title: IPEC1 cell - VerA_3uM_24hr - Rep3


title: HCT116-Control,12h-2

status: Public on May 31 2025

type: SRA

city: Kunming

first: Shimin

last: Gong

address: Wujiaying

country: China

institute: Life Sciences, Yunnan University

library_source: transcriptomic

data_processing:
Raw reads were trimmed for adaptor sequence and the low-quality reads were excluded using Trim galore (Version:1.3.0)
Then, the reads were mapped to human and Neurospora crassa(spike-in) using STAR (Version: 2.7.10b)
Assembly: hg38
Supplementary files format and content: raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: colon

extract_protocol:
The HCT116-AID2 cell lines were induced by 1 µg/ml of doxycycline for 24h, and wereadded or not added (as the control) to 10 µM 5-Ph-IAA (MCE, HY-134653) for several hours. Then transferring cultures to fresh medium supplemented with 10μg/mLactinomycin D (HY-17559, MCE). Samples were harvested at time points of 0, 4, 8 and 12h followingactinomycin Dtreatment. Three replicates were collected at each time point.To determine decay rate of RNA, 500ng HCT116-AID2 cellRNA and 50ngNeurospora RNA were input RT reaction. For tested genes, random RT primers were employed in RT reaction.
the VAHTS Universal V8 RNA-seq Library Prep Kit (Vazyme, NRM605)

tag: tissue

value: colon

tag: cell line

tag: genotype

value: Contro

tag: treatment

value: Actinomycin-D


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 120 min, total RNA, biol replicate 1

city: Brighton

first: Ruslan

last: Evans

state: East Sussex

address: Lewes Road

department: School of Applied Science

country: United Kingdom

institute: University of Brighton

data_processing:
Reads were quantified against S. coelicolor transcriptome gene annotations from NCBI reference NC_003888.3 using kallisto quant version 0.46.2.
Kallisto quantifications were converted to gene level by tximport version 1.20.0 then analysed for differential expression using DESeq2 version 1.32.0.
Translational Efficiency was evaluated using the deltaTE protocol described in 'deltaTE: Detection of Translationally Regulated Genes by Integrative Analysis of Ribo-seq and RNA-seq Data' Chothani et al. , Current Protocols in Molecular Biology e108 vol 129, 2019'.
Assembly: GCF_000203835.1_ASM20383v1  NC_003888.3
Supplementary files format and content: comma separated files. Table of fold-change and adj pval for each gene for Translational Efficiency, total RNA, and RPF fraction.
Supplementary files format and content: tab-delimited text files. Matrix table of counts for every gene generated by kallisto quant.

organism: Streptomyces coelicolor

growth_protocol: Spores were pre-germinated in 2 x YT medium for 7 hrs at 30°C and 250 rpm then used to inoculate 200ml of SMM medium (Practical Streptomyces Genetics, Kieser et al. 2000, ISBN 9780708406236) in 500 ml spring containing conical flasks at a concentration of approx. 500,000 cfu / ml and incubated for 18 h 20 min at 30°C / 250 rpm.

extract_protocol:
For total RNA extraction (transcriptome analysis), bacterial cultures were treated with RNA protect bacteria reagent ( Qiagen #76506) and incubated for 10 min at room temperature. Cultures were centrifuged and the pellets were stored at -80°C. Pellets from 15 ml of bacterial cultures were resuspended in 200 µl of lysozyme dissolved in TE buffer at a concentration of 0.015 g per ml and incubated at room temperature for 15 min. 600 µl of RNeasy Lysis Buffer (RLT buffer, Qiagen #79216) containing 10 µl / ml β-mercaptoethanol was added and the mixture mixed by vortex mixer then transferred to a 2 ml microfuge tube containing 5 mm stainless steel beads (Qiagen #69989) and placed in a Tissuelyser LT (Qiagen #85600) for efficient mechanical cell disruption / homogenisation for 2 min at 30 rpm. The suspension was then centrifuged at 16,627 RCF for 2 min, the supernatant was recovered and its volume estimated. One volume of acid pH 4.5 phenol:chloroform:isoamyl alcohol (125:24:1, Fisher #AM9720) was added and the mixture mixed by vortex mixer for 30 seconds, then centrifuged at 4°C for 5 min at 16,627 RCF. The upper phase containing the nucleic acids was removed and retained leaving behind the proteins in the interface, and the phenol/chloroform extraction repeated twice more. Then one volume of chloroform was added, the mixture mixed by vortex mixer then centrifuged at 4°C for 2 min at 16,627 RCF, and the upper phase was again transferred to a fresh RNase-free microfuge tube. From this point onward the standard manufacturer’s instructions were followed for the miRNAeasy RNA extraction kit (Qiagen #217004). The total RNA was eluted in 30 µl of nuclease free water and stored at -80°C. Genomic DNA was removed using the Turbo DNA free kit (Invitrogen AM1907). For the Riboseq protocol the protocol followed was based on that described in Jeong et al. Nature Communications 2016. Briefly, the mycelium was ground in lysis buffer and stored at -80°C as described in the treatment protocol. The ground mycelium was defrosted in ice and centrifuged at 20,000 RCF at 4°C. The supernatant was recovered and the RNA concentration was determined by NanoDrop spectrophotometer or Qubit fluorometer. 50 µg of cell lysate was incubated with 400 U of MNase for 2 h at 37°C. The digestion was stopped by adding 2.5 µl of EGTA 0.5M. The monosomes were isolated through Sephacryl S400 Microspin columns (GE cat 27-5140-01) in Recovery buffer (50mM Tris-HCl (pH8); 1% Triton X100; 50mM MgCl2; 25mM EGTA; 250mM NaCl) and the purified ribosomes were stored at -80°C. The ribosome protected RNA was isolated by column purification using the miRNeasy kit (Qiagen #217004) according to manufacturer’s protocol, and RNA between 15 and 45 nt was size selected by electrophoresis in 15% acrylamide gel in TBE. RNA was extracted from the gel in 500 µl of gel extraction buffer (0.25% SDS, 0.3M NaOAc pH 5.5, 1 mM EDTA) and precipitated by adding 16 µl of 5M NaCl, 45 µl 3M NaOAc, 4 µl glycoblue (15 mg / ml, Fisher #10391565) and 1.2 ml absolute ethanol and incubating at -80°C for 1 h. The RNA was centrifuged for 30 min at 20,000 RCF at 4°C. The RNA pellet was washed twice with ice cold 70% ethanol and air dried before resuspension in 9 - 11 µl of RNAse free water. The RNA was subsequently rRNA depleted using NEBNext Core Reagent Set (NEB #E7865) with custom DNA probes designed to cover Streptomyces specific rRNA and tRNA sequences. The RNA was subsequently treated with Polynucleotide Kinase for 1h at 37°C and the RNA was purified from the enzyme and the buffer using miRNeasy mini columns. The RNA was eluted in 30 µl of RNase free water, dehydrated and resuspended in 6 µl of nuclease-free water and used for library construction using the NEB NEBNext Small RNA Library Prep Set for Illumina (cat E7330S) following the manufacturer instructions.
Total RNA were depleted of rRNA by using the NEBNext Core Reagent Set (NEB #E7865) with custom DNA probes designed to cover Streptomyces specific rRNA and tRNA sequences and library constructions were carried out using the NEB directional RNAseq kit (NEB #E7760) and NEB NEBNext Small RNA Library Prep Set for Illumina (NEB #E7330S) following the manufacturer instructions.
directional RNA-seq for total RNA and miRNAseq library prep for the ribosome protected RNAs

treatment_protocol: 15ml of cultures taken immediately prior to the cold-shock as a 'time=0' reference were preserved with RNAProtect (Qiagen #76506) for total RNA extraction. 105ml of culture was taken at the same point for use as a 'time=0' reference in ribosome profiling experiments, vacuum filtered to remove medium and the cells immediately frozen in liquid nitrogen. The frozen cells were ground using a pestle and mortar whilst being kept frozen by adding liquid nitrogen. The pulverized mycelium was dissolved in a lysis buffer (20mM Tris pH 7.6; 5mM MgCl2; 140mM NaCl; 1% Triton X100;chloramphenicol 34 µg / ml) and frozen at -80°C. Cultures (30 ml) were exposed to cold-shock by the addition of 3 volumes of fresh media equilibrated at 4°C to rapidly reduce the temperature to 10°C, whilst control cultures had fresh media at 30°C added. After 120 min 15 ml of cultures was removed for total RNA analysis and preserved as before, and 105 ml of culture was removed for ribosome profiling experiments and processed as before.

tag: medium

value: SMM

value: control

tag: time (min)

tag: fraction

value: total RNA

tag: biol replicate

tag: strain


title: Multiome_WT3, Paired scRNA/ATACseq

city: Saint Louis

first: Alina

last: Ulezko Antonova

state: MO

address: 660 S. Euclid Ave

department: Path/Immuno

country: USA

institute: WUSM

data_processing:
The CellRanger Software Suite (v6.0.0) from 10x Genomics was used for sample demultiplexing, barcode processing, and single cell counting.
Assembly: mm10
Supplementary files format and content: For GEX, tab-delimeted files contain the features, barcodes and count matrix files contained in the "filtered_feature_bc_matrix" subfolder of the CellRanger "outs" folder.
Supplementary files format and content: For ATAC, tab-delimeted files contain the fragment files and the frament file indices of the CellRanger "outs" folder.
Library strategy: Multiome scRNA/ATAC-seq

molecule: nuclear RNA

organism: Mus musculus

source_name: Small intestine lamina propria

extract_protocol:
Nuclei extraction was performed as described in the 10x Genomics demonstrated protocol (CG000365).
For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle was used. Briefly, barcoded cDNA was amplified for 6 cycles before being purified using SPRIselect beads and the precise concentration of each library was determined.

value: Small intestine lamina propria

tag: cell type

value: WT


title: M201, CD8 T cells, PD-L1−

city: Heraklion

first: Matthieu

middle: David

last: Lavigne

address: Nikolaou Plastira 100

country: Greece

institute: IMBB-FORTH

description:
Library name: NGS-2344
Column name in raw_counts_All_Samples.txt: M201

data_processing:
Raw sequencing data were assessed for quality using FastQC version 0.12.0 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Adapter sequences and low-quality bases were trimmed with Cutadapt version 1.16 (DOI: https://doi.org/10.14806/ej.17.1.200). Ribosomal RNA sequences were identified and filtered out using RiboDetector version 0.3.1 (https://doi.org/10.1093/nar/gkac112). The resulting single-end reads were aligned to the human reference genome (hg38) using Rsubread version 2.12.3 with default settings. Gene-level counts were obtained using the 'featureCounts' function within the Rsubread package.
Differential expression analysis  (DEA) was conducted by running EdgeR63 version 3.40.2. For the comparison of PD-L1+ vs. PD-L1− CD8 positive sorted cells, DEGs in either group of the comparison were defined by applying the following thresholds: |Log2FC| >1.5 and FDR<0.05, which was considered statistically significant. For the comparison of NR and R, PD-L1+ CD8 T cell samples were divided according to the RECIST 1.1 criteria. DEGs in either group were identified using the thresholds |Log2FC|>0.5 and FDR<0.05, which were considered statistically significant. Heatmaps and boxplots were created in R with an in-house–developed script which is based on the complex heatmap R package.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: CD8+ T cells

extract_protocol:
RNA from FACS-sorted CD8 PD-L1 positive or negative cells (21x103 on average).  NSCLC was isolated using Nucleospin RNA XS kit (Macherey-Nagel), according to the manufacturer instructions. The quality and quantity of isolated RNA was measured using  2100 Bioanalyser  (Agilent)  and RNA 6000 Pico Kit reagents (Agilent).
RNA samples with RNA integrity number (RIN)>7 were used for library construction using the 3′ mRNA-Seq Library Prep Kit FWD for Illumina (QuantSeq-LEXOGEN) as per the manufacturer’s instructions. Amplification was controlled for obtaining optimal unbiased libraries across samples by assessing the number of cycles (ranging from 20-24) required by qPCR. DNA High Sensitivity Kit for bioanalyzer was used to assess the quantity and quality of libraries, according to the manufacturer’s instructions (Agilent). Libraries were multiplexed and sequenced on an Illumina Nextseq 500 at the genomics facility of IMBB FORTH according to the manufacturer’s instructions.

tag: patient id

tag: sample id_(p=_plus;_m=minus)

value: CD8+ T cells

tag: group id

tag: ici response

value: NR


title: HCT116-Control,8h-3


title: HCT116-Control,8h-2


title: P222, CD8 T cells, PD-L1+

description:
Library name: NGS-2357
Column name in raw_counts_All_Samples.txt: P222

value: R


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 0 min, total RNA, biol replicate 2


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 0 min, total RNA, biol replicate 1


title: M014, CD8 T cells, PD-L1−

description:
Library name: NGS-2340
Column name in raw_counts_All_Samples.txt: M014


title: P215, CD8 T cells, PD-L1+

description:
Library name: NGS-2355
Column name in raw_counts_All_Samples.txt: P215


title: IPEC1 cell - DMSO_0_24hr - Rep5

type: RNA

city: Toulouse

first: Laura

last: Soler Vasco

state: Haute Garonne

address: 180 Chemin de Tournefeuille

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 custom GE microarray (8X60K, Design 037880 enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_20120213). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 26 out of 32 microarrays or with a minimal weight of 2 per group from at least one experimental group. At this step, 43416 spots out of 61625 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 43418 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Sus scrofa

source_name: IPEC1 cell

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: The non-tumorigenic and non-transformed intestinal cell line IPEC1 was chosen as a model due to their competence in terms of cytochrome P450 and p53 status and thus well-suited for the study of AF and other pro-toxicants. IPEC1 cells were grown in 100 × 20 mm Petri dishes (Cellstar, Greiner Bio-One, Germany) using DMEM/HAMs F12 medium (Sigma,), supplemented with 5% fetal bovine serum (FBS, Eurobio, Courtaboeuf, France), 1% streptomycin/penicillin (Eurobio), 1% L-glutamine (Eurobio), 1% insulin transferrin-selenium (Sigma), and 5 μg/mL epidermal growth factor (Becton-Dickinson, Le Pont de Claix, France). Cells were consistently maintained under controlled conditions at 39 °C in a humidified environment containing 5% CO2. To mimic real conditions, IPEC1 cells were differentiated into monolayers using transwell devices prior to exposure to toxins as previously described (Al-Ayoubi et al., 2022).  In brief, 2.105 cells were initially seeded in Transwell inserts featuring 0.4 μm polyethylene terephthalate membranes (Coring Falcon, Corning, NY, USA). Once confluence was attained, cells were systematically differentiated into monolayers within the same medium, enriched with 20 μg/mL dexamethasone but devoid of FBS. This differentiation process remained until a stable transepithelial electrical resistance was established, which normally takes 8-10 days.

extract_protocol: For total RNA extraction, cells were washed in phosphate-buffered saline (PBS; Sigma) and lysed in Extract-All reagent (Eurobio; Les Ulis, France). the total RNA extraction was followed according to Chomczynski and Sacchi (1987).  Following extraction, the concentration and quality of the RNA were assessed using a Dropsense 96 UV/VIS droplet reader (Trinean, Belgium) and an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA). The mean (± SD) RNA Integrity Number (RIN) was 9.53 ± 0.36.

treatment_protocol: Monolayers were washed with Phosphate saline buffer exposed apically to 1 µM and 3 µM VerA, 1 µM AFB1, or solvent control (DMSO) for 6 or 24 h in cell culture medium without serum (SVF) nor phenol rouge. These conditions were not cytotoxic as described previously (Al-Ayoubi et al., 2023).

value: DMSO

tag: time

tag: dose


title: M198, CD8 T cells, PD-L1−

description:
Library name: NGS-2342
Column name in raw_counts_All_Samples.txt: M198


title: IPEC1 cell - VerA_3uM_6hr - Rep4

value: VerA


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 120 min, total RNA, biol replicate 2


title: HCT116-Control,8h-1


title: HCT116-Control,4h-3


title: S. coelicolor A3(2) grown in liquid SMM medium, cold-shock, 120 min, RPF fraction, biol replicate 2, tech replicate 4

molecule: cytoplasmic RNA

value: cold-shock

value: RPF

tag: tech replicate


title: HCT116-Control,4h-2

tag: tissue


title: IPEC1 cell - DMSO_0_6hr - Rep1


title: IPEC1 cell - AFB1_1uM_24hr - Rep3


title: IPEC1 cell - VerA_1uM_6hr - Rep4


title: IPEC1 cell - AFB1_1uM_6hr - Rep5


title: IPEC1 cell - DMSO_0_6hr - Rep2


title: P208, CD8 T cells, PD-L1+

description:
Library name: NGS-2349
Column name in raw_counts_All_Samples.txt: P208


title: HCT116-Control,4h-1

tag: cell line


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 120 min, RPF fraction, biol replicate 2, tech replicate 4


title: S. coelicolor A3(2) grown in liquid SMM medium, cold-shock, 120 min, RPF fraction, biol replicate 1, tech replicate 4


title: P209, CD8 T cells, PD-L1+

description:
Library name: NGS-2351
Column name in raw_counts_All_Samples.txt: P209

tag: genotype


title: P212, CD8 T cells, PD-L1+

description:
Library name: NGS-2353
Column name in raw_counts_All_Samples.txt: P212


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 0 min, RPF fraction, biol replicate 2, tech replicate 4

tag: treatment


title: HCT116-Contro, 0h-2


title: P198, CD8 T cells, PD-L1+

description:
Library name: NGS-2343
Column name in raw_counts_All_Samples.txt: P198


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 0 min, RPF fraction, biol replicate 1, tech replicate 4

tag: medium


title: HCT116-Contro, 0h-3


title: P202, CD8 T cells, PD-L1+

description:
Library name: NGS-2347
Column name in raw_counts_All_Samples.txt: P202


title: Brain_mouse6_section2

city: New York

first: Sarah

last: Stanley

state: NY

address: 1230 York Avenue

department: Dept of Molecular Genetics

institute: Rockefeller University

description: FFPE mouse brains with AAV hSyn-mCherry injection into the ventromedial hypothalamus

hyb_protocol: Hybridized for 20 hrs

scan_protocol: Xenium In Situ Analyzer

data_processing: Spatial transcriptomic data was processed with Xenium analyzer (10X Genomics).

label: Xenium Mouse Brain panel modified with 100 custom gene targets

source_name: Brain

label_protocol: Xenium Slides were deparaffinized and decrosslinked, then processed according to the manufacturer’s V1 protocol using the Mouse Brain panel modified with 100 custom gene targets.

growth_protocol: Mice (8+ weeks old) were housed under controlled light conditions (12 h light/12 h dark) and temperature (22°C) and fed ad libitum on standard mouse chow. Unless noted, all animals were male and were kept group housed. All other mice were kept group housed. Mice used were C57BL/6J (Jax# 000664). Animal care and experimental procedures were performed with the approval of the Animal Care and Use Committee of Icahn School of Medicine at Mount Sinai under established guidelines.

extract_protocol: Mice were injected with a AAVretro-mCherry into the VMH. After 4-weeks to allow for viral expression, the mice were perfused, and brains were collected. Brains were post-fixed overnight and then paraffin embedded. In brief, FFPE blocks with coronal embedded mouse brains were sectioned at 5 µm (Leica Histocore biocut), placing 3 brain sections per Xenium slide; serial sections were cut onto on standard charged slides and used for Immunofluorescence Control Slides. Xenium slides were baked for 3 hrs at 42°C for section adherence and stored in desiccator until use (no more than 4 wks).

treatment_protocol: Mice were injected with a AAVretro-mcherry into the VMH. After 4-weeks to allow for viral expression, the mice were perfused, and brains were collected. Brains were post-fixed overnight and then paraffin embedded. In brief, FFPE blocks with coronal embedded mouse brains were sectioned at 5 µm (Leica Histocore biocut), placing 3 brain sections per Xenium slide; serial sections were cut onto on standard charged slides and used for Immunofluorescence Control Slides. Xenium slides were baked for 3 hrs at 42°C for section adherence and stored in desiccator until use (no more than 4 wks).

value: Brain


title: P201, CD8 T cells, PD-L1+

description:
Library name: NGS-2345
Column name in raw_counts_All_Samples.txt: P201


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 120 min, RPF fraction, biol replicate 1, tech replicate 4

tag: time (min)


title: IPEC1 cell - VerA_3uM_6hr - Rep2


title: IPEC1 cell - AFB1_1uM_6hr - Rep3


title: S. coelicolor A3(2) grown in liquid SMM medium, cold-shock, 120 min, RPF fraction, biol replicate 2, tech replicate 3

tag: fraction


title: P014, CD8 T cells, PD-L1+

description:
Library name: NGS-2341
Column name in raw_counts_All_Samples.txt: P014


title: IPEC1 cell - DMSO_0_24hr - Rep2


title: IPEC1 cell - VerA_1uM_6hr - Rep3


title: Brain_mouse5_section2


title: S. coelicolor A3(2) grown in liquid SMM medium, cold-shock, 120 min, RPF fraction, biol replicate 1, tech replicate 3

tag: biol replicate


title: Brain_mouse4_section2


title: HCT116-Contro, 0h-1


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 120 min, RPF fraction, biol replicate 2, tech replicate 3

tag: strain


title: TSLC_p15_rep1

city: Kyoto-shi

first: Masatoshi

last: Ohgushi

state: Kyoto

address: 53 Shogoin Kawahara-cho

country: Japan

institute: Kyoto University

description:
Library name: Sample 3
Column name in All_TPM_TSLC.csv: TSLC_P15_rep1

data_processing:
BaseSpace Onsite (Illumina) were used for basecalling and generation of fastq files
Sequence reads were aligned against GRCh38 genome assembly using STAR (version 2.6.1d).
Read counts and TPM (transcripts per million) values of each gene were quantified and calculated using RSEM (version 1.3.3)
Assembly: GRCh38 genome assembly
Supplementary files format and content: csv file includes TPM valuse for each Sample

source_name: TS-like cells

growth_protocol: TSLCs were cultured in TSC medium (DMEM/F12 supplemented with 0.1mM 2-mercaptoethanol, 0.2% FBS, 0.3% BSA, 1% ITS-X supplement, 1.5 mg/ml L-ascorbic acid, 50 ng/ml EGF, 2 µM CHIR99021, 0.5 µM A83-01, 1 µM SB431542, 0.8 µM VPA and 5 µM Y27632) in humidified atmosphere with 5% Co2 at 37C.

extract_protocol:
Total RNAs were extracted using RNeasy micro kit (QUIAGEN) following the manufacturer's protocol
Sequencing libraries were prepared from 1 μg total RNAs using the TruSeq Standard mRNA LT Sample Preparation Kit (Illumina)

tag: cell type

value: TS-like cells


title: TSLC_p15_rep2

description:
Library name: Sample 4
Column name in All_TPM_TSLC.csv: TSLC_P15_rep2


title: Physco_hypo3

city: Groningen

first: Hans

last: van Veen

address: Nijenborgh 7

department: GELIFES

country: Netherlands

institute: University of Groningen

data_processing:
Kallisto read allignment, edgeR differenital expression
Assembly: Marchantia polymorpha v3.1 (Phytozome genome ID: 320); Physcomitrium patens v3.3 (Phytozome genome ID: 318); Selaginella moellendorffii v1.0 (Phytozome genome ID: 91); Pteris vittata (TSA); Equisetum hyemale (TSA)
Supplementary files format and content: processed_Ehym.txt
Supplementary files format and content: processed_Mpol.txt
Supplementary files format and content: processed_Ppat.txt
Supplementary files format and content: processed_Pvit.txt
Supplementary files format and content: processed_Smoe.txt

organism: Physcomitrium patens

source_name: shoot

extract_protocol:
Thermo Scientific™ GeneJET Plant RNA Purification Kit (Pteris, Marcha, Physco, Sella); Sigma Spectrum RNA extraction (Equi)
mRNA stranded library preparation (poly A enrichment)

value: shoot


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 120 min, RPF fraction, biol replicate 1, tech replicate 3


title: TSLC_p10_rep2

description:
Library name: Sample 2
Column name in All_TPM_TSLC.csv: TSLC_P10_rep2


title: Brain_mouse6_section1


title: IPEC1 cell - VerA_1uM_24hr - Rep3


title: Brain_mouse5_section1


title: Physco_hypo1


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 0 min, RPF fraction, biol replicate 2, tech replicate 3


title: TSLC_p10_rep1

description:
Library name: Sample 1
Column name in All_TPM_TSLC.csv: TSLC_P10_rep1


title: Brain_mouse4_section1


title: Physco_air3

value: aerobic conditions (21% O2)


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 0 min, RPF fraction, biol replicate 1, tech replicate 3


title: Brain_mouse3_section2


title: IPEC1 cell - VerA_3uM_24hr - Rep2


title: Physco_air2


title: IPEC1 cell - AFB1_1uM_24hr - Rep2


title: Lovo, IgG, Rep2

city: London

first: Van

middle: Thuy Mai

last: Nguyen

address: 237 Fulham Rd, Chester Beatty Laboratories, third floor

department: Cancer Biology

institute: Institute of cancer research

library_source: genomic

data_processing:
Paired-end fastq files were aligned to hg38 reference genome using Bowtie2
Peaks were called using MACS2 using callpeak function
Bigwig files were generated from bam files using Deeptools with option of bamCoverage
DeSeq2 analysis from DiffBind R package was used to compare differential binding between conditions
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: Cut and Run

molecule: genomic DNA

growth_protocol: Cells were cultured in growth medium supplemented with 10% FBS and 1% glutamine, and grown at 37 degree incubators with 5% CO2.

extract_protocol:
Cells were nuclei extracted with nuclei extraction buffer (20mM HEPES pH 7.9, 10mM KCl, 0.1% Triton X-100, 20% Glycerol and 1mM MnCl2). Cut and Run were performed and DNA were spike-in with Ecoli
CUT& RUN libraries were prepared with 10ng CUT& RUN DNA using NEBNext Ultra II DNA library prep kit (NEB)

treatment_protocol: Cells were treated with the indicated agents for 16 hours before harvest. Cells were pretreated with DMSO or EZH2i (tazemetostat at 5uM) for 5 days, and then seeded into 15cm plates. The following day, cells were treated with DMSO or MEKi (trametinib), with and without EZH2i.

value: colon

value: Lovo


title: Brain_mouse2_section2


title: S. coelicolor A3(2) grown in liquid SMM medium, cold-shock, 120 min, RPF fraction, biol replicate 2, tech replicate 2

value: SMM


title: P2C, 211116, S8

city: Bethesda

first: Ousmane

middle: Hamadoun

last: Cisse

state: MD

address: 10 Center Dr,

institute: National Institutes of Health

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Hiseq X  output.
To remove macaque DNA, ChIP-seq reads were aligned to the macaque genome (GCF_000772875.2)  using Bowtie2 version 2.2.5. Only unmapped  reads were retained.
ChIP-seq reads were aligned to the Pneumocystis sp macacae (taxon ID 2698480)  genome using bwa mem version 0.7.17-r1188
Peaks were called uing MACS v3.0.0a5 with the significance cut-off q-value <=0.05 (narrowPeak files)
bigWig files were generated using the bamCoverage from deepTools package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate (bins per millions; bin size; 50 bp)
Assembly: GCA_018127085.1
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

organism: Pneumocystis sp. 'macacae'

source_name: lungs

extract_protocol:
Cells were fixed with formaldehyde for 10 minutes using the active motif Low cell ChIP-seq (cat # 53084). After quenching and cell lysis, chromatin was sonicated using a Q800R3 Sonicator (Qsonica) with recirculating chiller.
ChIP-seq libraries were prepared using the active motif Low cell ChIP-seq (cat # 53084) that include the Next Gen DNA library kit and Next Gen Indexing kit. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using SPRIselect  beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: lungs

value: infected macaque P2C

value: infection level 5+

value: collect date:2021

tag: chip antibody

value: H3K4me2 (Abcam # ab8580)


title: Lovo, IgG, Rep1


title: S. coelicolor A3(2) grown in liquid SMM medium, cold-shock, 120 min, RPF fraction, biol replicate 1, tech replicate 2


title: Lovo, H3K27me3, COMBO, Rep2

value: COMBO


title: Brain_mouse1_section2


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 120 min, RPF fraction, biol replicate 2, tech replicate 2

value: control


title: P2C, 211116, S7

value: H3K9me2 (Abcam # ab1220)


title: Lovo, H3K27me3, COMBO, Rep1


title: Lovo, H3K27me3, MEKi, Rep2

value: AKTi


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 0 min, RPF fraction, biol replicate 2, tech replicate 2

value: RPF


title: Brain_mouse1_section1

value: Brain


title: Lovo, H3K27me3, MEKi, Rep1


title: P2C, 211116, S4

value: Mis12 antibody 2  (Genescript # U0148GF150)


title: Brain_mouse2_section1


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 0 min, RPF fraction, biol replicate 1, tech replicate 2


title: Mk, Old, Rep2

city: CHICAGO

first: Constantinos

last: chronis

state: IL

address: 900 S Ashland Ave, Mbrb 2370

department: Biochemistry and Molecular Genetics

institute: UIC

data_processing:
Basecalled data provided following sequencing in NovaseqX illunina instrument
Reads from RNA-seq experiments were mapped to the mouse genome (mm9) using TopHat software and only those reads that aligned with no more than two sequence mismatches were retained. RPKM values of mm9 RefSeq genes were calculated as described
fastq files were trimmed of their adapters with TrimGalore and then were aligned with STAR  to the GRCm39 genome
DEseq2 was used to identify differential gene expression with p-val <0.05 and fold-change >1.2
Assembly: GRCm39
Supplementary files format and content: TPM values are provided as part of table1

molecule: polyA RNA

source_name: Bone marrow Old MK cells

growth_protocol: FACS isolated young and old Mk cells were used for RNA extraction and gene expression comparisons

extract_protocol:
oligodt-selected mRNA
RNA was treated on column with 0.5 kunitz units of DNAse prior to elution according to manufacturers instructions. RNA from Young and Old FACS-isolated Mks  was extracted. Messenger RNA was captured using oligodT Dynabeads (Life Technologies). Strand-specific RNA-seq libraries were constructed using a TruSeq Stranded mRNA library Prep Kit, following the manufacturers instructions (RS-122-2101)

value: Bone marrow Old MK cells


title: Lovo, H3K27me3, EZH2i, Rep1


title: P2C, 211116, S2

value: Mis12 antibody 1  (Genescript # U0148GF150)


title: Lovo, H3K27me3, DMSO, Rep2

value: colon

value: DMSO


title: S. coelicolor A3(2) grown in liquid SMM medium, cold-shock, 120 min, RPF fraction, biol replicate 2, tech replicate 1

value: SMM

value: cold-shock


title: Mk, Young, Rep2

source_name: Bone marrow Young MK cells

value: Bone marrow Young MK cells


title: S. coelicolor A3(2) grown in liquid SMM medium, cold-shock, 120 min, RPF fraction, biol replicate 1, tech replicate 1


title: P2C, 211116, S3

value: lungs

value: infected macaque P2C

value: infection level 5+

value: pre immune serum Mis12 ab1 (input)


title: P2C, 211116, S5

value: collect date:2021

value: pre immune serum Mis12 ab2 (input)


title: Lovo, H3K27me3, EZH2i, Rep2

value: Lovo


title: Brain_mouse3_section1


title: Sella_hypo3

organism: Selaginella moellendorffii

value: shoot


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 120 min, RPF fraction, biol replicate 2, tech replicate 1

value: control

value: RPF


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 120 min, RPF fraction, biol replicate 1, tech replicate 2


title: P2C, 211116, S6

value: no antibody (input)


title: Sella_hypo1


title: Lovo, H3K27me3, DMSO, Rep1


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 120 min, RPF fraction, biol replicate 1, tech replicate 1


title: CLIP-seq TRMT10A replicate2

city: philadelphia

first: Fange

last: Liu

state: PA

address: 415 curie blvd, Clinical Research Building Rm 350

institute: UPENN

data_processing:
Raw reads were first trimmed according to recommended settings using cutadpt.
Processed reads were then mapped to the hg38 genome using Tophat2.
Cuffdiff was used to caculate the gene expression level changes.
Genome_build: hg38
Supplementary_files_format_and_content: peak, enrichment ratio

source_name: HEK 293T

growth_protocol: HEK293T cells were grown in DMEM (Gibco, 11965) media supplemented with 10% FBS (Gibco, 10438-026) and 1× Pen/Strep (Gibco, 15140).

extract_protocol: Total RNA was purified by TRIzol reagent (Invitrogen), following the manufacture’s instruction. mRNA was extracted from the total RNA by using Dynabeads mRNA Purification Kit (Ambion) following the instruction. The rRNA was further removed by RiboMinus Eukaryote Kit (Invitrogen).

treatment_protocol: Lipofectamine RNAiMax (13778150) ordered from Invitrogen was used for siRNA transfection, following the manufacturer’s instruction.

value: HEK 293T

tag: sirna


title: Sella_air3

value: aerobic conditions (21% O2)


title: Bend.3 cells stably expressing negative control 3A

city: shantou

first: xiaoqiang

last: xiao

state: Guangdong

address: North dongxia road

institute: Joint Shantou International Eye Center,Shantou University and the Chinese University of Hong Kong

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) [1] by (1) Removing reads containing sequencing adapter;
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) [2]. Bowtie2 (v2.2.5) [3] was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)

extract_protocol:
using TRIZol reagent  for total RNA extraction
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

value: stable cell line

value: corresponding empty vector


title: Mk, Old, Rep1

value: Bone marrow Old MK cells


title: CLIP-seq TRMT10A replicate1


title: Sella_air1


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 0 min, RPF fraction, biol replicate 2, tech replicate 1

value: SMM


title: Bend.3 cells stably expressing negative control 2A


title: S. coelicolor A3(2) grown in liquid SMM medium, control, 0 min, RPF fraction, biol replicate 1, tech replicate 1


title: input-seq Ctrl KD

value: Ctrl KD


title: Pteris_hypo3

organism: Pteris vittata


title: m6A-IP-seq Ctrl KD


title: Pteris_hypo1


title: Bend.3 cells stably expressing negative control 1A


title: Marcha_hypo2

organism: Marchantia polymorpha


title: Bend.3 cells stably expressing circular Slc17a5 3A

value: circSlc17a5 stably expressing


title: Pteris_air3


title: input-seq TRMT10A KD

value: TRMT10A KD


title: Bend.3 cells stably expressing circular Slc17a5 2A


title: Bend.3 cells stably expressing circular Slc17a5 1A


title: ClaI-1B - Brown, biorep 2

status: Public on May 30 2025

city: Vienna

first: Trinh

last: Phan-Canh

email: phancanht99@univie.ac.at, phancanhtrinh@gmail.com, karl.kuchler@univie.ac.at, karl.kuchler@univie.ac.at

state: Vienna

address: Dr.-Bohr-Gasse 9

department: Max Perutz Labs Vienna, Campus Vienna Biocenter

country: Austria

institute: Medical University of Vienna

data_processing:
The quality of raw reads were analyzed using FastQC (Andrews, 2010).
TrueSeq (Illumina) adapters were trimmed by using cutadapt v2.8 (https://cutadapt.readthedocs.io/en/stable/; settings: -q 30 -O 1). The reads were then mapped to C. auris genome (B8441) using NextGenMap (Sedlazeck et al., 2013), settings: -b -Q 30.
Optical read duplicates were removed using Picard tools (Broad Institute, https://broadinstitute.github.io/picard/, settings: MarkDuplicates REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT). Read counting was done using HTseq (Anders et al., 2014) in the union mode and the genomic annotation from C. auris B8441 (settings: -f bam -t gene -i ID).
Assembly: Differential gene expression analysis was done using the glm approach in edgeR (Robinson et al., 2009)
Supplementary files format and content: tab delimited .txt files containing the output of the HTSeq analysis (read counts)
Assembly: Candida auris B8441 - Genome version: s01-m01-r22 from Candida Genome Database
Supplementary files format and content: Matrix files are provided for each sample, comprising two columns: GeneID (Candida Genome Database) and raw read count.

organism: Candidozyma auris

source_name: fungal cell

growth_protocol: YPD, 30°C, 200 rpm, exponential phase

extract_protocol:
The total RNA was isolated from frozen samples using TRIZOL reagent.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: comparing different genotypes

value: fungal cell

tag: phase

value: planktonic cell at exponential phase

value: YPD


title: ClaI-1B - Brown, biorep 1


title: ClaI-1W - White, biorep 2


title: ClaI-1W - White, biorep 1


title: Marcha_hypo1


title: Marcha_air2


title: Mk, Young, Rep1

value: Bone marrow Young MK cells


title: m6A-IP-seq TRMT10A KD


title: ClaI-1P - Parent, biorep 2


title: ClaI-1W - White, biorep 3


title: ClaI-1B - Brown, biorep 3


title: Pteris_air1

value: shoot


title: crz2∆, biol rep 3

growth_protocol: YPD, 37°C, 200 rpm, exponential phase


title: WT, biol rep 2

source_name: 1133/P/13R, clinical isolate

value: 1133/P/13R, clinical isolate

value: WT


title: WT, biol rep 3


title: 1133/P/13R - ClaI-1P::wor1∆, biol rep 2

treatment_protocol: comparing different genotypes and phenotypes


title: 1133/P/13R - ClaI-1P::wor1∆, biol rep 1


title: WT, biol rep 1


title: 1133/P/13R - ClaI-1P::wor1∆, biol rep 3


title: 1133/P/13R - ClaI-1P::hyr3∆, biol rep 1


title: crz2∆, biol rep 2


title: 1133/P/13R - ClaI-1P::hyr3∆, biol rep 2


title: 462/P/14 - ClaI-2P::hyr3∆, biol rep 2


title: crz2∆, biol rep 1


title: ClaI-1P - Parent, biorep 1


title: 1133/P/13R - ClaI-1P::hyr3∆, biol rep 3


title: 462/P/14 - ClaI-2P::hyr3∆, biol rep 1


title: 1133/P/13R - ClaI-1P::msn4∆, biol rep 3


title: 1133/P/13R - ClaI-1P::msn4∆, biol rep 1


title: Marcha_air1


title: 1133/P/13R - ClaI-1P::msn4∆, biol rep 2


title: 462/P/14 - ClaI-2P::hyr3∆, biol rep 3


title: 1133/P/13R - ClaI-1B, biol rep 3


title: 1133/P/13R - ClaI-1B, biol rep 2


title: 1133/P/13R - ClaI-1B, biol rep 1


title: 462/P/14 - ClaI-2B, biol rep 1


title: 462/P/14 - ClaI-2B, biol rep 3


title: 1133/P/13R - ClaI-1P, biol rep 3


title: 1133/P/13R - ClaI-1P, biol rep 2


title: 462/P/14 - ClaI-2P, biol rep 2


title: 462/P/14 - ClaI-2P, biol rep 3


title: 462/P/14 - ClaI-2P, biol rep 1


title: 462/P/14 - ClaI-2B, biol rep 2


title: 1133/P/13R - ClaI-1P, biol rep 1


title: HYF2_IncreasedCopyNumber C

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

description: Library name: 4C_NODup_NP-OE-TF2

data_processing:
Transcript abundances were quantified based on version ucsf_hc.01_1.G217B of the Histoplasma G217B transcriptome (S5 Data of [PMID:26177267 Gilmore et al]).  Relative abundances (reported as TPM values [PMID:21816040 Li and Dewey]) and estimated counts (est_counts) of each transcript in each sample were estimated by alignment free comparison of k-mers between the reads and mRNA sequences using KALLISTO version 0.46.2 [PMID:27043002 Bray et al].  Further analysis was restricted to transcripts with estimated counts ≥ 10 in at least three samples.
Differentially expressed genes were identified by comparing replicate means for contrasts of interest using LIMMA version 3.46.0 [PMID:16646809 Symth, PMID:25605792 Ritchie et al].  Genes were considered significantly differentially expressed if they were statistically significant (at 5% FDR) with an effect size of at least 1.5x (absolute log2 fold change ≥ 0.585) for a given contrast.
Assembly: Version ucsf_hc.01_1.G217B of the Hc G217B transcriptome (S5 Data of PMID:26177267)
Supplementary files format and content: The results of the LIMMA analysis are in processed data file Table_SHAS09.txt, an Excel-compatible tab-delimited text conforming to JavaTreeView extended CDT format. Each row is a transcript, with the UNIQID column giving the ucsf_hc.01_1.G217B systematic gene name. The NAME column gives short names taken from Data S1 of [PMID:35089059] with additional names and corrections based on human curation. The next 9 columns give KALLISTO estimated counts for each transcript in each sample.  The next columns give LIMMA BH-adjusted p-values for differential expression in each of the 2 contrasts, and the corresponding LIMMA-fit log2 ratios are given in the final 2 columns.  Description and HcG217B_pred (WUSTL G217B predicted gene accessions), HcG217B_rc (Edwards et al G217B transcript accessions [PMID: 24112604]), and HcG217B_acc (UCSF1 gene accessions [PMID:35089059]); and Ryp1_ChIP, Ryp2_ChIP, Ryp3_ChIP, and Ryp4_C (indicating genes with promoters bound by Ryp TFs in [PMID: 23935449]) are taken from Data S1 of [PMID:35089059].  UCSF2_acc and UCSF3_acc give gene accessions from the G217B assemblies of [bioRxiv: 2025.05.05.652209v1].  CR is "critical_region" for genes in the critical region, "chr7" for genes on chromosome 7 but outside of the critical region, and blank for all other genes.  GWEIGHT is a place-holder column for JavaTreeView compatibility.  The estimated counts in this file are sufficient to recapitulate the LIMMA analysis.

organism: Histoplasma ohiense

growth_protocol: HYF1 increased copy number, HYF2 increased copy number, and control samples for RNA sequencing were collected from cultures started at OD600 of 0.2 then grown for 2 days in standard yeast conditions in HMM media not supplemented with GlcNAc.

extract_protocol:
Cells were collected by filtration, flash frozen in liquid nitrogen, and stored at -80°C prior to RNA extraction.
Libraries for RNAseq were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA). Average fragment size and presence of excess adapter was determined with High Sensitivity DNA Bioanalyzer chip from Agilent Technologies (Santa Clara, CA). Library concentration was measured by Qubit dsDNA BR Quantification Assay Kit (Invitrogen) then pooled with equal DNA mass from each library. The final libraries were submitted to the UCSF Center for Advanced Technology for sequencing on an Illumina Novaseq X 10B sequencer.

tag: replicate

value: C


title: Control A

description: Library name: 5A_NODup_NP-OE-EV

value: Control

value: A


title: HYF2_IncreasedCopyNumber A

description: Library name: 4A_NODup_NP-OE-TF2


title: HYF1_IncreasedCopyNumber C

description: Library name: 3C_NODup_NP-OE-TF1


title: Control B

description: Library name: 5B_NODup_NP-OE-EV

value: B


title: HYF1_IncreasedCopyNumber A

description: Library name: 3A_NODup_NP-OE-TF1


title: Control C

description: Library name: 5C_NODup_NP-OE-EV


title: Liquid culture from hyphae with single copy of chr7 after seven days transitioning to yeast at 37C, replicate B

description: Library name: 32_H_A23_Smooth_D7_37C

data_processing:
Transcript abundances were quantified based on version ucsf_hc.01_1.G217B of the Histoplasma G217B transcriptome (S5 Data of [PMID:26177267 Gilmore et al]).  Relative abundances (reported as TPM values [PMID:21816040 Li and Dewey]) and estimated counts (est_counts) of each transcript in each sample were estimated by alignment free comparison of k-mers between the reads and mRNA sequences using KALLISTO version 0.46.2 [PMID:27043002 Bray et al].  Further analysis was restricted to transcripts with estimated counts ≥ 10 in at least three samples.
Differentially expressed genes were identified by comparing replicate means for contrasts of interest using LIMMA version 3.46.0 [PMID:16646809 Symth, PMID:25605792 Ritchie et al].  Genes were considered significantly differentially expressed if they were statistically significant (at 5% FDR) with an effect size of at least 1.5x (absolute log2 fold change ≥ 0.585) for a given contrast.
Assembly: Version ucsf_hc.01_1.G217B of the Hc G217B transcriptome (S5 Data of PMID:26177267)
Supplementary files format and content: The results of the LIMMA analysis are in processed data file Table_SHAS07.txt, an Excel-compatible tab-delimited text conforming to JavaTreeView extended CDT format. Each row is a transcript, with the UNIQID column giving the ucsf_hc.01_1.G217B systematic gene name. The NAME column gives short names taken from Data S1 of [PMID:35089059] with additional names and corrections based on human curation. The next 36 columns give KALLISTO estimated counts for each transcript in each sample.  The next columns give LIMMA BH-adjusted p-values for differential expression in each of the 20 contrasts, and the corresponding LIMMA-fit log2 ratios are given in the final 20 columns.  Description and HcG217B_pred (WUSTL G217B predicted gene accessions), HcG217B_rc (Edwards et al G217B transcript accessions [PMID: 24112604]), and HcG217B_acc (UCSF1 gene accessions [PMID:35089059]); and Ryp1_ChIP, Ryp2_ChIP, Ryp3_ChIP, and Ryp4_C (indicating genes with promoters bound by Ryp TFs in [PMID: 23935449]) are taken from Data S1 of [PMID:35089059].  UCSF2_acc and UCSF3_acc give gene accessions from the G217B assemblies of [bioRxiv: 2025.05.05.652209v1].  CR is "critical_region" for genes in the critical region, "chr7" for genes on chromosome 7 but outside of the critical region, and blank for all other genes.  GWEIGHT is a place-holder column for JavaTreeView compatibility.  The estimated counts in this file are sufficient to recapitulate the LIMMA analysis.

growth_protocol: To obtain matched steady-state yeast and hyphae, cultures were started from single yeast colonies and grown as yeast for two days. From this, plates without GlcNAc at 37°C and with GlcNAc at 25°C were started in parallel and grown for 20 days. Hyphal cultures were then started from 25°C plates, grown for 2 days in liquid HMM supplemented with GlcNAc to ensure full hyphal conversion, passaged 1:6 to HMM without GlcNAc for five days, full hyphal growth was confirmed by microscopy, and hyphae were passaged 1:25 in media without GlcNAc and grown for seven days. Yeast cultures were started from 37°C plates and passaged 1:25 3 times a week in media without GlcNAc for the same two weeks as the hyphal cultures. Steady state and two-day transition timepoints were taken from two-day old cultures. Seven-day transition cultures were collected after seven days in conditions inducing the opposite morphology without passaging. Each condition was assessed in biological triplicate, media was not supplemented with GlcNAc for any of these conditions.

tag: initial morphology

value: hyphae

value: single copy

tag: growth condition


title: Liquid culture from hyphae with duplication of chr7 after seven days transitioning to yeast at 37C, replicate B

description: Library name: 35_H_A23_Rough_D7_37C

value: duplication


title: Liquid culture from hyphae with single copy of chr7 after seven days transitioning to yeast at 37C, replicate C

description: Library name: 33_H_A23_Smooth_D7_37C


title: Liquid culture from hyphae with duplication of chr7 after seven days transitioning to yeast at 37C, replicate C

description: Library name: 36_H_A23_Rough_D7_37C


title: Liquid culture from hyphae with single copy of chr7 after seven days transitioning to yeast at 37C, replicate A

description: Library name: 31_H_A23_Smooth_D7_37C


title: Liquid culture from hyphae with duplication of chr7 after seven days transitioning to yeast at 37C, replicate A

description: Library name: 34_H_A23_Rough_D7_37C


title: Liquid culture from hyphae with duplication of chr7 after two days at 25C, replicate B

description: Library name: 29_H_A23_Rough_D2_25C

value: two days at 25C


title: Liquid culture from hyphae with duplication of chr7 after two days at 25C, replicate C

description: Library name: 30_H_A23_Rough_D2_25C


title: Liquid culture from hyphae with duplication of chr7 after two days transitioning to yeast at 37C, replicate C

description: Library name: 24_H_A23_Rough_D2_37C

value: two days transitioning to yeast at 37C


title: Liquid culture from hyphae with single copy of chr7 after two days at 25C, replicate C

description: Library name: 27_H_A23_Smooth_D2_25C


title: Liquid culture from hyphae with duplication of chr7 after two days transitioning to yeast at 37C, replicate A

description: Library name: 22_H_A23_Rough_D2_37C


title: Liquid culture from hyphae with duplication of chr7 after two days at 25C, replicate A

description: Library name: 28_H_A23_Rough_D2_25C


title: Liquid culture from hyphae with single copy of chr7 after two days transitioning to yeast at 37C, replicate C

description: Library name: 21_H_A23_Smooth_D2_37C


title: Liquid culture from hyphae with single copy of chr7 after two days at 25C, replicate A

description: Library name: 25_H_A23_Smooth_D2_25C


title: Liquid culture from hyphae with single copy of chr7 after two days at 25C, replicate B

description: Library name: 26_H_A23_Smooth_D2_25C


title: Liquid culture from hyphae with duplication of chr7 after two days transitioning to yeast at 37C, replicate B

description: Library name: 23_H_A23_Rough_D2_37C


title: HYF1_IncreasedCopyNumber B

description: Library name: 3B_NODup_NP-OE-TF1


title: HYF2_IncreasedCopyNumber B

description: Library name: 4B_NODup_NP-OE-TF2


title: Liquid culture from yeast with duplication of chr7 after seven days transitioning to hyphae at 25C, replicate C

description: Library name: 18_Y_A23_Rough_D7_25C

value: yeast


title: Liquid culture from yeast with duplication of chr7 after seven days transitioning to hyphae at 25C, replicate A

description: Library name: 16_Y_A23_Rough_D7_25C

value: fungal cell


title: Liquid culture from yeast with duplication of chr7 after seven days transitioning to hyphae at 25C, replicate B

description: Library name: 17_Y_A23_Rough_D7_25C


title: Liquid culture from yeast with duplication of chr7 after two days transitioning to hyphae at 25C, replicate B

description: Library name: 11_Y_A23_Rough_D2_25C

value: two days transitioning to hyphae at 25C


title: Liquid culture from yeast with single copy of chr7 after seven days transitioning to hyphae at 25C, replicate C

description: Library name: 15_Y_A23_Smooth_D7_25C


title: Liquid culture from yeast with single copy of chr7 after two days transitioning to hyphae at 25C, replicate C

description: Library name: 09_Y_A23_Smooth_D2_25C


title: Liquid culture from yeast with single copy of chr7 after seven days transitioning to hyphae at 25C, replicate A

description: Library name: 13_Y_A23_Smooth_D7_25C


title: Liquid culture from yeast with duplication of chr7 after two days transitioning to hyphae at 25C, replicate C

description: Library name: 12_Y_A23_Rough_D2_25C


title: Liquid culture from yeast with single copy of chr7 after seven days transitioning to hyphae at 25C, replicate B

description: Library name: 14_Y_A23_Smooth_D7_25C


title: Liquid culture from yeast with single copy of chr7 after two days transitioning to hyphae at 25C, replicate B

description: Library name: 08_Y_A23_Smooth_D2_25C


title: Liquid culture from yeast with single copy of chr7 after two days transitioning to hyphae at 25C, replicate A

description: Library name: 07_Y_A23_Smooth_D2_25C


title: Liquid culture from yeast with single copy of chr7 after two days at 37C, replicate A

description: Library name: 01_Y_A23_Smooth_D2_37C

value: two days at 37C


title: Liquid culture from yeast with duplication of chr7 after two days at 37C, replicate B

description: Library name: 05_Y_A23_Rough_D2_37C


title: Liquid culture from yeast with duplication of chr7 after two days transitioning to hyphae at 25C, replicate A

description: Library name: 10_Y_A23_Rough_D2_25C


title: Liquid culture from yeast with single copy of chr7 after two days at 37C, replicate B

description: Library name: 02_Y_A23_Smooth_D2_37C


title: Liquid culture from yeast with duplication of chr7 after two days at 37C, replicate C

description: Library name: 06_Y_A23_Rough_D2_37C


title: Liquid culture from hyphae with single copy of chr7 after two days transitioning to yeast at 37C, replicate A

description: Library name: 19_H_A23_Smooth_D2_37C


title: for EFG1, R1::efg1∆, biol rep 2

source_name: White form

value: White form

value: planktonic cell at exponential phase


title: Liquid culture from yeast with duplication of chr7 after two days at 37C, replicate A

description: Library name: 04_Y_A23_Rough_D2_37C


title: for EFG1, R1::efg1∆, biol rep 3


title: for EFG1, WT R1, biol rep 1


title: Liquid culture from hyphae with single copy of chr7 after two days transitioning to yeast at 37C, replicate B

description: Library name: 20_H_A23_Smooth_D2_37C


title: for EFG1, WT R1, biol rep 3


title: for RCA1, R2::rca1∆ clone 2, biol rep 3


title: for EFG1, R1::efg1∆, biol rep 1


title: WT_5w_batch2

city: Tsukuba

first: Hiromi

last: Yanagisawa

address: 1-1-1 Tennodai

department: TARA center

institute: University of Tsukuba

description:
Library name: Sample8
10 x Genomics

library_source: transcriptomic single cell

data_processing:
The sequenced data were processed into expression matrices with the Cell Ranger Single cell software suite 6.1.2 (https://www.10xgenomics.com).
Assembly: Mouse mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: Asc Aorta

extract_protocol:
The pooled ascending aortas of mutant and wild-type mice were dissected and incubated in enzyme solution (20 mg/mL collagenase type A, 5 mg/ mL elastase, 60 U/mL DNase) for 1 hour at 37ºC. The cell suspension was filtered through a 70 µm strainer and stained with 7-Aminoactinomycin D to discriminate a live/dead cell. Live cells were sorted using FACS machine (BD LSRFortessa X-20) into 0.4% BSA in PBS.
Single cells were processed through the Chromium™ Single Cell Platform (10x Genomics) as per the manufacturer’s protocol. Single cell suspensions were partitioned into Gel Beads in Emulsion in the Chromium™ system, followed by cDNA amplification, shearing and 5’ adaptor and sample index attachment.

value: Asc Aorta

tag: age


title: for EFG1, WT R1, biol rep 2

value: WT


title: AD_5w_batch2

description:
Library name: Sample7
10 x Genomics

tag: tissue

value: Mutant (AD)


title: for RCA1, R2::rca1∆ clone 2, biol rep 2

tag: cell line


title: for RCA1, R2::rca1∆ clone 2, biol rep 1

tag: genotype


title: AD_5w_batch1

description:
Library name: Sample5
10 x Genomics


title: AD_3w_batch2

description:
Library name: Sample4
10 x Genomics


title: for RCA1, R2::rca1∆ clone 1, biol rep 1


title: Liquid culture from yeast with single copy of chr7 after two days at 37C, replicate C

description: Library name: 03_Y_A23_Smooth_D2_37C

value: C


title: WT_3w_batch2

description:
Library name: Sample3
10 x Genomics


title: AD_3w_batch1

description:
Library name: Sample2
10 x Genomics


title: for RCA1, R1::rca1∆, biol rep 1


title: WT_3w_batch1

description:
Library name: Sample1
10 x Genomics


title: Astro_SD_C3

city: Philadelphia

first: Utham Kashyap

last: Valekunja

address: 3400 Civic Center Boulevard,

department: Department of Systems Pharmacology & Therapeutics, Perelman School of Medicine,

institute: University of Pennsylvania

data_processing:
The reads were aligned to the Mouse genome GRCm39 using STAR version 2.7.10a. Transcript abundance was quantified as FPKM, TPM, and counts using StringTie v2.2.1. Genes with counts below 10 in all the samples were excluded from further analysis.  Differential expression analysis was performed on the above filtered counts table using R package DESeq2 v1.44.0 to compare SD versus NS conditions. Log fold changes were adjusted using the lfcShrink function within the DESeq2 package. Genes with an FDR-adjusted p-value less than 0.05 were considered differentially expressed.
Assembly: GRCm39
Supplementary files format and content: gene_abund.tsv
Supplementary files format and content: counts.gtf

source_name: Cerebral Cortex

extract_protocol:
Astrocytes and neuron samples were lysed using TRIzol®, and RNA was extracted with the Direct-zol™ RNA MiniPrep Kit (Zymo Research), following the manufacturer’s instructions.
Library preparation and RNA-sequencing Astrocytes and neuron samples were lysed using TRIzol®, and RNA was extracted with the Direct-zol™ RNA MiniPrep Kit (Zymo Research), following the manufacturer’s instructions. 1μg of RNA was used to prepare total RNA libraries with the KAPA-RiboErase Hyper Prep kit, as per the manufacturer’s protocol. The libraries were sequenced on an Illumina HiSeq 4000, generating 100bp pair-ended reads. The reads were aligned to the Mouse genome GRCm39 using STAR version 2.7.10a. Transcript abundance was quantified as FPKM, TPM, and counts using StringTie v2.2.1. Genes with counts below 10 in all the samples were excluded from further analysis.  Differential expression analysis was performed on the above filtered counts table using R package DESeq2 v1.44.0 to compare SD versus NS conditions. Log fold changes were adjusted using the lfcShrink function within the DESeq2 package. Genes with an FDR-adjusted p-value less than 0.05 were considered differentially expressed.

value: Cerebral Cortex

value: Astrocyte

tag: treatment

value: SD


title: for RCA1, R1::rca1∆, biol rep 2


title: Neuro_SD_C3

value: Neuron


title: for RCA1, WT R2, biol rep 3


title: Neuro_NS_C3

value: NS


title: for RCA1, WT R2, biol rep 2


title: Astro_SD_C2


title: for RCA1, WT R2, biol rep 1


title: for RCA1, WT R1, biol rep 2


title: Astro_SD_C1


title: WT_5w_batch1

description:
Library name: Sample6
10 x Genomics


title: for RCA1, WT R1, biol rep 3


title: Astro_NS_C3


title: Patient3, MarcoLo,  Marco-IBA+, 013

city: ROCHESTER

first: William

last: Sherman

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description:
Library name: L3_MarcoLo_013 | Marco-IBA+
FFPE GeoMx sequencing

data_processing:
Sequencing data were processed following the NanoString Standard Standalone Pipeline (2.3.3.10) and Illumina's bcl2fastq (2.20.0.422) to perform the initial demultiplex.
Digital count conversion (DCC) files were processed in R (4.2.2) using GeomxTools (3.2.0) and NanoStringNCTools (1.6.1).
QC and normalization was done following NanoString guidelines for Data QC for NGS Readout.
Differential expression analysis was performed using GeomxTools (3.2.0).
Assembly: mm10
Supplementary files format and content: comma-separated files with normalized GeoMx-Seq gene expression
Library strategy: Spatial Transcriptomics

source_name: liver

extract_protocol:
Library prep was completed following the NanoString Library Prep protocol
GeoMx-Seq

treatment_protocol: ROI segmentation was automatically performed by the GeoMx DSP analysis suite software based on the morphology markers signal, and the ROIs were divided into four segments: DESMIN+ (DESMIN+/MARCO-/IBA1-), MARCO+ (DESMIN-/MARCO+/IBA1+), MARCO- (DESMIN-/MARCO-/IBA1+) and ELSE (DESMIN-/MARCO-/IBA1-). 13-14 ROIs were selected on each liver sample; 6/7 were MARCO-High, and 6/7 were MARCO-Low, with 216 segments (libraries).

value: liver

tag: disease

value: fibrosis

value: Macrophage

value: treated CCl4


title: Astro_NS_C2


title: for RCA1, R2::rca1∆ clone 1, biol rep 2


title: Patient3, MarcoLo,  Marco+IBA+, 013

description:
Library name: L3_MarcoLo_013 | Marco+IBA+
FFPE GeoMx sequencing


title: for RCA1, R1::rca1∆, biol rep 3


title: for RCA1, R2::rca1∆ clone 1, biol rep 3


title: for RCA1, WT R1, biol rep 1


title: Neuro_SD_C1


title: Patient3, MarcoLo,  Marco-IBA-Des-, 005

description:
Library name: L3_MarcoLo_005 | Else
FFPE GeoMx sequencing

value: Other


title: Patient3, MarcoLo,  Marco-IBA-Des-, 006

description:
Library name: L3_MarcoLo_006 | Else
FFPE GeoMx sequencing


title: SNL_2

city: Nanchong

first: Guohui

last: Jiang

address: 234 Fujiang Road

department: Institute of Neurological Diseases

institute: North Sichuan Medical College

data_processing:
RSEM
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Hippocampal tissue

extract_protocol:
Total RNA was harvested using TRIzol (invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit folowing manufacturer's protocols.

treatment_protocol: The total was divided into three groups. In the Sham group, only the L5 spinal nerve was identified without ligation, followed by solvent intervention post-surgery. The SNL group underwent spinal nerve ligation modeling, followed by solvent intervention post-surgery. The CBD group received a 5mg/kg CBD intraperitoneal injection for 15 days after spinal nerve ligation.

value: Hippocampal tissue

tag: group

value: SNL


title: Patient3, MarcoLo,  Marco-IBA+, 005

description:
Library name: L3_MarcoLo_005 | Marco-IBA+
FFPE GeoMx sequencing


title: SNL_3


title: Patient3, MarcoLo,  Marco+IBA+, 005

description:
Library name: L3_MarcoLo_005 | Marco+IBA+
FFPE GeoMx sequencing


title: Sham_3

value: sham-operated


title: Neuro_SD_C2


title: Neuro_NS_C1


title: Patient3, MarcoLo,  Marco-IBA-Des-, 003

description:
Library name: L3_MarcoLo_003 | Else
FFPE GeoMx sequencing


title: Patient3, MarcoLo,  Des+, 005

description:
Library name: L3_MarcoLo_005 | Des+
FFPE GeoMx sequencing

value: HSC


title: Sham_1


title: CBD_3

value: CBD (5mg/kg, ip)


title: Patient3, MarcoLo,  Des+, 003

description:
Library name: L3_MarcoLo_003 | Des+
FFPE GeoMx sequencing


title: Patient3, MarcoLo,  Marco+IBA+, 003

description:
Library name: L3_MarcoLo_003 | Marco+IBA+
FFPE GeoMx sequencing


title: Patient3, MarcoLo,  Marco-IBA+, 003

description:
Library name: L3_MarcoLo_003 | Marco-IBA+
FFPE GeoMx sequencing


title: Patient3, MarcoLo,  Marco-IBA-Des-, 001

description:
Library name: L3_MarcoLo_001 | Else
FFPE GeoMx sequencing


title: CBD_2


title: Astro_NS_C1


title: Patient3, MarcoLo,  Marco-IBA-Des-, 007

description:
Library name: L3_MarcoLo_007 | Else
FFPE GeoMx sequencing


title: CBD_1


title: Neuro_NS_C2


title: Patient3, MarcoLo,  Des+, 001

description:
Library name: L3_MarcoLo_001 | Des+
FFPE GeoMx sequencing


title: Control_rna_rep3_ΔHDcomparison

city: Columbus

first: Genevieve

last: Kendall

state: Ohio

address: 575 Children's Crossroads

department: Center for Childhood Cancer Research

institute: Nationwide Children's Hospital

description:
Library name: GCK-NGS368
Id geneSymbol CNTLrep1 CNTLrep2 CNTLrep3 HDmutrep1 HDmutrep2 HDmutrep3 HDmutrep4 HDmutrep5 P3Frep1 P3Frep2 P3Frep3 norm.CNTLrep1 norm.CNTLrep2 norm.CNTLrep3 norm.HDmutrep1 norm.HDmutrep2 norm.HDmutrep3 norm.HDmutrep4 norm.HDmutrep5 norm.P3Frep1 norm.P3Frep2 norm.P3Frep3 baseMean CNTL HDmut P3F FoldChange log2FoldChange pvalue padj dispGeneEst dispFit dispMAP dispersion betaConv maxCooks

data_processing:
FASTQC and MultiQC assessed quality
TrimGalore removed adapter sequences
Reads were alligned with STAR
Reads were assigned to genomic feature by featureCount
Differential gene expression was completed with DESeq2
Assembly: danRer11
Supplementary files format and content: tab-delimb text file include raw counts, normalized counts, and differential expression analysis
Supplementary files format and content: bigwig on normalized counts for each replicate

organism: Danio rerio

source_name: Whole Embryo

growth_protocol: WIK adults were in-crossed and embryos were injected at the single-cell stage with mRNA. Embryos were incubated at 32ºC for 5.25 hours

extract_protocol:
RNA was isolated from snap-frozen embryo alliquots with the QIAGEN Rneasy Mini kit with on-colun DNAse digestion
Libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and a polyA enrichment step

treatment_protocol: Embryos were injected with 100 ng/uL PAX3::FOXO1-2A-sfGFP mRNA or equal molarity of pCS2+MCS-P2A-sfGFP mRNA

value: Whole Embryo

value: WIK (Wild-type)

tag: developmental stage

value: 6 hours post-fertilization

value: Injected with 32 ng/uL pCS2+MCS-P2A-sfGFP mRNA


title: Control_rna_rep2_ΔHDcomparison

description:
Library name: GCK-NGS367
Id geneSymbol CNTLrep1 CNTLrep2 CNTLrep3 HDmutrep1 HDmutrep2 HDmutrep3 HDmutrep4 HDmutrep5 P3Frep1 P3Frep2 P3Frep3 norm.CNTLrep1 norm.CNTLrep2 norm.CNTLrep3 norm.HDmutrep1 norm.HDmutrep2 norm.HDmutrep3 norm.HDmutrep4 norm.HDmutrep5 norm.P3Frep1 norm.P3Frep2 norm.P3Frep3 baseMean CNTL HDmut P3F FoldChange log2FoldChange pvalue padj dispGeneEst dispFit dispMAP dispersion betaConv maxCooks


title: Patient3, MarcoLo,  Marco-IBA+, 001

description:
Library name: L3_MarcoLo_001 | Marco-IBA+
FFPE GeoMx sequencing


title: SNL_1


title: Control_rna_rep1_ΔHDcomparison

description:
Library name: GCK-NGS366
Id geneSymbol CNTLrep1 CNTLrep2 CNTLrep3 HDmutrep1 HDmutrep2 HDmutrep3 HDmutrep4 HDmutrep5 P3Frep1 P3Frep2 P3Frep3 norm.CNTLrep1 norm.CNTLrep2 norm.CNTLrep3 norm.HDmutrep1 norm.HDmutrep2 norm.HDmutrep3 norm.HDmutrep4 norm.HDmutrep5 norm.P3Frep1 norm.P3Frep2 norm.P3Frep3 baseMean CNTL HDmut P3F FoldChange log2FoldChange pvalue padj dispGeneEst dispFit dispMAP dispersion betaConv maxCooks


title: Sham_2


title: PAX3FOXO1_rna_rep3_ΔHDcomparison

description:
Library name: GCK-NGS365
Id geneSymbol CNTLrep1 CNTLrep2 CNTLrep3 HDmutrep1 HDmutrep2 HDmutrep3 HDmutrep4 HDmutrep5 P3Frep1 P3Frep2 P3Frep3 norm.CNTLrep1 norm.CNTLrep2 norm.CNTLrep3 norm.HDmutrep1 norm.HDmutrep2 norm.HDmutrep3 norm.HDmutrep4 norm.HDmutrep5 norm.P3Frep1 norm.P3Frep2 norm.P3Frep3 baseMean CNTL HDmut P3F FoldChange log2FoldChange pvalue padj dispGeneEst dispFit dispMAP dispersion betaConv maxCooks

value: Injected with 100 ng/uL PAX3::FOXO1 mRNA


title: Patient3, MarcoHi,  Marco-IBA-Des-, 007

description:
Library name: L3_MarcoHi_007 | Else
FFPE GeoMx sequencing


title: Patient3, MarcoHi,  Marco-IBA+, 007

description:
Library name: L3_MarcoHi_007 | Marco-IBA+
FFPE GeoMx sequencing


title: PAX3FOXO1_rna_rep2_ΔHDcomparison

description:
Library name: GCK-NGS364
Id geneSymbol CNTLrep1 CNTLrep2 CNTLrep3 HDmutrep1 HDmutrep2 HDmutrep3 HDmutrep4 HDmutrep5 P3Frep1 P3Frep2 P3Frep3 norm.CNTLrep1 norm.CNTLrep2 norm.CNTLrep3 norm.HDmutrep1 norm.HDmutrep2 norm.HDmutrep3 norm.HDmutrep4 norm.HDmutrep5 norm.P3Frep1 norm.P3Frep2 norm.P3Frep3 baseMean CNTL HDmut P3F FoldChange log2FoldChange pvalue padj dispGeneEst dispFit dispMAP dispersion betaConv maxCooks


title: PAX3FOXO1ΔHD_rna_rep5

description:
Library name: GCK-NGS358
Id geneSymbol CNTLrep1 CNTLrep2 CNTLrep3 HDmutrep1 HDmutrep2 HDmutrep3 HDmutrep4 HDmutrep5 P3Frep1 P3Frep2 P3Frep3 norm.CNTLrep1 norm.CNTLrep2 norm.CNTLrep3 norm.HDmutrep1 norm.HDmutrep2 norm.HDmutrep3 norm.HDmutrep4 norm.HDmutrep5 norm.P3Frep1 norm.P3Frep2 norm.P3Frep3 baseMean CNTL HDmut P3F FoldChange log2FoldChange pvalue padj dispGeneEst dispFit dispMAP dispersion betaConv maxCooks

value: Injected with 94 ng/uL PAX3::FOXO1ΔHD-2A-sfGFP mRNA


title: Patient3, MarcoHi,  Marco+IBA+, 007

description:
Library name: L3_MarcoHi_007 | Marco+IBA+
FFPE GeoMx sequencing


title: Patient3, MarcoHi,  Des+, 006

description:
Library name: L3_MarcoHi_006 | Des+
FFPE GeoMx sequencing


title: Patient3, MarcoHi,  Marco-IBA-Des-, 006

description:
Library name: L3_MarcoHi_006 | Else
FFPE GeoMx sequencing


title: PAX3FOXO1ΔHD_rna_rep3

description:
Library name: GCK-NGS356
Id geneSymbol CNTLrep1 CNTLrep2 CNTLrep3 HDmutrep1 HDmutrep2 HDmutrep3 HDmutrep4 HDmutrep5 P3Frep1 P3Frep2 P3Frep3 norm.CNTLrep1 norm.CNTLrep2 norm.CNTLrep3 norm.HDmutrep1 norm.HDmutrep2 norm.HDmutrep3 norm.HDmutrep4 norm.HDmutrep5 norm.P3Frep1 norm.P3Frep2 norm.P3Frep3 baseMean CNTL HDmut P3F FoldChange log2FoldChange pvalue padj dispGeneEst dispFit dispMAP dispersion betaConv maxCooks


title: Patient3, MarcoHi,  Des+, 005

description:
Library name: L3_MarcoHi_005 | Des+
FFPE GeoMx sequencing


title: Patient3, MarcoLo,  Marco+IBA+, 001

description:
Library name: L3_MarcoLo_001 | Marco+IBA+
FFPE GeoMx sequencing


title: Patient3, MarcoHi,  Marco-IBA-Des-, 005

description:
Library name: L3_MarcoHi_005 | Else
FFPE GeoMx sequencing


title: PAX3FOXO1ΔHD_foxo1_input_rep2

description: Library name: GCK-NGS372

data_processing:
Reads were alligned with Bowtie2
PCR duplicates were removed with PICARD
FASTQ files were scaled according to spike-in ratiowith PICARD
Peaks were called and bigwigs were generate with MACS2
Differential enrichment analysis was completed with diffBind
Assembly: danRer11
Supplementary files format and content: bigWig for signal visualization of each replicate
Supplementary files format and content: concensus peaks per condition between the replicates

extract_protocol:
Embryos were dissociated into single cells, fixed in 1% formaldehyde for 10 min, and quenched in 125 mM glycine. RH30 were cultured and fixed in a similar manner.  For the anti-FOXO1 ChIP-seq 2,000,000 zebrafish cells and 250,000 RH30 cells were sonicated with a bioruptor PICO and incubated with 4 μG anti-FOXO1 (Cell Signaling, C29H4). For the anti-H3K27ac ChIP-seq 1,000,000 zebrafish cells and1,000,000 RH30 cells were sonicated with a EpiShear probe sonicator and incubated with 4 μG anti-H3K27ac (Active Motif, 39133).
DNA libraries underwent end-repair with either the End-It DNA End-Repair Kit (Lucigen, ER81050) or NEBNext End Repair (NEB, E6050S), A-tailing, and adapter ligation for Illumina sequencing. Libraries were selected with 1.8X AMPure beads selection, amplfied by qRT-PCR with Illumina sequencing adapters, and selected with a 1.0X AMPure beads selection.

treatment_protocol: Embryos were injected with 100 ng/uL PAX3::FOXO1-2A-sfGFP mRNA or equal molarity of CNTL-sfGFP or pCS2+MCS-P2A-sfGFP mRNA.

value: WIK (Wildtype)

value: Input DNA


title: Patient3, MarcoHi,  Marco+IBA+, 006

description:
Library name: L3_MarcoHi_006 | Marco+IBA+
FFPE GeoMx sequencing

value: liver

value: fibrosis


title: PAX3FOXO1ΔHD_rna_rep1

description:
Library name: GCK-NGS354
Id geneSymbol CNTLrep1 CNTLrep2 CNTLrep3 HDmutrep1 HDmutrep2 HDmutrep3 HDmutrep4 HDmutrep5 P3Frep1 P3Frep2 P3Frep3 norm.CNTLrep1 norm.CNTLrep2 norm.CNTLrep3 norm.HDmutrep1 norm.HDmutrep2 norm.HDmutrep3 norm.HDmutrep4 norm.HDmutrep5 norm.P3Frep1 norm.P3Frep2 norm.P3Frep3 baseMean CNTL HDmut P3F FoldChange log2FoldChange pvalue padj dispGeneEst dispFit dispMAP dispersion betaConv maxCooks


title: PAX3FOXO1ΔHD_rna_rep2

description:
Library name: GCK-NGS355
Id geneSymbol CNTLrep1 CNTLrep2 CNTLrep3 HDmutrep1 HDmutrep2 HDmutrep3 HDmutrep4 HDmutrep5 P3Frep1 P3Frep2 P3Frep3 norm.CNTLrep1 norm.CNTLrep2 norm.CNTLrep3 norm.HDmutrep1 norm.HDmutrep2 norm.HDmutrep3 norm.HDmutrep4 norm.HDmutrep5 norm.P3Frep1 norm.P3Frep2 norm.P3Frep3 baseMean CNTL HDmut P3F FoldChange log2FoldChange pvalue padj dispGeneEst dispFit dispMAP dispersion betaConv maxCooks


title: Patient3, MarcoHi,  Marco-IBA-Des-, 004

description:
Library name: L3_MarcoHi_004 | Else
FFPE GeoMx sequencing

value: treated CCl4


title: Patient3, MarcoHi,  Marco+IBA+, 005

description:
Library name: L3_MarcoHi_005 | Marco+IBA+
FFPE GeoMx sequencing

value: Macrophage


title: Patient3, MarcoHi,  Marco-IBA+, 005

description:
Library name: L3_MarcoHi_005 | Marco-IBA+
FFPE GeoMx sequencing


title: PAX3FOXO1ΔHD_foxo1_input_rep1

description: Library name: GCK-NGS370


title: PAX3FOXO1ΔHD_foxo1_chip_rep1

description: Library name: GCK-NGS369

value: FOXO1 (Cell Signaling, C29H4)


title: Patient3, MarcoHi,  Des+, 007

description:
Library name: L3_MarcoHi_007 | Des+
FFPE GeoMx sequencing


title: Patient3, MarcoHi,  Marco-IBA+, 004

description:
Library name: L3_MarcoHi_004 | Marco-IBA+
FFPE GeoMx sequencing


title: Tg_c591_11_TransTag

city: Denton

first: Fanju

last: Meng

state: Texas

address: 1155 Union Circle #305220

department: Department of Biological Sciences

institute: University of North Texas

data_processing:
Briefly, a customized bash script was used to identify chimeric reads and remove Tn5 adapter and Tol2 sequences (https://github.com/fanjumeng/TransTag). The output file from this script contains genomic reads flanking transgene insertion sites, and can be uploaded into the Shiny App (https://menglab.shinyapps.io/transtag_alignmentfree/)  for further processing
Assembly: Zv11
Supplementary files format and content: txt files

source_name: Tail fin

growth_protocol: Adult zebrafish were maintained on a 14h:10h light:dark cycle

extract_protocol:
50 mL of alkaline lysis buffer (25mM NaOH, pH=12) were added to samples, and samples were heated at 95℃ for 30minutes. After brief vortex, 50 mL of neutralizing buffer (100mM Tris-HCl, pH=8) was added. Genomic DNAs were further purified using Zymo Research DNA Clean and Concentrator kit.
About 100ng genomic DNAs were used as inputs to generate TransTag libraries to identify transgene insertion sites following the protocol provided in this manuscript

treatment_protocol: A small fin clips from adult fish were collected to extract genomic DNAs

value: Tail fin

value: Adult


title: PAX3FOXO1_rna_rep1_ΔHDcomparison

description:
Library name: GCK-NGS363
Id geneSymbol CNTLrep1 CNTLrep2 CNTLrep3 HDmutrep1 HDmutrep2 HDmutrep3 HDmutrep4 HDmutrep5 P3Frep1 P3Frep2 P3Frep3 norm.CNTLrep1 norm.CNTLrep2 norm.CNTLrep3 norm.HDmutrep1 norm.HDmutrep2 norm.HDmutrep3 norm.HDmutrep4 norm.HDmutrep5 norm.P3Frep1 norm.P3Frep2 norm.P3Frep3 baseMean CNTL HDmut P3F FoldChange log2FoldChange pvalue padj dispGeneEst dispFit dispMAP dispersion betaConv maxCooks


title: Patient3, MarcoHi,  Des+, 004

description:
Library name: L3_MarcoHi_004 | Des+
FFPE GeoMx sequencing

value: HSC


title: Tg_c635_9_TransTag

value: Tg(QUAS:GFP, cmlc:GFP)c635


title: Patient3, MarcoHi,  Marco+IBA+, 004

description:
Library name: L3_MarcoHi_004 | Marco+IBA+
FFPE GeoMx sequencing


title: Tg_c403_5_TransTag


title: PAX3FOXO1ΔHD_rna_rep4

description:
Library name: GCK-NGS357
Id geneSymbol CNTLrep1 CNTLrep2 CNTLrep3 HDmutrep1 HDmutrep2 HDmutrep3 HDmutrep4 HDmutrep5 P3Frep1 P3Frep2 P3Frep3 norm.CNTLrep1 norm.CNTLrep2 norm.CNTLrep3 norm.HDmutrep1 norm.HDmutrep2 norm.HDmutrep3 norm.HDmutrep4 norm.HDmutrep5 norm.P3Frep1 norm.P3Frep2 norm.P3Frep3 baseMean CNTL HDmut P3F FoldChange log2FoldChange pvalue padj dispGeneEst dispFit dispMAP dispersion betaConv maxCooks

value: Whole Embryo


title: Tg_c594_7_TransTag


title: Tg_c787_3_TransTag

value: Tg(QUAS:mApple, he1.1:CFP)c787


title: Patient3, MarcoHi,  Marco-IBA-Des-, 002

description:
Library name: L3_MarcoHi_002 | Else
FFPE GeoMx sequencing

value: Other


title: Patient3, MarcoHi,  Des+, 003

description:
Library name: L3_MarcoHi_003 | Des+
FFPE GeoMx sequencing


title: Tg_c636_1_TransTag

value: Tg(QUAS:mApple-CAAX, he1.1:mCherry)c636


title: Patient3, MarcoHi,  Marco-IBA+, 003

description:
Library name: L3_MarcoHi_003 | Marco-IBA+
FFPE GeoMx sequencing


title: Patient3, MarcoHi,  Des+, 002

description:
Library name: L3_MarcoHi_002 | Des+
FFPE GeoMx sequencing


title: Patient3, MarcoHi,  Marco-IBA+, 002

description:
Library name: L3_MarcoHi_002 | Marco-IBA+
FFPE GeoMx sequencing


title: Patient3, MarcoHi,  Marco+IBA+, 002

description:
Library name: L3_MarcoHi_002 | Marco+IBA+
FFPE GeoMx sequencing


title: H2AZmCherry_TransTag


title: mitfamCherry_crestinEGFP_TransTag

value: mitfa:mCherry and crestin:EGFP compound transgenic line


title: Patient3, MarcoHi,  Marco-IBA-Des-, 001

description:
Library name: L3_MarcoHi_001 | Else
FFPE GeoMx sequencing


title: Patient3, MarcoHi,  Marco+IBA+, 001

description:
Library name: L3_MarcoHi_001 | Marco+IBA+
FFPE GeoMx sequencing


title: Patient3, MarcoHi,  Des+, 001

description:
Library name: L3_MarcoHi_001 | Des+
FFPE GeoMx sequencing


title: 6PPD_1

city: Guiyang

first: Mengzhu

last: Lv

address: No. 6, Ankang Avenue, Gui'an New District

institute: Guizhou Medical University

data_processing:
Self-house pipeline
Sequence reads were trimmed for adaptor sequence/low-quality seguence using fastp (parameter- Quality limit: 20)
Trimmed sequence reads were mapped to GRCz11.109 use HISAT2
Read count extraction and normalization were performed using featureCounts and StringTie
Assembly: GRCz11.109
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: Embryos were collected and cultured in egg water (0.06 mg/mL sea salt, 0.5 mg/L methylene blue) and incubated  before 24 hpf at 28°C. To inhibit pigmentation, embryos were treated with 0.003% 1-phenyl-2-thiourea (PTU, Aladdin) starting at 24 hpf.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: For transcriptomic analysis, three biological replicates were prepared for both the 500 μg/L 6PPD treatment group and the DMSO control group. The embryos were treated from 10 hpf to 2dpf.For each replicate, the heads of 150 embryos at 2 dpf were dissected, flash-frozen in liquid nitrogen.

value: Brain


title: Con_3

value: DMSO


title: PAX3FOXO1ΔHD_foxo1_chip_rep2

description: Library name: GCK-NGS371

value: WIK (Wildtype)

value: 6 hours post-fertilization

value: Injected with 94 ng/uL PAX3::FOXO1ΔHD-2A-sfGFP mRNA


title: Patient2, MarcoLo,  Marco-IBA-Des-, 006

description:
Library name: L2_MarcoLo_006 | Else
FFPE GeoMx sequencing

value: liver

value: healthy

value: control


title: Con_2


title: 6PPD_3


title: Patient2, MarcoLo,  Marco-IBA+, 006

description:
Library name: L2_MarcoLo_006 | Marco-IBA+
FFPE GeoMx sequencing

value: Macrophage


title: Patient2, MarcoLo,  Des+, 006

description:
Library name: L2_MarcoLo_006 | Des+
FFPE GeoMx sequencing


title: Con_1


title: Patient2, MarcoLo,  Marco+IBA+, 005

description:
Library name: L2_MarcoLo_005 | Marco+IBA+
FFPE GeoMx sequencing


title: Control_rna_rep4

description:
Id, geneSymbol, CNTLrep1, CNTLrep2, CNTLrep3, CNTLrepl4, P3Frep1, P3Frep2, P3Frep3,  P3Frepl4, norm.CNTLrep1, norm.CNTLrep2, norm.CNTLrep3, norm.CNTLrepl4, norm.P3Frep1, norm. P3Frep2, norm.P3Frep3, norm.P3Frepl4, baseMean, CNTL, P3F, FoldChange, log2FoldChange, pvalue, padj, dispGeneEst, dispFit, dispMAP, dispersion, betaCov, maxCooks
P3FvsCNTL.complete.txt

value: WIK (Wild-type)

value: Injected with 32 ng/uL pCS2+MCS-P2A-sfGFP mRNA


title: Patient3, MarcoHi,  Marco-IBA-Des-, 003

description:
Library name: L3_MarcoHi_003 | Else
FFPE GeoMx sequencing

value: fibrosis

value: treated CCl4


title: Patient2, MarcoLo,  Marco+IBA+, 006

description:
Library name: L2_MarcoLo_006 | Marco+IBA+
FFPE GeoMx sequencing


title: Control_rna_rep3

value: Whole Embryo


title: 6PPD_2


title: Patient2, MarcoLo,  Marco+IBA+, 004

description:
Library name: L2_MarcoLo_004 | Marco+IBA+
FFPE GeoMx sequencing


title: Patient2, MarcoLo,  Marco-IBA-Des-, 004

description:
Library name: L2_MarcoLo_004 | Else
FFPE GeoMx sequencing

value: Other


title: PAX3FOXO1_rna_rep4

value: Injected with 100 ng/uL PAX3::FOXO1 mRNA


title: PAX3FOXO1_rna_rep3

value: Injected with 100 ng/uL PAX3::FOXO1-2A-sfGFP mRNA


title: sox10Kaede_TransTag

value: Tail fin

value: Adult


title: Patient2, MarcoLo,  Marco-IBA-Des-, 003

description:
Library name: L2_MarcoLo_003 | Else
FFPE GeoMx sequencing


title: WT_TransTag

value: wild type


title: Control_rna_rep1

value: 6 hours post-fertilization


title: Control_rna_rep2


title: Patient4, MarcoLo,  Marco-IBA-Des-, 006

description:
Library name: L4_MarcoLo_006 | Else
FFPE GeoMx sequencing


title: PAX3FOXO1_rna_rep2


title: Patient4, MarcoLo,  Marco+IBA+, 003

description:
Library name: L4_MarcoLo_003 | Marco+IBA+
FFPE GeoMx sequencing


title: PAX3FOXO1_rna_rep1


title: Patient4, MarcoLo,  Marco-IBA-Des-, 002

description:
Library name: L4_MarcoLo_002 | Else
FFPE GeoMx sequencing


title: Control_foxo1_chip_rep2

description:
p3f.CNTL_2_signal.bigWig
p3f.CNTL_idrValues.bed

value: WIK (Wildtype)

value: FOXO1 (Cell Signaling, C29H4)


title: Patient4, MarcoLo,  Marco-IBA+, 002

description:
Library name: L4_MarcoLo_002 | Marco-IBA+
FFPE GeoMx sequencing

value: liver

value: healthy


title: Patient4, MarcoLo,  Des+, 002

description:
Library name: L4_MarcoLo_002 | Des+
FFPE GeoMx sequencing

value: HSC

value: control


title: PAX3FOXO1_foxo1_input_rep2

description:
p3f.P3F_2_signal.bigWig
pcP3F_diffBind.bed

value: Input DNA


title: Patient4, MarcoLo,  Marco+IBA+, 002

description:
Library name: L4_MarcoLo_002 | Marco+IBA+
FFPE GeoMx sequencing

value: Macrophage


title: Patient4, MarcoHi,  Marco-IBA-Des-, 007

description:
Library name: L4_MarcoHi_007 | Else
FFPE GeoMx sequencing


title: Control_foxo1_input_rep2

value: Injected with 32 ng/uL pCS2+MCS-P2A-sfGFP mRNA


title: Patient4, MarcoHi,  Des+, 007

description:
Library name: L4_MarcoHi_007 | Des+
FFPE GeoMx sequencing


title: PAX3FOXO1_foxo1_chip_rep2

value: Whole Embryo


title: Patient2, MarcoLo,  Des+, 003

description:
Library name: L2_MarcoLo_003 | Des+
FFPE GeoMx sequencing


title: PAX3FOXO1_foxo1_input_rep1

description:
p3f.P3F_1_signal.bigWig
pcP3F_diffBind.bed


title: Control_h3k27ac_chip_rep2

description:
h3k27ac.cntl_1.signal.bigWig
h3k27ac.cntl_consensus.bed

value: H3K27ac (Active Motif, 39133)


title: Patient4, MarcoHi,  Marco-IBA-Des-, 006

description:
Library name: L4_MarcoHi_006 | Else
FFPE GeoMx sequencing

value: Other


title: Patient4, MarcoHi,  Marco+IBA+, 007

description:
Library name: L4_MarcoHi_007 | Marco+IBA+
FFPE GeoMx sequencing


title: Control_h3k27ac_input_rep2


title: PAX3FOXO1_foxo1_chip_rep1

value: Injected with 100 ng/uL PAX3::FOXO1-2A-sfGFP mRNA


title: Control_foxo1_input_rep1

description:
p3f.CNTL_1_signal.bigWig
p3f.CNTL_idrValues.bed


title: Patient2, MarcoLo,  Des+, 002

description:
Library name: L2_MarcoLo_002 | Des+
FFPE GeoMx sequencing


title: PAX3FOXO1_h3k27ac_input_rep2

description:
h3k27ac.p3f_2.signal.bigWig
h3k27ac.p3f_consensus.bed


title: PAX3FOXO1_h3k27ac_chip_rep2


title: Patient2, MarcoLo,  Marco+IBA+, 003

description:
Library name: L2_MarcoLo_003 | Marco+IBA+
FFPE GeoMx sequencing


title: Patient4, MarcoLo,  Des+, 006

description:
Library name: L4_MarcoLo_006 | Des+
FFPE GeoMx sequencing


title: Control_h3k27ac_input_rep1


title: Patient2, MarcoLo,  Marco-IBA-Des-, 002

description:
Library name: L2_MarcoLo_002 | Else
FFPE GeoMx sequencing


title: Patient2, MarcoLo,  Marco-IBA+, 002

description:
Library name: L2_MarcoLo_002 | Marco-IBA+
FFPE GeoMx sequencing


title: Patient2, MarcoLo,  Marco+IBA+, 002

description:
Library name: L2_MarcoLo_002 | Marco+IBA+
FFPE GeoMx sequencing


title: Control_h3k27ac_chip_rep1


title: Patient2, MarcoLo,  Marco-IBA-Des-, 001

description:
Library name: L2_MarcoLo_001 | Else
FFPE GeoMx sequencing


title: PAX3FOXO1_h3k27ac_input_rep1

description:
h3k27ac.p3f_1.signal.bigWig
h3k27ac.p3f_consensus.bed


title: Patient2, MarcoLo,  Marco+IBA+, 001

description:
Library name: L2_MarcoLo_001 | Marco+IBA+
FFPE GeoMx sequencing


title: Control_foxo1_chip_rep1


title: Patient2, MarcoHi,  Marco-IBA-Des-, 008

description:
Library name: L2_MarcoHi_008 | Else
FFPE GeoMx sequencing


title: PAX3FOXO1_h3k27ac_chip_rep1


title: Control_atac_rep2

description: atac_cntl_overlap.optimal_peak.narrowPeak

data_processing:
FASTQ files were analyzed with the ENCODE ATAC-seq pipeline
Assembly: danRer11
Supplementary files format and content: bigWig for signal visualization of each replicate
Supplementary files format and content: concensus peaks per condition between the replicates

extract_protocol:
Embryos were dissociated into single cells and 50,000 injected cells were used per replicate. Cells underwent nuclear isolation, tn5 transposition reaction, and DNA isolation with the QIAGEN MinElute PCR Purification kit.
DNA libraries were amplified with Illumnia indexing primers by qRT-PCR and purified with 0.4X/1.2X and 1.8X AMPure bead selection.


title: Patient2, MarcoHi,  Marco-IBA-Des-, 007

description:
Library name: L2_MarcoHi_007 | Else
FFPE GeoMx sequencing


title: Patient2, MarcoHi,  Des+, 008

description:
Library name: L2_MarcoHi_008 | Des+
FFPE GeoMx sequencing


title: Patient2, MarcoHi,  Marco+IBA+, 008

description:
Library name: L2_MarcoHi_008 | Marco+IBA+
FFPE GeoMx sequencing


title: Patient2, MarcoHi,  Marco+IBA+, 007

description:
Library name: L2_MarcoHi_007 | Marco+IBA+
FFPE GeoMx sequencing


title: Control_atac_rep1


title: PAX3FOXO1_atac_rep2

description: atac_p3f.overlap.optimal_peak.narrowPeak


title: RNase J mutant + empty vector, pre-induced, biol rep 2

city: Hamilton

first: Marie

last: Elliot

state: Ontario

address: 1280 Main Street W

department: Biology

country: Canada

institute: McMaster University

description:
Library name: sample 22
rnj_VC_R2_pre.bam

data_processing:
Reads were aligned to the Streptomyces venezuelae NRRL B-65442 genome (NCBI accession: NZ_CP018074.1) using the BowTie2 program and the aligned files were sorted using SamTools. The number of reads aligning to genomic features were counted using the HTseq-count program for each replicate. The HTseq-count tables were then normalized and used for differential transcript level analysis with the program DESeq2.
For transcriptomic analysis comparing the post-induced samples to pre-induced samples, these data were filtered by significance (adjusted p-value < 0.05), expression (BaseMean > 50), and differential expression (log2 fold change > |2|)
Assembly: Streptomyces venezuelae NRRL B-65442 genome (NCBI accession: NZ_CP018074.1)
Supplementary files format and content: csv fle includes normalized counts (extracted from DESeq2 analysis) for each sample

organism: Streptomyces venezuelae

source_name: bacterial cell

growth_protocol: Streptomyces cultures were grown in MYM (1% malt extract, 0.4%yeast extract, 0.4% maltose) at 30°C. Overnight culured were diluted to 0.1 OD(600) and grown for 8 h at 200 RPM.

extract_protocol:
Cells were lysed by vortexing pellets for 2 min with an approximately equal volume of sterile glass beads and ice cold lysis solution (4M guanidine thiocyanate, 25 mM trisodium citrate, 0.5%v/v sodium N-lauroylsarcosinate, 0.8%v/v β-mercaptoethanol). An equal volume of phenol:chloroform:isoamyl alcohol (50:50:1, pH 4.6) was added to the lysate and samples were vortexed on and off in thirty second intervals to emulsify the solutions. Samples were then centrifuged at 7,800 ×g and the aqueous phase containing the RNA was recovered. Total RNA was precipitated by adding an equal volume of ice-cold isopropanol (100%), 0.1 volume of sodium acetate buffer (3 M, pH 6), and 2 μL of RNA grade glycogen (ThermoFisher Scientific).The total RNA sample was DNase treated post-extraction using TURBO DNase buffer and enzyme (Fisher Scientific). Total RNA was extracted from the reaction mixture with phenol:chloroform:isoamyl alcohol (50:50:1, pH=4.6).
RNA-sequencing was conducted by the MOBIX facility at McMaster University using paired-end technology on the Illumina MiSeq v3 platform.

treatment_protocol: Afte cells were subcultured for 8 h, theophylline was  added to a concentration of 4 mM to induce TipA translation. Cultures were then grown for an additional 2 h at 30°C before thiostrepton was added to a final concentration of 50 μg/mL to promote expression of FLAG-tagged RNases. Cells were collected at 0 min (pre-induction), and at 20 and 40 min post-thiostrepton addition.

value: bacterial cell

value: RNase J mutant


title: RNase J mutant + empty vector, 40 minutes, biol rep 2

description:
Library name: sample 24
rnj_VC_R2_40m.bam


title: Patient2, MarcoHi,  Marco-IBA-Des-, 006

description:
Library name: L2_MarcoHi_006 | Else
FFPE GeoMx sequencing


title: Patient2, MarcoHi,  Des+, 006

description:
Library name: L2_MarcoHi_006 | Des+
FFPE GeoMx sequencing


title: PAX3FOXO1_atac_rep1


title: RNase J mutant + empty vector, 20 minutes, biol rep 2

description:
Library name: sample 23
rnj_VC_R2_20m.bam


title: RNase J mutant + RNase J(3xFLAG), 40 minutes, biol rep 2

description:
Library name: sample 21
rnj_VC_R1_40m.bam


title: Patient2, MarcoHi,  Marco-IBA-Des-, 005

description:
Library name: L2_MarcoHi_005 | Else
FFPE GeoMx sequencing


title: RNase J mutant + RNase J(3xFLAG), pre-induced, biol rep 2

description:
Library name: sample 19
rnj_VC_R1_pre.bam


title: Patient2, MarcoHi,  Marco+IBA+, 005

description:
Library name: L2_MarcoHi_005 | Marco+IBA+
FFPE GeoMx sequencing


title: Patient2, MarcoHi,  Marco+IBA+, 006

description:
Library name: L2_MarcoHi_006 | Marco+IBA+
FFPE GeoMx sequencing


title: Patient2, MarcoHi,  Des+, 004

description:
Library name: L2_MarcoHi_004 | Des+
FFPE GeoMx sequencing


title: Patient2, MarcoHi,  Marco-IBA-Des-, 004

description:
Library name: L2_MarcoHi_004 | Else
FFPE GeoMx sequencing


title: RNase J mutant + empty vector, 20 minutes, biol rep 1

description:
Library name: sample 17
rnj_3xF_R2_20m.bam


title: RNase J mutant + empty vector, 40 minutes, biol rep 1

description:
Library name: sample 18
rnj_3xF_R2_40m.bam


title: RNase J mutant + RNase J(3xFLAG), 20 minutes, biol rep 2

description:
Library name: sample 20
rnj_VC_R1_20m.bam


title: Patient2, MarcoHi,  Marco-IBA-Des-, 003

description:
Library name: L2_MarcoHi_003 | Else
FFPE GeoMx sequencing


title: Patient2, MarcoHi,  Marco+IBA+, 003

description:
Library name: L2_MarcoHi_003 | Marco+IBA+
FFPE GeoMx sequencing


title: Patient2, MarcoHi,  Des+, 003

description:
Library name: L2_MarcoHi_003 | Des+
FFPE GeoMx sequencing


title: RNase J mutant + RNase J(3xFLAG), pre-induced, biol rep 1

description:
Library name: sample 13
rnj_3xF_R1_pre.bam


title: RNase J mutant + RNase J(3xFLAG), 20 minutes, biol rep 1

description:
Library name: sample 14
rnj_3xF_R1_20m.bam


title: RNase III mutant + empty vector, 40 minutes, biol rep 2

description:
Library name: sample 12
rnc_VC_R2_40m.bam

value: RNase III mutant


title: Patient2, MarcoHi,  Marco-IBA-Des-, 002

description:
Library name: L2_MarcoHi_002 | Else
FFPE GeoMx sequencing


title: RNase III mutant + empty vector, 20 minutes, biol rep 2

description:
Library name: sample 11
rnc_VC_R2_20m.bam


title: RNase III mutant + empty vector, pre-induced, biol rep 2

description:
Library name: sample 10
rnc_VC_R2_pre.bam


title: RNase J mutant + empty vector, pre-induced, biol rep 1

description:
Library name: sample 16
rnj_3xF_R2_pre.bam


title: Patient2, MarcoHi,  Marco+IBA+, 002

description:
Library name: L2_MarcoHi_002 | Marco+IBA+
FFPE GeoMx sequencing


title: RNase III mutant + RNase III(3xFLAG), 20 minutes, biol rep 2

description:
Library name: sample 8
rnc_VC_R1_20m.bam


title: Patient2, MarcoHi,  Marco-IBA-Des-, 001

description:
Library name: L2_MarcoHi_001 | Else
FFPE GeoMx sequencing


title: Patient2, MarcoHi,  Marco+IBA+, 001

description:
Library name: L2_MarcoHi_001 | Marco+IBA+
FFPE GeoMx sequencing


title: Patient2, MarcoHi,  Des+, 001

description:
Library name: L2_MarcoHi_001 | Des+
FFPE GeoMx sequencing


title: Patient1, MarcoLo,  Des+, 007

description:
Library name: L1_MarcoLo_007 | Des+
FFPE GeoMx sequencing

value: fibrosis

value: treated CCl4


title: RNase J mutant + RNase J(3xFLAG), 40 minutes, biol rep 1

description:
Library name: sample 15
rnj_3xF_R1_40m.bam


title: RNase III mutant + empty vector, 20 minutes, biol rep 1

description:
Library name: sample 5
rnc_3xF_R2_20m.bam


title: RNase III mutant + RNase III(3xFLAG), pre-induced, biol rep 2

description:
Library name: sample 7
rnc_VC_R1_pre.bam


title: Patient1, MarcoLo,  Marco-IBA-Des-, 007

description:
Library name: L1_MarcoLo_007 | Else
FFPE GeoMx sequencing


title: RNase III mutant + empty vector, 40 minutes, biol rep 1

description:
Library name: sample 6
rnc_3xF_R2_40m.bam


title: Patient1, MarcoLo,  Marco-IBA+, 007

description:
Library name: L1_MarcoLo_007 | Marco-IBA+
FFPE GeoMx sequencing


title: Patient1, MarcoLo,  Marco+IBA+, 007

description:
Library name: L1_MarcoLo_007 | Marco+IBA+
FFPE GeoMx sequencing


title: Patient1, MarcoLo,  Marco-IBA-Des-, 006

description:
Library name: L1_MarcoLo_006 | Else
FFPE GeoMx sequencing


title: Patient2, MarcoHi,  Marco+IBA+, 004

description:
Library name: L2_MarcoHi_004 | Marco+IBA+
FFPE GeoMx sequencing


title: RNase III mutant + empty vector, pre-induced, biol rep 1

description:
Library name: sample 4
rnc_3xF_R2_pre.bam


title: RNase III mutant + RNase III(3xFLAG), 40 minutes, biol rep 1

description:
Library name: sample 3
rnc_3xF_R1_40m.bam


title: Patient1, MarcoLo,  Des+, 006

description:
Library name: L1_MarcoLo_006 | Des+
FFPE GeoMx sequencing


title: RNase III mutant + RNase III(3xFLAG), 20 minutes, biol rep 1

description:
Library name: sample 2
rnc_3xF_R1_20m.bam


title: Patient1, MarcoLo,  Marco-IBA+, 006

description:
Library name: L1_MarcoLo_006 | Marco-IBA+
FFPE GeoMx sequencing


title: RNase III mutant + RNase III(3xFLAG), pre-induced, biol rep 1

description:
Library name: sample 1
rnc_3xF_R1_pre.bam


title: RNase J mutant sporulating, 24h, biol rep 2

description:
Library name: sample 16
rnj_24h_R2.bam

data_processing:
Reads were aligned to the Streptomyces venezuelae NRRL B-65442 genome (NCBI accession: NZ_CP018074.1) using the BowTie2 program and the aligned files were sorted using SamTools. The number of reads aligning to genomic features were counted using the HTseq-count program for each replicate. The HTseq-count tables were then normalized and used for differential transcript level analysis with the program DESeq2.
For transcriptomic analysis of the RNase mutants compared to wild type Streptomyces venezuelae these data were filtered by significance (adjusted p-value < 0.05), expression (BaseMean > 50), and differential expression (log2 fold change > |2|)
Assembly: Streptomyces venezuelae NRRL B-65442 genome (NCBI accession: NZ_CP018074.1)
Supplementary files format and content: csv fle includes normalized counts (extracted from DESeq2 analysis) for each sample

growth_protocol: Streptomyces venezuelae cultures were grown in MYM (1% malt extract, 0.4%yeast extract, 0.4% maltose) at 30°C. Overnight culured were diluted to 0.1 OD(600) and grown for 10-24 h at 200 RPM.

tag: time


title: Patient2, MarcoHi,  Des+, 002

description:
Library name: L2_MarcoHi_002 | Des+
FFPE GeoMx sequencing