene Expression Wash Buffer 2. Scanning and image analysis was performed using the Agilent DNA Microarray Scanner equipped with extended dynamic range (XDR) software according to the Agilent one Colour Gene Expression Protocol (December 2015; P/N G4140-90040).

data_processing:
Extraction from raw microarray image files was performed by using Agilent Feature Extraction Software (Version 10.7.1.1.) to generate raw microarray data. The matrix on sheet2 was generated with LIMMA read.maimages(source="agilent",  green.only=TRUE)
Gprocessed signal

molecule: total RNA

source_name: liver, day8, Cyclobutrifluram, 120ppm

label_protocol: Cyanine-3 (Cy3) labelled cRNA was prepared using the Agilent low input labelling kit (5190-2305) from 200 ng total RNA and purified using the Qiagen RNeasy mini kit (74104). Quantification of cRNA yields and specific activity (pmol Cy3 per μg cRNA) were measured by NanoDrop spectroscopy.

extract_protocol: Liver samples (40 – 60 mg each) were taken from the left lateral lobe, snap frozen in liquid nitrogen, and  processed for whole genome microarray analysis. Total RNA was extracted from each sample using the Qiagen miRNeasy Mini Kit (217004, v 12/2014) according to the manufacturer’s instructions.

value: liver

tag: gender

value: male

value: cyclobutrifluram

tag: dose (ppm)

tag: duration (days)


title: Brain, embryonic day 16, H3K4me3, rep4

description: Library name: Embryo, brain, H3K4me3, replicate 4

value: embryonic day 16


title: liver_day8_Cyclobutrifluram_120ppm_23B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916335_S01_GE1_107_Sep09_2_1


title: PBMC_nonBOS_Sam11

city: Chicago

first: Wei

last: Zhang

state: Illinois

address: 840 S. Wood Street

department: Pediatrics & Institute of Human Genetics

institute: University of Illinois

hyb_protocol: Total RNA was processed using the Illumina Total prep kit (Ambion) according to the manufacturer’s protocol. Illumina array hybridizations, washing, etc.

scan_protocol: Scanning were performed according to standard protocols provide by Illumina using a HiScan

data_processing: The raw microarray data were background corrected and quantile normalized across all samples using the Illumina Genome Studio. Gene expression of samples obtained from ‘BOS’ group was compared to non-‘BOS’ group using independent and unpaired T-test correction for multiple comparisons to estimate a false discovery rate as implemented in multiple variables linear regression analysis (MLR). Genes were retained for further analyses if FDR < 5%.

label: Cy3, Cy5

source_name: PBMCs

label_protocol: Same to Sample name. 52 pieces of PBMC cells mRNA (100 ng/ul) was randomized before undergoing hybridization to the Human HT-12 v4 Expression BeadChip Kit.

extract_protocol: PBMC cells were separated from patient blood samples using the Ficoll method (Amersham). Total RNA of PBMC cells was isolated using RNeasy Mini Kit according to the manufacturer’s directions (Qiagen).

tag: recipient

value: lung transplant recipient

value: Male

tag: age


title: PBMC_nonBOS_Sam7


title: PBMC_nonBOS_Sam9


title: PBMC_nonBOS_Sam6


title: PBMC_nonBOS_Sam8


title: Brain, embryonic day 16, H3K4me3, rep3

description: Library name: Embryo, brain, H3K4me3, replicate 3


title: liver_day8_Cyclobutrifluram_120ppm_22B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916366_S01_GE1_107_Sep09_1_2


title: Naïve CD8+ after 24h of treatment with RGX-104 versus DMSO, sample 08

first: Benjamin

middle: N

last: Ostendorf

institute: Charité University Medicine

description: Library name: 08_tx

data_processing:
Adapter and polyA trimming with BBDuk (v38.9; options k=13, ktrim=r, forcetrimleft=11, useshortkmers=t, mink=5, qtrim=t, trimq=10, minlength=20)
Alignment and read counting with STAR aligner (v2.7.8a; default settings apart from --outFilterMismatchNoverLmax 0.1)
Library size normalization in R v4.1.0 with DESeq2 v1.4
Assembly: GRCm38
Supplementary files format and content: TSV-formatted table with raw gene counts for every gene and every sample

source_name: Naive CD8+ T cells

growth_protocol: Naïve CD8+ T cells were were cultured the presence of DMSO (ctrl) or 2µM RGX-104 for 24 hours.

extract_protocol:
Naïve CD8+ cells were isolated using the MojoSort Mouse CD8 Naïve T Cell Isolation Kit (Biolegend, 480044) and RNA was isolated using the Monarch Total RNA extraction kit (Biolabs, T20105)
Quantseq 3’ mRNA-Seq Library Prep kit (113.96, Lexogen)

treatment_protocol: DMSO versus 2µM RGX-104.

value: Naive CD8+ T cells


title: PBMC_nonBOS_Sam10


title: NPC cells, CRMi003-A, control, vehicle [0.1% DMSO] treated for 6 hours, replicate 1

description:
Library name: NCRM1_DMSO_06A
Column_name in FPKM_joined.tab: FPKM_NCRM1_DMSO_06A

value: 0.1% DMSO for 6 hours


title: liver_day8_Cyclobutrifluram_120ppm_21B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916365_S01_GE1_107_Sep09_2_3


title: NPC cells, CRMi003-A, control, vehicle [0.1% DMSO] treated for 6 hours, replicate 2

description:
Library name: NCRM1_DMSO_06B
Column_name in FPKM_joined.tab: FPKM_NCRM1_DMSO_06B


title: NPC cells, CRMi003-A, control, untreated for 24 hours, replicate 3

description:
Library name: NCRM1_basal_24C
Column_name in FPKM_joined.tab: FPKM_NCRM1_basal_24C

value: no additives for 24 hours


title: liver_day3_Cyclobutrifluram_120ppm_30A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916362_S01_GE1_107_Sep09_2_2

source_name: liver, day3, Cyclobutrifluram, 120ppm


title: NPC cells, CRMi003-A, control, untreated for 24 hours, replicate 2

description:
Library name: NCRM1_basal_24B
Column_name in FPKM_joined.tab: FPKM_NCRM1_basal_24B

value: NPC generated from iPSC


title: NPC cells, CRMi003-A, control, vehicle [0.1% DMSO] treated for 6 hours, replicate 3

description:
Library name: NCRM1_DMSO_06C
Column_name in FPKM_joined.tab: FPKM_NCRM1_DMSO_06C

value: Neuronal precursor cells (NPCs)


title: Naïve CD8+ after 24h of treatment with RGX-104 versus DMSO, sample 07

description: Library name: 07_tx


title: Naïve CD8+ after 24h of treatment with RGX-104 versus DMSO, sample 06

description: Library name: 06_tx


title: Naïve CD8+ after 24h of treatment with RGX-104 versus DMSO, sample 05

description: Library name: 05_tx


title: NPC cells, HHUi002-A, MILS patient, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 2

description:
Library name: TDA3_10um_DRUG_06B
Column_name in FPKM_joined.tab: FPKM_TDA3_10um_DRUG_06B


title: liver_day3_Cyclobutrifluram_120ppm_28A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916129_S01_GE1_107_Sep09_1_4


title: genomic DNA from 3h_4

description: changes of genome-wide DNA methylation at 3hrs in placental trophoblast


title: Naïve CD8+ after 24h of treatment with RGX-104 versus DMSO, sample 04

description: Library name: 04_ctrl

value: control


title: NPC cells, CRMi003-A, control, untreated for 6 hours, replicate 3

description:
Library name: NCRM1_basal_06C
Column_name in FPKM_joined.tab: FPKM_NCRM1_basal_06C

value: wildtype

value: no additives for 6 hours


title: genomic DNA from 48h_1

description: changes of genome-wide DNA methylation at 48hrs in placental trophoblast

value: syncytiotrophoblasts


title: Naïve CD8+ after 24h of treatment with RGX-104 versus DMSO, sample 03

description: Library name: 03_ctrl


title: liver_day3_Cyclobutrifluram_120ppm_29A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916361_S01_GE1_107_Sep09_1_3


title: liver_day3_Cyclobutrifluram_120ppm_26A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916344_S01_GE1_107_Sep09_1_2


title: NPC cells, CRMi003-A, control, untreated for 6 hours, replicate 2

description:
Library name: NCRM1_basal_06B
Column_name in FPKM_joined.tab: FPKM_NCRM1_basal_06B


title: Naïve CD8+ after 24h of treatment with RGX-104 versus DMSO, sample 02

description: Library name: 02_ctrl


title: NPC cells, CRMi003-A, control, untreated for 24 hours, replicate 1

description:
Library name: NCRM1_basal_24A
Column_name in FPKM_joined.tab: FPKM_NCRM1_basal_24A


title: liver_day3_Cyclobutrifluram_120ppm_35A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916342_S01_GE1_107_Sep09_2_3


title: Naïve CD8+ after 24h of treatment with RGX-104 versus DMSO, sample 01

description: Library name: 01_ctrl


title: NPC cells, CRMi003-A, control, untreated for 6 hours, replicate 1

description:
Library name: NCRM1_basal_06A
Column_name in FPKM_joined.tab: FPKM_NCRM1_basal_06A


title: NPC cells, CRMi003-A, control, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 3

description:
Library name: NCRM1_1um_DRUG_24C
Column_name in FPKM_joined.tab: FPKM_NCRM1_1um_DRUG_24C


title: liver_day3_Cyclobutrifluram_120ppm_24A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916341_S01_GE1_107_Sep09_1_4


title: Liver, adult (3 months), H3K27me3, rep2

description: Library name: Adult, liver, H3K27me3, replicate 2

source_name: liver

value: adult (3 months)


title: liver_day3_Cyclobutrifluram_120ppm_27A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916345_S01_GE1_107_Sep09_2_1


title: liver_day3_Cyclobutrifluram_120ppm_23A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916335_S01_GE1_107_Sep09_1_1


title: Liver, adult (3 months), H3K27me3, rep1

description: Library name: Adult, liver, H3K27me3, replicate 1


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

description:
Library name: NCRM1_1um_DRUG_24A
Column_name in FPKM_joined.tab: FPKM_NCRM1_1um_DRUG_24A


title: Liver, embryonic day 16, H3K27me3, rep2

description: Library name: Embryo, liver, H3K27me3, replicate 2


title: liver_day3_Cyclobutrifluram_120ppm_21A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916365_S01_GE1_107_Sep09_1_3


title: NPC cells, CRMi003-A, control, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 3

description:
Library name: NCRM1_1um_DRUG_06C
Column_name in FPKM_joined.tab: FPKM_NCRM1_1um_DRUG_06C


title: liver_day29_PBcontrol_850ppm_20C

description:
liver gene expression after 29 days exposed to PBcontrol 850 ppm
US45102884_257480916364_S01_GE1_107_Sep09_2_2

source_name: liver, day29, PBcontrol, 850ppm

value: phenobarbital


title: Liver, embryonic day 16, H3K27me3, rep1

description: Library name: Embryo, liver, H3K27me3, replicate 1

value: liver


title: NPC cells, CRMi003-A, control, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 2

description:
Library name: NCRM1_1um_DRUG_06B
Column_name in FPKM_joined.tab: FPKM_NCRM1_1um_DRUG_06B


title: Liver, adult (3 months), H3K27ac, rep2

description: Library name: Adult, liver, H3K27ac, replicate 2


title: liver_day29_PBcontrol_850ppm_19C

description:
liver gene expression after 29 days exposed to PBcontrol 850 ppm
US45102884_257480916363_S01_GE1_107_Sep09_2_4

value: male


title: NPC cells, CRMi003-A, control, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 1

description:
Library name: NCRM1_1um_DRUG_06A
Column_name in FPKM_joined.tab: FPKM_NCRM1_1um_DRUG_06A


title: PBMC_BOS_Sam29


title: liver_day3_Cyclobutrifluram_120ppm_22A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916330_S01_GE1_107_Sep09_2_2

value: cyclobutrifluram


title: Liver, adult (3 months), H3K27ac, rep1

description: Library name: Adult, liver, H3K27ac, replicate 1


title: PBMC_nonBOS_Sam5


title: PBMC_nonBOS_Sam4


title: PBMC_nonBOS_Sam2


title: liver_day29_PBcontrol_850ppm_18C

description:
liver gene expression after 29 days exposed to PBcontrol 850 ppm
US45102884_257480916354_S01_GE1_107_Sep09_2_1


title: PBMC_nonBOS_Sam1


title: Liver, embryonic day 16, H3K27ac, rep2

description: Library name: Embryo, liver, H3K27ac, replicate 2

value: embryonic day 16


title: liver_day29_PBcontrol_850ppm_17C

description:
liver gene expression after 29 days exposed to PBcontrol 850 ppm
US45102884_257480916353_S01_GE1_107_Sep09_1_2


title: PBMC_BOS_Sam28

value: lung transplant recipient

value: Female


title: Liver, embryonic day 16, H3K27ac, rep1

description: Library name: Embryo, liver, H3K27ac, replicate 1


title: PBMC_nonBOS_Sam3

value: Male


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

description:
Library name: NCRM1_10um_DRUG_24A
Column_name in FPKM_joined.tab: FPKM_NCRM1_10um_DRUG_24A


title: PBMC_BOS_Sam27


title: NPC cells, CRMi003-A, control, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 2

description:
Library name: NCRM1_1um_DRUG_24B
Column_name in FPKM_joined.tab: FPKM_NCRM1_1um_DRUG_24B


title: PBMC_BOS_Sam30


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

description:
Library name: NCRM1_10um_DRUG_24C
Column_name in FPKM_joined.tab: FPKM_NCRM1_10um_DRUG_24C


title: liver_day29_PBcontrol_850ppm_16C

description:
liver gene expression after 29 days exposed to PBcontrol 850 ppm
US45102884_257480916346_S01_GE1_107_Sep09_2_3


title: PBMC_BOS_Sam24


title: PBMC_nonBOS_Sam13


title: Liver, adult (3 months), H3K9ac, rep2

description: Library name: Adult, liver, H3K9ac, replicate 2


title: PBMC_BOS_Sam26


title: PBMC_BOS_Sam20


title: PBMC_BOS_Sam25


title: liver_day29_PBcontrol_850ppm_15C

description:
liver gene expression after 29 days exposed to PBcontrol 850 ppm
US45102884_257480916345_S01_GE1_107_Sep09_1_4


title: PBMC_BOS_Sam19


title: Liver, adult (3 months), H3K9ac, rep1

description: Library name: Adult, liver, H3K9ac, replicate 1


title: NPC cells, CRMi003-A, control, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 3

description:
Library name: NCRM1_10um_DRUG_06C
Column_name in FPKM_joined.tab: FPKM_NCRM1_10um_DRUG_06C


title: PBMC_BOS_Sam21


title: PBMC_BOS_Sam18


title: liver_day29_PBcontrol_850ppm_14C

description:
liver gene expression after 29 days exposed to PBcontrol 850 ppm
US45102884_257480916342_S01_GE1_107_Sep09_1_1


title: PBMC_BOS_Sam22


title: NPC cells, CRMi003-A, control, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 2

description:
Library name: NCRM1_10um_DRUG_06B
Column_name in FPKM_joined.tab: FPKM_NCRM1_10um_DRUG_06B


title: Liver, embryonic day 16, H3K9ac, rep2

description: Library name: Embryo, liver, H3K9ac, replicate 2


title: liver_day29_PBcontrol_850ppm_13C

description:
liver gene expression after 29 days exposed to PBcontrol 850 ppm
US45102884_257480916337_S01_GE1_107_Sep09_2_2


title: NPC cells, CRMi003-A, control, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 1

description:
Library name: NCRM1_10um_DRUG_06A
Column_name in FPKM_joined.tab: FPKM_NCRM1_10um_DRUG_06A


title: Liver, embryonic day 16, H3K9ac, rep1

description: Library name: Embryo, liver, H3K9ac, replicate 1


title: PBMC_BOS_Sam16


title: PBMC_BOS_Sam23


title: Liver, adult (3 months), H3K4me3, rep2

description: Library name: Adult, liver, H3K4me3, replicate 2


title: liver_day29_PBcontrol_850ppm_12C

description:
liver gene expression after 29 days exposed to PBcontrol 850 ppm
US45102884_257480916336_S01_GE1_107_Sep09_1_3


title: PBMC_BOS_Sam17


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


title: liver_day29_PBcontrol_850ppm_11C

description:
liver gene expression after 29 days exposed to PBcontrol 850 ppm
US45102884_257480916366_S01_GE1_107_Sep09_2_4


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

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

value: NPC generated from iPSC


title: PBMC_BOS_Sam15


title: Liver, adult (3 months), H3K4me3, rep1

description: Library name: Adult, liver, H3K4me3, replicate 1


title: Liver, embryonic day 16, H3K4me3, rep2

description: Library name: Embryo, liver, H3K4me3, replicate 2


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

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

value: Neuronal precursor cells (NPCs)


title: liver_day8_PBcontrol_850ppm_20B

description:
liver gene expression after 8 days exposed to PBcontrol 850 ppm
US45102884_257480916364_S01_GE1_107_Sep09_2_3

source_name: liver, day8, PBcontrol, 850ppm


title: NPC cells, MDCi009-A, MILS patient, vehicle [0.1% DMSO] treated for 6 hours, replicate 3

description:
Library name: C11_DMSO_06C
Column_name in FPKM_joined.tab: FPKM_C11_DMSO_06C

value: 0.1% DMSO for 6 hours


title: Liver, embryonic day 16, H3K4me3, rep1

description: Library name: Embryo, liver, H3K4me3, replicate 1


title: liver_day8_PBcontrol_850ppm_18B

description:
liver gene expression after 8 days exposed to PBcontrol 850 ppm
US45102884_257480916354_S01_GE1_107_Sep09_1_1


title: liver_day8_PBcontrol_850ppm_19B

description:
liver gene expression after 8 days exposed to PBcontrol 850 ppm
US45102884_257480916363_S01_GE1_107_Sep09_1_4


title: NPC cells, MDCi009-A, MILS patient, vehicle [0.1% DMSO] treated for 6 hours, replicate 2

description:
Library name: C11_DMSO_06B
Column_name in FPKM_joined.tab: FPKM_C11_DMSO_06B


title: NPC cells, MDCi009-A, MILS patient, vehicle [0.1% DMSO] treated for 6 hours, replicate 1

description:
Library name: C11_DMSO_06A
Column_name in FPKM_joined.tab: FPKM_C11_DMSO_06A


title: Kidney, adult (3 months), H3K27me3, rep1

description: Library name: Adult, kidney, H3K27me3, replicate 1

source_name: kidney

value: kidney


title: liver_day8_PBcontrol_850ppm_16B

description:
liver gene expression after 8 days exposed to PBcontrol 850 ppm
US45102884_257480916346_S01_GE1_107_Sep09_1_3


title: NPC cells, MDCi009-A, MILS patient, untreated for 24 hours, replicate 3

description:
Library name: C11_basal_24C
Column_name in FPKM_joined.tab: FPKM_C11_basal_24C

value: no additives for 24 hours


title: Kidney, embryonic day 16, H3K27me3, rep2

description: Library name: Embryo, kidney, H3K27me3, replicate 2


title: liver_day8_PBcontrol_850ppm_15B

description:
liver gene expression after 8 days exposed to PBcontrol 850 ppm
US45102884_257480915114_S01_GE1_107_Sep09_2_3


title: NPC cells, MDCi009-A, MILS patient, untreated for 24 hours, replicate 2

description:
Library name: C11_basal_24B
Column_name in FPKM_joined.tab: FPKM_C11_basal_24B


title: Kidney, embryonic day 16, H3K27me3, rep1

description: Library name: Embryo, kidney, H3K27me3, replicate 1


title: NPC cells, MDCi009-A, MILS patient, untreated for 24 hours, replicate 1

description:
Library name: C11_basal_24A
Column_name in FPKM_joined.tab: FPKM_C11_basal_24A


title: liver_day8_PBcontrol_850ppm_14B

description:
liver gene expression after 8 days exposed to PBcontrol 850 ppm
US45102884_257480916129_S01_GE1_107_Sep09_1_3


title: Kidney, adult (3 months), H3K27ac, rep2

description: Library name: Adult, kidney, H3K27ac, replicate 2


title: liver_day8_PBcontrol_850ppm_13B

description:
liver gene expression after 8 days exposed to PBcontrol 850 ppm
US45102884_257480916337_S01_GE1_107_Sep09_1_2


title: PBMC_BOS_Sam14


title: Kidney, adult (3 months), H3K27me3, rep2

description: Library name: Adult, kidney, H3K27me3, replicate 2


title: liver_day8_PBcontrol_850ppm_17B

description:
liver gene expression after 8 days exposed to PBcontrol 850 ppm
US45102884_257480916352_S01_GE1_107_Sep09_2_2


title: liver_day8_PBcontrol_850ppm_12B

description:
liver gene expression after 8 days exposed to PBcontrol 850 ppm
US45102884_257480916335_S01_GE1_107_Sep09_2_3


title: Kidney, adult (3 months), H3K27ac, rep1

description: Library name: Adult, kidney, H3K27ac, replicate 1


title: NPC cells, MDCi009-A, MILS patient, untreated for 6 hours, replicate 2

description:
Library name: C11_basal_06B
Column_name in FPKM_joined.tab: FPKM_C11_basal_06B

value: no additives for 6 hours


title: PBMC_BOS_Sam11


title: PBMC_BOS_Sam12


title: PBMC_BOS_Sam10


title: PBMC_BOS_Sam6


title: PBMC_BOS_Sam8


title: PBMC_BOS_Sam9


title: liver_day8_PBcontrol_850ppm_11B

description:
liver gene expression after 8 days exposed to PBcontrol 850 ppm
US45102884_257480916366_S01_GE1_107_Sep09_1_4


title: PBMC_BOS_Sam4


title: NPC cells, MDCi009-A, MILS patient, untreated for 6 hours, replicate 1

description:
Library name: C11_basal_06A
Column_name in FPKM_joined.tab: FPKM_C11_basal_06A


title: PBMC_BOS_Sam7


title: liver_day3_PBcontrol_850ppm_20A

description:
liver gene expression after 3 days exposed to PBcontrol 850 ppm
US45102884_257480915114_S01_GE1_107_Sep09_1_4

source_name: liver, day3, PBcontrol, 850ppm


title: PBMC_BOS_Sam5


title: Kidney, adult (3 months), H3K9ac, rep2

description: Library name: Adult, kidney, H3K9ac, replicate 2

value: adult (3 months)


title: NPC cells, MDCi009-A, MILS patient, untreated for 6 hours, replicate 3

description:
Library name: C11_basal_06C
Column_name in FPKM_joined.tab: FPKM_C11_basal_06C


title: liver_day3_PBcontrol_850ppm_19A

description:
liver gene expression after 3 days exposed to PBcontrol 850 ppm
US45102884_257480916362_S01_GE1_107_Sep09_2_4

value: phenobarbital


title: NPC cells, MDCi009-A, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 2

description:
Library name: C11_1um_DRUG_24B
Column_name in FPKM_joined.tab: FPKM_C11_1um_DRUG_24B


title: liver_day3_PBcontrol_850ppm_18A

description:
liver gene expression after 3 days exposed to PBcontrol 850 ppm
US45102884_257480916353_S01_GE1_107_Sep09_2_1

value: liver


title: MTX_150_BR2TR2

city: Syracuse

first: Wenyi

last: Feng

state: NY

address: 750 East Adams Street

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

description:
MTX_150_BR2TR2 denotes BR2TR2 RNA-seq sample treated with 150 µg/mL MTX
MTX_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.

data_processing:
alignment by Bowtie2, reads per transcript calculated using featureCounts
Assembly: sacCer3
Supplementary files format and content: DESeq2results

organism: Saccharomyces cerevisiae

growth_protocol: WT yeast cells from the W303 background were grown either in YEPD or SC media at 30 °C.

extract_protocol:
10 mL cell pellet stored -80 ºC  RNA was using hot phenol method
Library construction and sequencing on the isolated RNA was performed by the SUNY Molecular Analysis Core.

treatment_protocol: Cells were grown to an OD~0.3 before addition of either the replication inhibitor or vehicle control.  Post addition of the either,  the cells were continued to grow for the determined IC50 timepoint prior to harvesting.

tag: strain

value: WT

tag: background

tag: media

value: SC

value: MTX

tag: technical replicate


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

description:
Library name: C11_1um_DRUG_24A
Column_name in FPKM_joined.tab: FPKM_C11_1um_DRUG_24A

tag: tissue


title: Kidney, adult (3 months), H3K9ac, rep1

description: Library name: Adult, kidney, H3K9ac, replicate 1


title: MTX_150_BR2TR1

description:
MTX_150_BR2TR1 denotes BR2TR1 RNA-seq sample treated with 150 µg/mL MTX
MTX_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: Kidney, embryonic day 16, H3K9ac, rep2

description: Library name: Embryo, kidney, H3K9ac, replicate 2

value: embryonic day 16


title: PBMC_BOS_Sam13

value: lung transplant recipient

value: Female


title: Kidney, embryonic day 16, H3K27ac, rep2

description: Library name: Embryo, kidney, H3K27ac, replicate 2


title: liver_day3_PBcontrol_850ppm_17A

description:
liver gene expression after 3 days exposed to PBcontrol 850 ppm
US45102884_257480916352_S01_GE1_107_Sep09_1_2

value: male


title: Kidney, embryonic day 16, H3K27ac, rep1

description: Library name: Embryo, kidney, H3K27ac, replicate 1


title: NPC cells, MDCi009-A, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 3

description:
Library name: C11_1um_DRUG_24C
Column_name in FPKM_joined.tab: FPKM_C11_1um_DRUG_24C

tag: cell line

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


title: MTX_150_BR1TR2

description:
MTX_150_BR1TR2 denotes BR1TR2 RNA-seq sample treated with 150 µg/mL MTX
MTX_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: liver_day3_PBcontrol_850ppm_16A

description:
liver gene expression after 3 days exposed to PBcontrol 850 ppm
US45102884_257480916345_S01_GE1_107_Sep09_2_3


title: NPC cells, MDCi009-A, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 2

description:
Library name: C11_1um_DRUG_06B
Column_name in FPKM_joined.tab: FPKM_C11_1um_DRUG_06B

value: NPC generated from iPSC

tag: cell type


title: MTX_150_BR1TR1

description:
MTX_150_BR1TR1 denotes BR1TR1 RNA-seq sample treated with 150 µg/mL MTX
MTX_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: NPC cells, MDCi009-A, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 1

description:
Library name: C11_1um_DRUG_06A
Column_name in FPKM_joined.tab: FPKM_C11_1um_DRUG_06A

value: Neuronal precursor cells (NPCs)

tag: genotype


title: Kidney, adult (3 months), H3K4me3, rep2

description: Library name: Adult, kidney, H3K4me3, replicate 2


title: CM_BR2TR2

description:
CM_BR2TR2 denotes BR2TR1 RNA-seq sample treated with 0.1N NAOH (Control for MTX)
CM_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.

source_name: CM

tag: treatment

value: 0.1N NaOH


title: Kidney, adult (3 months), H3K4me3, rep1

description: Library name: Adult, kidney, H3K4me3, replicate 1

value: kidney


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

description:
Library name: C11_10um_DRUG_24C
Column_name in FPKM_joined.tab: FPKM_C11_10um_DRUG_24C

tag: biological replicate


title: liver_day3_PBcontrol_850ppm_14A

description:
liver gene expression after 3 days exposed to PBcontrol 850 ppm
US45102884_257480916341_S01_GE1_107_Sep09_1_1


title: CM_BR2TR1

description:
CM_BR2TR1 denotes BR2TR1 RNA-seq sample treated with 0.1N NAOH (Control for MTX)
CM_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: liver_day3_PBcontrol_850ppm_13A

description:
liver gene expression after 3 days exposed to PBcontrol 850 ppm
US45102884_257480916336_S01_GE1_107_Sep09_2_2


title: Kidney, embryonic day 16, H3K4me3, rep2

description: Library name: Embryo, kidney, H3K4me3, replicate 2

tag: developmental timepoint


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

description:
Library name: C11_10um_DRUG_24B
Column_name in FPKM_joined.tab: FPKM_C11_10um_DRUG_24B


title: Kidney, embryonic day 16, H3K4me3, rep1

description: Library name: Embryo, kidney, H3K4me3, replicate 1

tag: antibody


title: CM_BR1TR2_

description:
CM_BR1TR2 denotes BR1TR2 RNA-seq sample treated with 0.1N NAOH (Control for MTX)
CM_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: liver_day3_PBcontrol_850ppm_12A

description:
liver gene expression after 3 days exposed to PBcontrol 850 ppm
US45102884_257480916335_S01_GE1_107_Sep09_1_3

tag: gender


title: NPC cells, MDCi009-A, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 3

description:
Library name: C11_1um_DRUG_06C
Column_name in FPKM_joined.tab: FPKM_C11_1um_DRUG_06C


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

description:
Library name: C11_10um_DRUG_24A
Column_name in FPKM_joined.tab: FPKM_C11_10um_DRUG_24A


title: CM_BR1TR1

description:
CM_BR1TR1 denotes BR1TR1 RNA-seq sample treated with 0.1N NAOH (Control for MTX)
CM_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: PBMC_BOS_Sam3

value: Male


title: Brain, adult (3 months), H3K27me3, rep2

description: Library name: Adult, brain, H3K27me3, replicate 2

value: brain


title: liver_day3_PBcontrol_850ppm_11A

description:
liver gene expression after 3 days exposed to PBcontrol 850 ppm
US45102884_257480916330_S01_GE1_107_Sep09_2_4

tag: dose (ppm)


title: Kidney, embryonic day 16, H3K9ac, rep1

description: Library name: Embryo, kidney, H3K9ac, replicate 1


title: PBMC_BOS_Sam2


title: DOX_25_BR2TR2

description:
DOX_25_BR2TR2 denotes BR2TR2 RNA-seq sample treated with 25 µg/mL DOX
DOX_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.

value: DOX


title: liver_day3_PBcontrol_850ppm_15A

description:
liver gene expression after 3 days exposed to PBcontrol 850 ppm
US45102884_257480916344_S01_GE1_107_Sep09_1_4

value: phenobarbital

tag: duration (days)


title: NPC cells, MDCi009-A, MILS patient, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 2

description:
Library name: C11_10um_DRUG_06B
Column_name in FPKM_joined.tab: FPKM_C11_10um_DRUG_06B


title: PBMC_BOS_Sam1

tag: recipient


title: DOX_25_BR2TR1

description:
DOX_25_BR2TR1 denotes BR2TR1 RNA-seq sample treated with 25 µg/mL DOX
DOX_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: Brain, embryonic day 16, H3K27me3, rep2

description: Library name: Embryo, brain, H3K27me3, replicate 2


title: NPC cells, MDCi009-A, MILS patient, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 1

description:
Library name: C11_10um_DRUG_06A
Column_name in FPKM_joined.tab: FPKM_C11_10um_DRUG_06A


title: DOX_25_BR1TR2

description:
DOX_25_BR1TR2 denotes BR1TR2 RNA-seq sample treated with 25 µg/mL DOX
DOX_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: Brain, embryonic day 16, H3K27me3, rep1

description: Library name: Embryo, brain, H3K27me3, replicate 1


title: NPC cells, MDCi008-A, MILS patient, vehicle [0.1% DMSO] treated for 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%)

value: 0.1% DMSO for 24 hours


title: Brain, adult (3 months), H3K27ac, rep2

description: Library name: Adult, brain, H3K27ac, replicate 2

value: adult (3 months)


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

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


title: DOX_25_BR1TR1

description:
DOX_25_BR1TR1 denotes BR1TR1 RNA-seq sample treated with 25 µg/mL DOX
DOX_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.

value: WT

value: SC


title: liver_day29_control_0ppm_7C

description:
liver gene expression after 29 days exposed to control 0 ppm
US45102884_257480916346_S01_GE1_107_Sep09_2_2

source_name: liver, day29, control, 0ppm

value: liver

value: control


title: CD_BR2TR2

description:
CD_BR2TR2 denotes BR2TR2 RNA-seq sample treated with AgD H2O (Control for DOX)
CD_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.

source_name: CD


title: NPC cells, MDCi009-A, MILS patient, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 3

description:
Library name: C11_10um_DRUG_06C
Column_name in FPKM_joined.tab: FPKM_C11_10um_DRUG_06C


title: Brain, adult (3 months), H3K27ac, rep1

description: Library name: Adult, brain, H3K27ac, replicate 1


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

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


title: liver_day29_control_0ppm_6C

description:
liver gene expression after 29 days exposed to control 0 ppm
US45102884_257480915114_S01_GE1_107_Sep09_2_1

value: male


title: NPC cells, MDCi008-A, MILS patient, vehicle [0.1% DMSO] treated for 6 hours, replicate 3

description:
Library name: B12_DMSO_06C
Column_name in FPKM_joined.tab: FPKM_B12_DMSO_06C

value: 0.1% DMSO for 6 hours


title: Brain, embryonic day 16, H3K27ac, rep2

description: Library name: Embryo, brain, H3K27ac, replicate 2

value: embryonic day 16


title: Brain, adult (3 months), H3K27me3, rep1

description: Library name: Adult, brain, H3K27me3, replicate 1


title: liver_day29_control_0ppm_5C

description:
liver gene expression after 29 days exposed to control 0 ppm
US45102884_257480916343_S01_GE1_107_Sep09_2_4


title: CD_BR1TR2

description:
CD_BR1TR2 denotes BR1TR2 RNA-seq sample treated with AgD H2O (Control for DOX)
CD_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: CD_BR2TR1

description:
CD_BR2TR1 denotes BR2TR1 RNA-seq sample treated with AgD H2O (Control for DOX)
CD_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: liver_day29_control_0ppm_10C

description:
liver gene expression after 29 days exposed to control 0 ppm
US45102884_257480916363_S01_GE1_107_Sep09_2_3


title: liver_day29_control_0ppm_4C

description:
liver gene expression after 29 days exposed to control 0 ppm
US45102884_257480916337_S01_GE1_107_Sep09_2_1


title: Brain, embryonic day 16, H3K27ac, rep1

description: Library name: Embryo, brain, H3K27ac, replicate 1


title: Brain, adult (3 months), H3K9ac, rep2

description: Library name: Adult, brain, H3K9ac, replicate 2


title: liver_day29_control_0ppm_9C

description:
liver gene expression after 29 days exposed to control 0 ppm
US45102884_257480916362_S01_GE1_107_Sep09_1_4


title: NPC cells, MDCi008-A, MILS patient, vehicle [0.1% DMSO] treated for 6 hours, replicate 2

description:
Library name: B12_DMSO_06B
Column_name in FPKM_joined.tab: FPKM_B12_DMSO_06B

value: NPC generated from iPSC

value: Neuronal precursor cells (NPCs)


title: liver_day29_control_0ppm_3C

description:
liver gene expression after 29 days exposed to control 0 ppm
US45102884_257480916129_S01_GE1_107_Sep09_1_1


title: NPC cells, MDCi008-A, MILS patient, vehicle [0.1% DMSO] treated for 6 hours, replicate 1

description:
Library name: B12_DMSO_06A
Column_name in FPKM_joined.tab: FPKM_B12_DMSO_06A


title: liver_day29_control_0ppm_8C

description:
liver gene expression after 29 days exposed to control 0 ppm
US45102884_257480916353_S01_GE1_107_Sep09_1_1


title: Brain, adult (3 months), H3K9ac, rep1

description: Library name: Adult, brain, H3K9ac, replicate 1


title: liver_day29_control_0ppm_2C

description:
liver gene expression after 29 days exposed to control 0 ppm
US45102884_257480916366_S01_GE1_107_Sep09_2_3


title: NPC cells, MDCi008-A, MILS patient, untreated for 24 hours, replicate 3

description:
Library name: B12_basal_24C
Column_name in FPKM_joined.tab: FPKM_B12_basal_24C

value: no additives for 24 hours


title: Brain, embryonic day 16, H3K9ac, rep2

description: Library name: Embryo, brain, H3K9ac, replicate 2


title: liver_day29_control_0ppm_1C

description:
liver gene expression after 29 days exposed to control 0 ppm
US45102884_257480916364_S01_GE1_107_Sep09_1_1


title: NPC cells, MDCi008-A, MILS patient, untreated for 24 hours, replicate 2

description:
Library name: B12_basal_24B
Column_name in FPKM_joined.tab: FPKM_B12_basal_24B


title: Brain, embryonic day 16, H3K9ac, rep1

description: Library name: Embryo, brain, H3K9ac, replicate 1


title: AD_50_BR1TR2

description:
AD_50_BR1TR2 denotes BR1TR2 RNA-seq sample treated with 50 µg/mL AD
AD_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.

value: AD


title: liver_day8_control_0ppm_9B

description:
liver gene expression after 8 days exposed to control 0 ppm
US45102884_257480916361_S01_GE1_107_Sep09_2_4

source_name: liver, day8, control, 0ppm


title: liver_day8_control_0ppm_10B

description:
liver gene expression after 8 days exposed to control 0 ppm
US45102884_257480916363_S01_GE1_107_Sep09_1_3


title: Brain, adult (3 months), H3K4me3, rep2

description: Library name: Adult, brain, H3K4me3, replicate 2

value: brain


title: NPC cells, MDCi008-A, MILS patient, untreated for 24 hours, replicate 1

description:
Library name: B12_basal_24A
Column_name in FPKM_joined.tab: FPKM_B12_basal_24A


title: CA_BR2TR2

description:
CA_BR2TR2 denotes BR2TR2 RNA-seq sampletreated with 2%  acetone as solvent
CA_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.

source_name: CA

value: 2% Acetone


title: Brain, adult (3 months), H3K4me3, rep1

description: Library name: Adult, brain, H3K4me3, replicate 1


title: liver_day8_control_0ppm_8B

description:
liver gene expression after 8 days exposed to control 0 ppm
US45102884_257480916352_S01_GE1_107_Sep09_2_1


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

description:
Library name: NCRM1_10um_DRUG_24B
Column_name in FPKM_joined.tab: FPKM_NCRM1_10um_DRUG_24B

source_name: NPC generated from iPSC

value: wildtype


title: NPC cells, MDCi008-A, MILS patient, untreated for 6 hours, replicate 2

description:
Library name: B12_basal_06B
Column_name in FPKM_joined.tab: FPKM_B12_basal_06B

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

value: no additives for 6 hours


title: CD_BR1TR1

description:
CD_BR1TR1 denotes BR1TR1 RNA-seq sample treated with AgD H2O (Control for DOX)
CD_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: Brain, embryonic day 16, H3K4me3, rep2

description: Library name: Embryo, brain, H3K4me3, replicate 2


title: CA_BR2TR1

description:
CA_BR2TR1 denotes BR2TR1 RNA-seq sampletreated with 2%  acetone as solvent
CA_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: AD_50_BR2TR2

description:
AD_50_BR2TR2 denotes BR2TR2 RNA-seq sample treated with 50 µg/mL AD
AD_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: liver_day8_control_0ppm_7B

description:
liver gene expression after 8 days exposed to control 0 ppm
US45102884_257480916346_S01_GE1_107_Sep09_1_2


title: Brain, embryonic day 16, H3K4me3, rep1

description: Library name: Embryo, brain, H3K4me3, replicate 1


title: NPC cells, MDCi008-A, MILS patient, untreated for 6 hours, replicate 1

description:
Library name: B12_basal_06A
Column_name in FPKM_joined.tab: FPKM_B12_basal_06A


title: CA_BR1TR2

description:
CA_BR1TR2 denotes BR1TR2 RNA-seq sampletreated with 2%  acetone as solvent
CA_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: liver_day8_control_0ppm_6B

description:
liver gene expression after 8 days exposed to control 0 ppm
US45102884_257480916344_S01_GE1_107_Sep09_2_3


title: NPC cells, MDCi008-A, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 3

description:
Library name: B12_1um_DRUG_24C
Column_name in FPKM_joined.tab: FPKM_B12_1um_DRUG_24C


title: CA_BR1TR1

description:
CA_BR1TR1 denotes BR1TR1 RNA-seq sampletreated with 2%  acetone as solvent
CA_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: AD_50_BR2TR1

description:
AD_50_BR2TR1 denotes BR2TR1 RNA-seq sample treated with 50 µg/mL AD
AD_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: liver_day8_control_0ppm_5B

description:
liver gene expression after 8 days exposed to control 0 ppm
US45102884_257480916129_S01_GE1_107_Sep09_2_4


title: CPT_100_BR2TR2

description:
CPT_100_BR2TR2 denotes BR2TR2 RNA-seq sample treated with 100µg/mL CPT
CPT_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.

value: YEPD

value: CPT


title: liver_day8_control_0ppm_4B

description:
liver gene expression after 8 days exposed to control 0 ppm
US45102884_257480916337_S01_GE1_107_Sep09_1_1


title: AD_50_BR1TR1

description:
AD_50_BR1TR1 denotes BR1TR1 RNA-seq sample treated with 50 µg/mL AD
AD_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.

value: WT

value: SC


title: NPC cells, MDCi008-A, MILS patient, untreated for 6 hours, replicate 3

description:
Library name: B12_basal_06C
Column_name in FPKM_joined.tab: FPKM_B12_basal_06C


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

description:
Library name: B12_1um_DRUG_24A
Column_name in FPKM_joined.tab: FPKM_B12_1um_DRUG_24A


title: total RNAseq in Klf9KI hearts from 4weeks old mice, n=3

city: Newark

first: Danish

last: Sayed

state: NJ

address: 185 south orange avenue

department: CBMM

institute: Rutgers-NJMS

description: Library name: Klf9KI (4weeks)

data_processing:
ChIP-Seq: Sequence analysis – 75-nt sequence generated by sequencing reads were mapped to the genome using BWA algorithm, and the information stored in BAM format. Only reads which align with no more than two mismatches and map uniquely are used in analysis. Peak Finding – Genomic regions with enrichments in tag numbers are termed ‘intervals', and defined by the chromosome number, start and end coordinate. 24237848 normalized tags were used for peak calling using MACS 2.1.0 algorithm with default cutoff p value 1e-7. Peak filtering was performed by removing false ChIP-Seq peaks as defined within the ENCODE blacklist. Merged region analysis – To compare peak metrics between two samples, overlapping Intervals are grouped into ‘Merged Regions', which are defined by start coordinate of the most upstream interval and end coordinate of the most downstream interval (=union of overlapping intervals; “merged peaks”). In locations where only one sample has an interval, this interval defines Merged Region. The MaxTags filter out the regions with low signal values, which are expected to be more variable and therefore lead to unreliable, often exaggerated ratios. To calculate the maximum number of tags (reads) multiply the average value of the tag per sample with the length of the regions and divide by constant 224. The 224 value represents the average length of the sequenced fragment in base pairs.
RNAseq:- Sequenced reads were processed through fastp software to remove possible adapter sequences and nucleotides with poor quality to obtain clean reads. Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. Alignment information for each read was stored in the BAM format. The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Distribution of read counts in libraries was examined before and after normalization. The original read counts were normalized to adjust for various factors such as variations of sequencing yield between samples. These normalized read counts were used to accurately determine differentially expressed genes using DESeq2 R package (1.20.0). Log2 fold change between the groups was calculated and the Wald test was used to determine statistical significance (p-value). Adjusted p values were calculated using Benjamini-Hochberg procedure.
Assembly: mm10
Supplementary files format and content: Klf9-ChIP-Seq: Excel sheet with merged regions, MaxTags
Supplementary files format and content: RNAseq: Excel sheet with all comparisons

source_name: heart

extract_protocol:
Mice were saced and hearts were snapped forzen in liquid nitorgen and sent to Active Motif, Inc for processing and Klf9-ChIP-Seq. For RNAseq, hearts were extracted from Wt-Cre (control) and Klf9KI mice and send for RNA extraction and RNAseq to Novogene, Inc
library construction for ChIP-seq was performed by Active motif, InC. RNAseq libraries were prepared by Novogene. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non-strand specific library or dUTP for strand specific library. These libraries were ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The libraries were checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: ChIP-Seq: Mice were subjected to sham ot Transconstrictive operations (TAC) for 2wks

value: heart

value: alphaMHC-Cre +Klf9KI( Tg)


title: total RNAseq in Klf9KI hearts from 8week old mice, n=3

description: Library name: Klf9KI (8week


title: NPC cells, MDCi008-A, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 2

description:
Library name: B12_1um_DRUG_24B
Column_name in FPKM_joined.tab: FPKM_B12_1um_DRUG_24B


title: CPT_100_BR2TR1

description:
CPT_100_BR2TR1 denotes BR2TR1 RNA-seq sample treated with 100µg/mL CPT
CPT_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: CPT_100_BR1TR2

description:
CPT_100_BR1TR2 denotes BR1TR2 RNA-seq sample treated with 100µg/mL CPT
CPT_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: total RNAseq in Wt-Cre hearts from 8weeks old mice, n=3

description: Library name: Wt-Cre (8weeks)

value: alphaMHC-Cre (Wt-control)


title: total RNAseq in Klf9KI hearts from 1week old mice, n=3

description: Library name: Klf9KI (1week)


title: NPC cells, MDCi008-A, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 3

description:
Library name: B12_1um_DRUG_06C
Column_name in FPKM_joined.tab: FPKM_B12_1um_DRUG_06C


title: liver_day8_control_0ppm_2B

description:
liver gene expression after 8 days exposed to control 0 ppm
US45102884_257480916366_S01_GE1_107_Sep09_1_3

value: liver

value: male

value: control


title: CPT_100_BR1TR1

description:
CPT_100_BR1TR1 denotes BR1TR1 RNA-seq sample treated with 100µg/mL CPT
CPT_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: liver_day8_control_0ppm_1B

description:
liver gene expression after 8 days exposed to control 0 ppm
US45102884_257480916365_S01_GE1_107_Sep09_2_4


title: total RNAseq in Wt-Cre hearts from 4weeks old mice, n=3

description: Library name: Wt-Cre (4weeks)


title: NPC cells, MDCi008-A, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 2

description:
Library name: B12_1um_DRUG_06B
Column_name in FPKM_joined.tab: FPKM_B12_1um_DRUG_06B

value: NPC generated from iPSC

value: Neuronal precursor cells (NPCs)


title: CC_BR2TR2

description:
CC_BR2TR2 denotes BR2TR2 RNA-seq sample treated with 1N NAOH (Control for CPT)
CC_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.

source_name: CC

value: 1N NaoH


title: total RNAseq in Wt-Cre hearts from 1week old mice, n=3

description: Library name: Wt-Cre (1week)


title: liver_day3_control_0ppm_10A

description:
liver gene expression after 3 days exposed to control 0 ppm
US45102884_257480916362_S01_GE1_107_Sep09_2_3

source_name: liver, day3, control, 0ppm


title: NPC cells, MDCi008-A, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 1

description:
Library name: B12_1um_DRUG_06A
Column_name in FPKM_joined.tab: FPKM_B12_1um_DRUG_06A


title: CC_BR2TR1

description:
CC_BR2TR1 denotes BR2TR1 RNA-seq sample treated with 1N NAOH (Control for CPT)
CC_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


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

description:
Library name: B12_10um_DRUG_24C
Column_name in FPKM_joined.tab: FPKM_B12_10um_DRUG_24C


title: Cerebellum synaptosome PostNB, replicate 9

city: Urbana

first: Boxuan

last: Zhao

state: IL

address: 505 S Goodwin Ave

institute: UIUC

description:
Library name: cseq36 Syn_Post_nb
cseq36_Spost
single-synaptosome RNA-seq (ssRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode
Since only the neuronal barcodes, and not the mRNA, were sequenced for the synaptosomes, the feature.tsv files for the ssRNA-seq samples are empty.

library_source: other

data_processing:
Raw sequencing data was processed using Cell Ranger (v7.1.0) with custom genome references including SynBar and Cre genes. Nuclear libraries were processed using force-cells parameter of actual loaded amount, while synaptosomal libraries used expect-cells parameter of actual loaded amount. Barcode sequences were extracted from filtered nuclear and unfiltered synaptosomal BAM files using custom Python scripts. Sequences were collapsed using Hamming distance 1 within samples to account for sequencing errors.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

molecule: other

source_name: Cerebellum

extract_protocol:
After perfusion with ice-cold PBS, target brain regions (right one-third cerebellum or bilateral pons) were dissected, homogenized in SET buffer (sucrose, Tris-HCl, EDTA, protease and RNase inhibitors), and centrifuged to separate nuclear (P1) and synaptosomal (S1) fractions. Nuclei were isolated from P1 by brief rinsing and resuspension in nuclear lysis buffer, followed by homogenization (cerebellum) or gentle mixing (pons), dilution, incubation on ice, filtration, centrifugation, washing, and staining with SiR-DNA in washing and staining buffer prior to flow cytometry. Synaptosomes were isolated from S1 by centrifugation to obtain synaptosomal pellet (P2), which was resuspended in washing and staining buffer, blocked with Fc receptor blocker, stained with anti-V5-Alexa Fluor 647 and anti-HA-PE antibodies, washed, and incubated with CellBrite 405 membrane dye. Nuclei were sorted by DNA content (SiR-DNA) and GFP expression, while synaptosomes were sorted based on scatter profiles, membrane integrity (CellBrite 405), and double-positivity for V5 and HA, and all sorted samples were collected into tubes containing appropriate collection buffers for downstream processing.
Libraries were generated using the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1, Chromium Next GEM Chip G, and 10x Chromium Controller (10x Genomics) according to manufacturer's protocol with modifications. For each experiment, approximately 20,000-30,000 individually sorted GFP-positive nuclei or double-positive synaptosomes were loaded into each channel of the chip. For nuclear libraries, cDNA was amplified, size-selected using SPRIselect beads to separate transcriptome and barcode components, and independently constructed into mRNA libraries and barcode libraries. Synaptosome libraries were constructed using barcode-specific amplification without template switching oligonucleotides.

value: Cerebellum

tag: library type

value: NB


title: liver_day3_control_0ppm_9A

description:
liver gene expression after 3 days exposed to control 0 ppm
US45102884_257480916361_S01_GE1_107_Sep09_1_4


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

description:
Library name: B12_10um_DRUG_24B
Column_name in FPKM_joined.tab: FPKM_B12_10um_DRUG_24B

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


title: CC_BR1TR2

description:
CC_BR1TR2 denotes BR1TR2 RNA-seq sample treated with 1N NAOH (Control for CPT)
CC_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.

tag: strain


title: liver_day3_control_0ppm_8A

description:
liver gene expression after 3 days exposed to control 0 ppm
US45102884_257480916352_S01_GE1_107_Sep09_1_1


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

description:
Library name: B12_10um_DRUG_24A
Column_name in FPKM_joined.tab: FPKM_B12_10um_DRUG_24A


title: liver_day3_control_0ppm_7A

description:
liver gene expression after 3 days exposed to control 0 ppm
US45102884_257480916345_S01_GE1_107_Sep09_2_2


title: liver_day8_control_0ppm_3B

description:
liver gene expression after 8 days exposed to control 0 ppm
US45102884_257480916335_S01_GE1_107_Sep09_2_2


title: Pons nucleus PreNB, replicate 7

description:
Library name: cseq36 PN_Pre_nb
cseq36_PN
single-nucleus RNA-seq (snRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode

source_name: Pons

value: Pons


title: MMS_002_BR2TR2

description:
MMS_002_BR2TR2 denotes BR2TR2 RNA-seq sample treated with 0.002% MMS
MMS_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.

tag: background

value: YEPD

value: MMS


title: CC_BR1TR1

description:
CC_BR1TR1 denotes BR1TR1 RNA-seq sample treated with 1N NAOH (Control for CPT)
CC_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.

value: WT

tag: media


title: NPC cells, MDCi008-A, MILS patient, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 3

description:
Library name: B12_10um_DRUG_06C
Column_name in FPKM_joined.tab: FPKM_B12_10um_DRUG_06C


title: Pons nucleus mRNA, replicate 7

description:
Library name: cseq36 PN_mRNA
cseq36_PN
single-nucleus RNA-seq (snRNA-seq)
polyA RNA
mRNA: read 1 file contains cell barcode and UMI; read 2 file contains transcript sequence

library_source: transcriptomic single cell

value: mRNA


title: NPC cells, MDCi008-A, MILS patient, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 2

description:
Library name: B12_10um_DRUG_06B
Column_name in FPKM_joined.tab: FPKM_B12_10um_DRUG_06B


title: liver_day3_control_0ppm_5A

description:
liver gene expression after 3 days exposed to control 0 ppm
US45102884_257480916342_S01_GE1_107_Sep09_2_4


title: MMS_002_BR2TR1

description:
MMS_002_BR2TR1 denotes BR2TR1 RNA-seq sample treated with 0.002% MMS
MMS_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.

tag: technical replicate


title: MMS_002_BR1TR2

description:
MMS_002_BR1TR2 denotes BR1TR2 RNA-seq sample treated with 0.002% MMS
MMS_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: NPC cells, MDCi008-A, MILS patient, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 1

description:
Library name: B12_10um_DRUG_06A
Column_name in FPKM_joined.tab: FPKM_B12_10um_DRUG_06A

tag: tissue


title: liver_day3_control_0ppm_4A

description:
liver gene expression after 3 days exposed to control 0 ppm
US45102884_257480916336_S01_GE1_107_Sep09_2_1


title: liver_day3_control_0ppm_6A

description:
liver gene expression after 3 days exposed to control 0 ppm
US45102884_257480916344_S01_GE1_107_Sep09_1_3


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

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

tag: cell line

value: wildtype

value: 0.1% DMSO for 24 hours


title: Cerebellum nucleus mRNA, replicate 7

description:
Library name: cseq36 CN_mRNA
cseq36_CN
single-nucleus RNA-seq (snRNA-seq)
polyA RNA
mRNA: read 1 file contains cell barcode and UMI; read 2 file contains transcript sequence


title: Cerebellum nucleus PostNB, replicate 7

description:
Library name: cseq36 CN_Post_nb
cseq36_CN
single-nucleus RNA-seq (snRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode


title: liver_day3_control_0ppm_3A

description:
liver gene expression after 3 days exposed to control 0 ppm
US45102884_257480916335_S01_GE1_107_Sep09_1_2


title: Cerebellum synaptosome PostNB, replicate 8

description:
Library name: cseq35 Syn_4_Post_nb
cseq35_S4post
single-synaptosome RNA-seq (ssRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode
Since only the neuronal barcodes, and not the mRNA, were sequenced for the synaptosomes, the feature.tsv files for the ssRNA-seq samples are empty.


title: MMS_002_BR1TR1

description:
MMS_002_BR1TR1 denotes BR1TR1 RNA-seq sample treated with 0.002% MMS
MMS_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: HU_50mM_BR2TR2

description:
HU_50mM_BR2TR2 denotes BR2TR2 RNA-seq sample treated with 50mM HU
HU_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.

value: HU


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

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

tag: cell type


title: Cerebellum synaptosome PreNB, replicate 8

description:
Library name: cseq35 Syn_4_Pre_nb
cseq35_S4pre
single-synaptosome RNA-seq (ssRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode
Since only the neuronal barcodes, and not the mRNA, were sequenced for the synaptosomes, the feature.tsv files for the ssRNA-seq samples are empty.

tag: genotype


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

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

tag: treatment


title: liver_day3_control_0ppm_2A

description:
liver gene expression after 3 days exposed to control 0 ppm
US45102884_257480916330_S01_GE1_107_Sep09_2_3

value: liver


title: HU_50mM_BR2TR1

description:
HU_50mM_BR2TR1 denotes BR2TR1 RNA-seq sample treated with 50mM HU
HU_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.

tag: biological replicate


title: Cerebellum synaptosome PreNB, replicate 9

description:
Library name: cseq36 Syn_Pre_nb
cseq36_Spre
single-synaptosome RNA-seq (ssRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode
Since only the neuronal barcodes, and not the mRNA, were sequenced for the synaptosomes, the feature.tsv files for the ssRNA-seq samples are empty.


title: Cerebellum synaptosome PostNB, replicate 7

description:
Library name: cseq35 Syn_3_Post_nb
cseq35_S3post
single-synaptosome RNA-seq (ssRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode
Since only the neuronal barcodes, and not the mRNA, were sequenced for the synaptosomes, the feature.tsv files for the ssRNA-seq samples are empty.


title: liver_day3_control_0ppm_1A

description:
liver gene expression after 3 days exposed to control 0 ppm
US45102884_257480916365_S01_GE1_107_Sep09_1_4

value: male


title: NPC cells, BIHi269-B, control, vehicle [0.1% DMSO] treated for 6 hours, replicate 3

description:
Library name: 269B_DMSO_06C
Column_name in FPKM_joined.tab: FPKM_269B_DMSO_06C

value: 0.1% DMSO for 6 hours


title: HU_50mM_BR1TR2

description:
HU_50mM_BR1TR2 denotes BR1TR2 RNA-seq sample treated with 50mM HU
HU_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: Cerebellum synaptosome PreNB, replicate 7

description:
Library name: cseq35 Syn_3_Pre_nb
cseq35_S3pre
single-synaptosome RNA-seq (ssRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode
Since only the neuronal barcodes, and not the mRNA, were sequenced for the synaptosomes, the feature.tsv files for the ssRNA-seq samples are empty.


title: SPLASH, HeLa, Whole Cell, NaAsO2, biological replicate 2, technical replicate 2

city: Singapore

first: Jovi

last: Lim

address: 60 Biopolis St

country: Singapore

institute: Genome Institute of Singapore

description:
Library name: SPLASH_NaAsO2_biorep2_techrep2
Paired-end reads were merged into single-end reads (with a minimum overlap of 10bp) using SeqPrep software

data_processing:
Briefly, icSHAPE libraries were de-duplicated and adapter-trimmed. Remaining reads were mapped to genome. RT stops and base coverage were called out for each nucleotide. Genomic coordinates were converted to transcript coordinate for downstream analysis.
Assembly: ENSEMBL GRCh38 release 98
Supplementary files format and content: Processed data consists of icSHAPE reactivity for all detected transcripts in each sample i.e. files ending with "shape.txn.txt". Each row in the files represent one transcript. Each entry (tab delimited) in each row represent the reactivity of each nucleotide. SPLASH txt files contain the information of all detected chimeras in each sample. eCLIP txt.gz files contain the enriched windows for each sample (refer to software Skipper for details https://doi.org/10.1016/j.xgen.2023.100317). Translation Efficiency data are recorded in "tpm_te.csv"  files. Transcript per million (TPM) was quantified for each gene. Translation efficiency was quantified by dividing TPM of Ribo-seq samples with that of RNA-seq.

source_name: Cervix

extract_protocol:
RNA was harvested using TRIzol/TRIzol LS reagent following manufacturer's instructions. The amount of 500ng and 1,500ng RNA were used for generating icSHAPE and SPLASH libraries, repectively. For SRSF1 eCLIP libraries, cells were fixed with UV (254nm, 400mJ/cm^2) in prior to proceeding to immunoprecipitation and library preparation.
icSHAPE library preparation was carried out according to the protocol described before (Flynn, et al, 2016); SPLASH library preparation was performed according to the protocol described before (Aw, et al, 2016); eCLIP library preparation was performed according to the protocol described before (Blue, et al, 2022).

value: Cervix

value: HeLa

value: Cervical adenocarcinoma

value: wt

value: Psoralen

tag: group

value: SPLASH, HeLa, Whole Cell, NaAsO2


title: Cerebellum synaptosome PostNB, replicate 6

description:
Library name: cseq35 Syn_2_Post_nb
cseq35_S2post
single-synaptosome RNA-seq (ssRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode
Since only the neuronal barcodes, and not the mRNA, were sequenced for the synaptosomes, the feature.tsv files for the ssRNA-seq samples are empty.

value: Cerebellum

value: NB


title: HU_50mM_BR1TR1

description:
HU_50mM_BR1TR1 denotes BR1TR1 RNA-seq sample treated with 50mM HU
HU_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.

value: YEPD


title: NPC cells, BIHi269-B, control, vehicle [0.1% DMSO] treated for 6 hours, replicate 2

description:
Library name: 269B_DMSO_06B
Column_name in FPKM_joined.tab: FPKM_269B_DMSO_06B

value: NPC generated from iPSC

value: Neuronal precursor cells (NPCs)


title: C0_BR2TR1

description:
C0_BR2TR1 denotes BR2TR1 RNA-seq sample treated with AgD H2O (Control for HU and MMS)
C0_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.

value: WT


title: SPLASH, HeLa, Whole Cell, NaAsO2, biological replicate 2, technical replicate 1

description:
Library name: SPLASH_NaAsO2_biorep2_techrep1
Paired-end reads were merged into single-end reads (with a minimum overlap of 10bp) using SeqPrep software


title: NPC cells, BIHi269-B, control, vehicle [0.1% DMSO] treated for 6 hours, replicate 1

description:
Library name: 269B_DMSO_06A
Column_name in FPKM_joined.tab: FPKM_269B_DMSO_06A

value: wildtype


title: SPLASH, HeLa, Whole Cell, NaAsO2, biological replicate 1, technical replicate 2

description:
Library name: SPLASH_NaAsO2_biorep1_techrep2
Paired-end reads were merged into single-end reads (with a minimum overlap of 10bp) using SeqPrep software


title: Cerebellum synaptosome PostNB, replicate 5

description:
Library name: cseq35 Syn_1_Post_nb
cseq35_S1post
single-synaptosome RNA-seq (ssRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode
Since only the neuronal barcodes, and not the mRNA, were sequenced for the synaptosomes, the feature.tsv files for the ssRNA-seq samples are empty.


title: SPLASH, HeLa, Whole Cell, NaAsO2, biological replicate 1, technical replicate 1

description:
Library name: SPLASH_NaAsO2_biorep1_techrep1
Paired-end reads were merged into single-end reads (with a minimum overlap of 10bp) using SeqPrep software


title: Cerebellum synaptosome PreNB, replicate 6

description:
Library name: cseq35 Syn_2_Pre_nb
cseq35_S2pre
single-synaptosome RNA-seq (ssRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode
Since only the neuronal barcodes, and not the mRNA, were sequenced for the synaptosomes, the feature.tsv files for the ssRNA-seq samples are empty.


title: C0_BR1TR2

description:
C0_BR1TR2 denotes BR1TR2 RNA-seq sample treated with AgD H2O (Control for HU and MMS)
C0_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: C0_BR2TR2

description:
C0_BR2TR2 denotes BR2TR2 RNA-seq sample treated with AgD H2O (Control for HU and MMS)
C0_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: NPC cells, BIHi269-B, control, untreated for 24 hours, replicate 2

description:
Library name: 269B_basal_24B
Column_name in FPKM_joined.tab: FPKM_269B_basal_24B

value: no additives for 24 hours


title: Cerebellum synaptosome PreNB, replicate 5

description:
Library name: cseq35 Syn_1_Pre_nb
cseq35_S1pre
single-synaptosome RNA-seq (ssRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode
Since only the neuronal barcodes, and not the mRNA, were sequenced for the synaptosomes, the feature.tsv files for the ssRNA-seq samples are empty.


title: C0_BR1TR1

description:
C0_BR1TR1 denotes BR1TR1 RNA-seq sample treated with AgD H2O (Control for HU and MMS)
C0_featureCounts_transcript.txt
The 4 replicate experiments were pooled together while calculating the counts. Hence, there is only processed file per treatment.


title: NPC cells, BIHi269-B, control, untreated for 24 hours, replicate 1

description:
Library name: 269B_basal_24A
Column_name in FPKM_joined.tab: FPKM_269B_basal_24A


title: Pons nucleus PreNB, replicate 6

description:
Library name: cseq35 PN_Pre_nb
cseq35_PN
single-nucleus RNA-seq (snRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode

value: Pons


title: SPLASH, HeLa, Whole Cell, Untreated, biological replicate 2, technical replicate 2

description:
Library name: SPLASH_Untreated_biorep2_techrep2
Paired-end reads were merged into single-end reads (with a minimum overlap of 10bp) using SeqPrep software

value: SPLASH, HeLa, Whole Cell, Untreated


title: SPLASH, HeLa, Whole Cell, Untreated, biological replicate 2, technical replicate 1

description:
Library name: SPLASH_Untreated_biorep2_techrep1
Paired-end reads were merged into single-end reads (with a minimum overlap of 10bp) using SeqPrep software


title: NPC cells, BIHi269-B, control, untreated for 6 hours, replicate 3

description:
Library name: 269B_basal_06C
Column_name in FPKM_joined.tab: FPKM_269B_basal_06C

value: no additives for 6 hours


title: log2 enrichment of uracil in P. falciparum UNG-iKO strain, RAPA-treated sample

city: Budapest

first: Richard

last: Izrael

state: Pest

address: Magyar tudosok korutja 2

department: Institute of Molecular Life Sciences

country: Hungary

institute: HUN-REN Research Center for Natural Sciences

description: bigwig file of the log2 enrichment calculated from the RAPA-treated mock control UNG-iKO U-DNA-Seq dataset

data_processing:
Raw sequencing reads were mapped to the P. falciparum 3D7 reference genome (version 57) using bwa mem.
Duplicate reads were removed using picard-tools.
Coverage was calculated and normalized to genomic content using bamCoverage from deeptools.
Input vs. U-DNA-IP log2 enrichment was calculated using bigwigCompare from deeptools. Binsizes are indicated in the filename.
bigwig file of the log2 enrichment calculated from the merged dataset of the two independent 3D7 replicates is linked as Series supplementary file.
Assembly: P. falciparum 3D7 reference genome version 57
Supplementary files format and content: bigwig files include log2 of read enrichment calculated by comparing the input vs. U-DNA-IP samples
Supplementary files format and content: bigwig file of the log2 enrichment calculated from the merged dataset of the two independent 3D7 replicates

organism: Plasmodium falciparum

source_name: schizont-stage parasites

growth_protocol: Parasites were grown in complete medium until reaching at least 10% parasitemia. Percoll-sorbitol synchronized, late stage schizont parasites were isolated.

extract_protocol:
Genomic DNA was isolated using ZymoGene Quick DNA MiniPrep Plus kit and fragmented subsequently using sonication.
Library was generated using NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: UNG-iKO parasites were treated with rapamycin (RAPA) and DMSO as mock control to induce UNG knock-out. Genomic DNA was isolated after 88 hours of treatment.

value: schizont-stage parasites

value: UNG-KO induced knock-out

value: RAPA


title: NPC cells, BIHi269-B, control, untreated for 6 hours, replicate 2

description:
Library name: 269B_basal_06B
Column_name in FPKM_joined.tab: FPKM_269B_basal_06B


title: SPLASH, HeLa, Whole Cell, Untreated, biological replicate 1, technical replicate 2

description:
Library name: SPLASH_Untreated_biorep1_techrep2
Paired-end reads were merged into single-end reads (with a minimum overlap of 10bp) using SeqPrep software

value: Cervix

value: HeLa

value: Cervical adenocarcinoma

value: wt


title: log2 enrichment of uracil in P. falciparum UNG-iKO strain, RAPA-treated sample, input


title: SPLASH, HeLa, Whole Cell, Untreated, biological replicate 1, technical replicate 1

description:
Library name: SPLASH_Untreated_biorep1_techrep1
Paired-end reads were merged into single-end reads (with a minimum overlap of 10bp) using SeqPrep software

value: Psoralen


title: Cerebellum nucleus PostNB, replicate 6

description:
Library name: cseq35 CN_Post_nb
cseq35_CN
single-nucleus RNA-seq (snRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode

value: Cerebellum

value: NB


title: log2 enrichment of uracil in P. falciparum UNG-iKO strain, DMSO-treated control

description: bigwig file of the log2 enrichment calculated from the DMSO-treated mock control UNG-iKO U-DNA-Seq dataset

value: UNG-KO control

value: DMSO


title: NPC cells, BIHi269-B, control, untreated for 24 hours, replicate 3

description:
Library name: 269B_basal_24C
Column_name in FPKM_joined.tab: FPKM_269B_basal_24C

value: NPC generated from iPSC

value: Neuronal precursor cells (NPCs)

value: wildtype


title: Cerebellum nucleus mRNA, replicate 6

description:
Library name: cseq35 CN_mRNA
cseq35_CN
single-nucleus RNA-seq (snRNA-seq)
polyA RNA
mRNA: read 1 file contains cell barcode and UMI; read 2 file contains transcript sequence

value: mRNA


title: NPC cells, BIHi269-B, control, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 3

description:
Library name: 269B_1um_DRUG_24C
Column_name in FPKM_joined.tab: FPKM_269B_1um_DRUG_24C


title: 2-mother

city: Shanghai

first: Weiqi

address: 280 South Chongqing Road, Shanghai, China

department: Shanghai Institute of Immunology

institute: Shanghai Jiao Tong University School of Medicine

description: 10X Genomics

data_processing:
The scRNA-seq raw data was processed using Cell Ranger v.3.0.0 (10X Genomics)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: periphery blood

extract_protocol:
PBMCs from the son (PT) and mother (MOM) were purified by Ficoll and suspend the cells with ice-cold PBS+10%FBS+2mM buffer.
Single-cell RNA-seq libraries were prepared following the protocol provided by 10X Genomics Chromium Single Cell Immune Profiling Solution. Libraries were constructed with a Single Cell 3′ Reagent kit (v3). In each lane of a 10X Chromium instrument, Ficoll-purified PBMCs from the patient (PT) and mother (MOM) were encapsulated and single-cell libraries were sequenced on Illumina Hiseq X10 platform.

value: periphery blood

value: PBMCs


title: Cerebellum synaptosome PostNB, replicate 4

description:
Library name: cseq34 Syn_Post_nb
cseq34_Spost
single-synaptosome RNA-seq (ssRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode
Since only the neuronal barcodes, and not the mRNA, were sequenced for the synaptosomes, the feature.tsv files for the ssRNA-seq samples are empty.


title: log2 enrichment of uracil in P. falciparum UNG-iKO strain, DMSO-treated control, input

value: schizont-stage parasites


title: 1-son

description: 10X Genomics


title: log2 enrichment of uracil in P. falciparum 3D7 strain, second replicate, input

value: wild type


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

description:
Library name: 269B_1um_DRUG_24A
Column_name in FPKM_joined.tab: FPKM_269B_1um_DRUG_24A


title: NPC cells, BIHi269-B, control, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 3

description:
Library name: 269B_1um_DRUG_06C
Column_name in FPKM_joined.tab: FPKM_269B_1um_DRUG_06C


title: H9_HLCs

city: Guangzhou

first: Jian

last: Tu

state: Guangdong

address: #58 Zhongshan second road

institute: The First Affliated Hospitap of Sun Yat-sen University

description: GWS

data_processing:
The raw data quality control (QC), human reference genome (hg19) alignment, genotype joint genotype calling, and variant quality score recalibration were performed using the GATK Best Practices workflow. Somatic mutations were called using Mutect2 with default parameters
Assembly: hg19
Supplementary files format and content: vcf

extract_protocol:
The cells were washed with 1× PBS and extracted DNA using DNeasy Blood and Tissue kit (Qiagen, 69504)following the manufacturer's protocol.
Short-insert 500 bp whole genome libraries were constructed, flowcells were prepared, and sequencing clusters were generated following the manufacturer's protocols. The libraries were then sequenced using the Illumina HiSeq X-ten platform (PE150)
WGS are used to assess mutation burdens during HLCs differentiation process.

value: hESC

tag: differentiated cell type

value: hLCs

tag: time

value: HLCs


title: H9_day21

description: GWS


title: log2 enrichment of uracil in P. falciparum 3D7 strain, first replicate

description: bigwig file of the log2 enrichment calculated from the first replicate of the 3D7 U-DNA-Seq dataset


title: Pons nucleus mRNA, replicate 6

description:
Library name: cseq35 PN_mRNA
cseq35_PN
single-nucleus RNA-seq (snRNA-seq)
polyA RNA
mRNA: read 1 file contains cell barcode and UMI; read 2 file contains transcript sequence

value: Pons


title: H9_day0

description: GWS


title: Pons nucleus PreNB, replicate 5

description:
Library name: cseq34.2 PN_Pre_nb
cseq34_PN2
single-nucleus RNA-seq (snRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode


title: log2 enrichment of uracil in P. falciparum 3D7 strain, second replicate

description: bigwig file of the log2 enrichment calculated from the second replicate of the 3D7 U-DNA-Seq dataset


title: Pons nucleus mRNA, replicate 5

description:
Library name: cseq34.2 PN_mRNA
cseq34_PN2
single-nucleus RNA-seq (snRNA-seq)
polyA RNA
mRNA: read 1 file contains cell barcode and UMI; read 2 file contains transcript sequence


title: NPC cells, BIHi269-B, control, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 2

description:
Library name: 269B_1um_DRUG_06B
Column_name in FPKM_joined.tab: FPKM_269B_1um_DRUG_06B


title: NPC cells, BIHi269-B, control, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 1

description:
Library name: 269B_1um_DRUG_06A
Column_name in FPKM_joined.tab: FPKM_269B_1um_DRUG_06A


title: H1_HLCs

description: GWS


title: Cerebellum synaptosome PreNB, replicate 4

description:
Library name: cseq34 Syn_Pre_nb
cseq34_Spre
single-synaptosome RNA-seq (ssRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode
Since only the neuronal barcodes, and not the mRNA, were sequenced for the synaptosomes, the feature.tsv files for the ssRNA-seq samples are empty.


title: NPC cells, BIHi269-B, control, untreated for 6 hours, replicate 1

description:
Library name: 269B_basal_06A
Column_name in FPKM_joined.tab: FPKM_269B_basal_06A

value: no additives for 6 hours


title: Lib2_SkinWound

city: New York

first: Dr. Shruti

last: Naik

address: 1425 Madison Ave

department: Immunology and Immunotherapy

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: 2.F23710AA.SW
V1V3 16S rRNA sequencing of skin wound. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

data_processing:
The final library was sequenced on Illumina® Nextseq™ with a P1 reagent kit (600 cycles). The sequencing was performed with 30% PhiX spike-in.
QIIME2 pipeline (version: 2024.5) (PMID: 31341288) was used for training the classifier and for all downstream analysis of 16s data. Paired end demultiplexed FASTQ files were first imported into QIIME2 workflow, using import function with data type set to ‘SampleData[PairedEndSequencesWithQuality]’ and input format set to ‘PairedEndFastqManifestPhred33V2’. The data was denoised with DADA2 (PMID: 27214047) to trim and truncate reads to remove low quality reads. Output from DADA2 denoising included representative sequences, features table and DADA2 denoising stats.
New classifier was trained specifically for V1-V3 region of Bacterial genome using Silva 138 database (PMID: 23193283). The representative sequences were then tabulated to generate read counts using feature table function to generate feature counts tabulations based on the sample metadata. The representative reads / sequences were also aligned to the custom classifier generated for V1-V3 region and output taxonomic classifications were generated. The taxonomy data was then used to tabulate read counts and an output taxa bar plot was generated using the condition column from metadata to group the samples.
The taxonomy and feature data output from QIIME2 was then imported into an R programming environment and mia package (doi:10.18129/B9.bioc.mia) was used for subsequent analysis. ImportQIIME2 function was used to import the data into R. The imported microbiome data was stored in TreeSummarizedExperiment object in R.
Feature table and Taxonomic mapping were extracted from TreeSummarizedExperiment object in R.
Assembly: V1-V3 bacterial genomic region
Supplementary files format and content: Feature table with raw read counts (no normalization) stored in .csv file format.
Supplementary files format and content: Taxonomic mapping for features found in the read counts file, stored in .csv file format.
Library strategy: 16S rRNA-seq

organism: human skin metagenome

source_name: Skin wound

extract_protocol:
ZymoBIOMICS® DNA Miniprep Kit (Zymo Research, Irvine, CA) was used for low biomass samples such as skin swabs, as it permits for a lower elution volume, resulting in more concentrated DNA samples.
Bacterial 16S ribosomal RNA gene targeted sequencing was performed using the Quick-16S™ NGS Library Prep Kit (Zymo Research, Irvine, CA). The bacterial 16S primers amplified the V1-V3 region of the 16S rRNA gene. These primers have been custom-designed by Zymo Research to provide the best coverage of the 16S gene while maintaining high sensitivity.  The sequencing library was prepared using an innovative library preparation process in which PCR reactions were performed in real-time PCR machines to control cycles and therefore limit PCR chimera formation. The final PCR products were quantified with qPCR fluorescence readings and pooled together based on equal molarity. The final pooled library was cleaned with the Select-a-Size DNA Clean & Concentrator™ (Zymo Research, Irvine, CA), then quantified with TapeStation®(Agilent Technologies, Santa Clara, CA) and Qubit® (Thermo Fisher Scientific, Waltham, WA).

value: Skin wound

tag: injury time

tag: Sex

value: f

tag: site

value: finger

tag: injury type

value: cut

tag: age


title: Lib2_ContralateralSkin

description:
Library name: 2.F23710AA.Control
V1V3 16S rRNA sequencing of contralateral control skin. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

source_name: Contralateral skin

value: Contralateral skin


title: Pons nucleus PreNB, replicate 4

description:
Library name: cseq34.1 PN_Pre_nb
cseq34_PN1
single-nucleus RNA-seq (snRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode

tag: library type

value: NB


title: Cerebellum nucleus mRNA, replicate 5

description:
Library name: cseq34.2 CN_mRNA
cseq34_CN2
single-nucleus RNA-seq (snRNA-seq)
polyA RNA
mRNA: read 1 file contains cell barcode and UMI; read 2 file contains transcript sequence

value: Cerebellum


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

description:
Library name: 269B_10um_DRUG_24C
Column_name in FPKM_joined.tab: FPKM_269B_10um_DRUG_24C

value: NPC generated from iPSC

value: Neuronal precursor cells (NPCs)

value: wildtype


title: H1_day21

description: GWS


title: NPC cells, BIHi269-B, control, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 2

description:
Library name: 269B_1um_DRUG_24B
Column_name in FPKM_joined.tab: FPKM_269B_1um_DRUG_24B


title: H1_day0

description: GWS


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

description:
Library name: 269B_10um_DRUG_24B
Column_name in FPKM_joined.tab: FPKM_269B_10um_DRUG_24B


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

description:
Library name: 269B_10um_DRUG_24A
Column_name in FPKM_joined.tab: FPKM_269B_10um_DRUG_24A


title: Pons nucleus mRNA, replicate 4

description:
Library name: cseq34.1 PN_mRNA
cseq34_PN1
single-nucleus RNA-seq (snRNA-seq)
polyA RNA
mRNA: read 1 file contains cell barcode and UMI; read 2 file contains transcript sequence

value: mRNA


title: Lib15_ContralateralSkin

description:
Library name: 15.M30821SA.CS
V1V3 16S rRNA sequencing of contralateral control skin. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: m


title: log2 enrichment of uracil in P. falciparum 3D7 strain, first replicate, input

value: schizont-stage parasites

value: wild type


title: NPC cells, BIHi269-B, control, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 3

description:
Library name: 269B_10um_DRUG_06C
Column_name in FPKM_joined.tab: FPKM_269B_10um_DRUG_06C


title: Cerebellum nucleus PostNB, replicate 5

description:
Library name: cseq34.2 CN_Post_nb
cseq34_CN2
single-nucleus RNA-seq (snRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode


title: Lib15_SkinWound

description:
Library name: 15.M30821SA.SW
V1V3 16S rRNA sequencing of skin wound. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.


title: Cerebellum nucleus mRNA, replicate 4

description:
Library name: cseq34.1 CN_mRNA
cseq34_CN1
single-nucleus RNA-seq (snRNA-seq)
polyA RNA
mRNA: read 1 file contains cell barcode and UMI; read 2 file contains transcript sequence