title: BrUseq, CFAP20KO, rep3

data_processing:
For all sequencing data, a sequencing quality profile was generated using FastQC (Version 0.11.9). Sequences were trimmed using TrimGalore (Version 0.6.5) and were aligned to the Human Genome 38 using STAR (Version 2.7.7a) with genome file GCA_000001405.15_GRCh38 and splice junction file Homo_sapiens.GRCh38.94.correctedContigs.gtf. Bam files were converted into stranded TagDirectories and UCSC genome tracks using HOMER tools (Version 4.8.2). Example genome tracks were generated in IGV (Version 2.4.3).
OK-seq data in untreated RPE1 cells was downloaded from Chen et al. 2019 (datasets GSM3130725 and GSM3130726). Sequences were trimmed using TrimGalore (Version 0.6.5), and aligned to the Human Genome 38 using STAR (Version 2.7.7a) with genome file GCA_000001405.15_GRCh38. Duplicate reads were removed using Samtools (Version 1.11) with fixmate -m and markdup -r settings. Replication initiation zones were subsequently defined using the replication fork directionality analysis R toolkit (OKseqHMM; available on https://github.com/CL-CHEN-Lab/OK-Seq), with read coverage threshold 6 for GSM3130725 and 1 for GSM3130726, and smoothing window size 15 kb. Initiation zones present in both datasets were identified using mergePeaks of HOMER tools (Version 4.8.2), with -d given. Origins were defined as the center of initiation zones. For all origins, their nearest TSS was defined using annotatePeaks of HOMER tools, together with the distance between the TSS and the origin. Here, a negative distance represents an origin upstream of the TSS (co-directional transcription relative to replication), while a positive distance represents an origin downstream of a TSS (head-on transcription relative to replication). To allow for clean transcription versus replication analyses, we further selected only origins for which their nearest TSS was not preceded by another gene within 5kb upstream of the TSS. This resulted in a list of 2,040 origins.
A list of 49,948 gene-coordinates was obtained from the UCSC genome database selecting the 'knownCanonical' table containing the canonical transcription start sites per gene (Karolchik et al., 2004). To prevent contamination of binding profiles, genes were selected to be non-overlapping with at least 2 kb between genes and a minimal size of 3 kb (n=9,944). From this, a set of 3,000 actively transcribed genes was selected by calculating gene size-corrected read-densities of BrU-seq data in WT cells, using the AnnotatePeaks.pl tool of HOMER with default settings.
Read-density profiles around origin or TSS/TTS coordinates were defined using the AnnotatePeaks.pl tool of HOMER using the default normalization to 10 million reads. Individual datasets were subsequently processed into heatmaps or binding profiles using R (Version 4.0.5) and Rstudio (Version 1.1.423) (Team, 2019).
Splicing efficiencies for individual splice junctions were calculated in all BrU-seq datasets using the SPLICE-q.py tool (de Melo Costa et al., 2021) with splice coordinates from Homo_sapiens.GRCh38.94. Only splice sites with reads in at least 2 biological replicates of WT and CFAP20-KO cells were included in the analyses (n=~6700). Per experiment, Δsplice-q values were calculated by subtracting the splice-q value of WT samples from the splice-q values in CFAP20KO or rescue samples. Splice junctions with attenuated splicing were defined as junctions with a Δsplice-q between CFAP20-KO and WT of >0.15 or <-0.15 in all three replicate experiments; meaning a difference between the splicing efficiency of WT and CFAP20-KO of at least 15%. Heatmaps were generated of the splicing efficiency of the top 50 worse or better splicing junctions in CFAP20-KO cells versus WT cells. For visualization, in each heatmap, signal intensities per experiment were normalized to the average splicing efficiency in the 50 splice junction in WT cells to correct for experimental differences in overall splicing efficiency
Assembly: hg38
Supplementary files format and content:
SpliceJunctionDatafile_n6710.txt: tab-delimited text file containing splicing indexes for ~6700 splice junctions in indicated WT, CFAP20-KO or CFAP20rescue cells
OriginCenter_OKseq_Select5kbUpstreamTSSempty.txt: tab-delimited text file containing coordinates of origins identified as described.
BrUseq_ReadDensityAroundOKseqOrigins_200KbWindow_CFAP20KO_mock_rep*_TranscStrand.txt: tab-delimited text file containing the read-density/10M total reads of the transcribed strand at the indicated distance from the origin
BrUseq_ReadDensityAroundOKseqOrigins_200KbWindow_WT_mock_rep*_TranscStrand.txt: tab-delimited text file containing the read-density/10M total reads of the transcribed strand at the indicated distance from the origin
BrUseq_ReadDensityAroundTSS_200KbWindow_Above3kb_2kbGap_CFAP20KO_mock_rep*_TranscStrand.txt: tab-delimited text file containing the read-density/10M total reads of the transcribed strand at the indicated distance from ~9944 TSSs of >3kb with at least 2kb between genes
BrUseq_ReadDensityAroundTSS_200KbWindow_Above3kb_2kbGap_CFAP20Rescue_rep1_TranscStrand.txt: tab-delimited text file containing the read-density/10M total reads of the transcribed strand at the indicated distance from ~9944 TSSs of >3kb with at least 2kb between genes
BrUseq_ReadDensityAroundTSS_200KbWindow_Above3kb_2kbGap_WT_mock_rep*_TranscStrand.txt: tab-delimited text file containing the read-density/10M total reads of the transcribed strand at the indicated distance from ~9944 TSSs of >3kb with at least 2kb between genes

extract_protocol:
After incubation cells were lysed in Trizol (Thermo Fisher, 15596018) and BrU-containing RNA was isolated as previously described (Andrade-Lima et al., 2015, Nucleic Acids Res)
cDNA libraries were made from the BrU-labeled RNA using the Illumina TruSeq library kit and paired-end 151 bp sequenced using the Illumina NovaSeq platform at the University of Michigan Advanced Genomics Core. Paired-end sequencing data was used for downstream analyses.
nascent RNA-seq

treatment_protocol: Cells were grown to 80-90% confluency and pulse-labeled with 2 mM bromouridine (BrU, Sigma) in culture medium at 37°C for 30 min, followed by immediate harvest.

value: 30 minutes BrU pulse-labeled

tag: pulldown antibody

value: Mouse anti-BrdU; BD Pharmingen, 555627

tag: type of_material

value: Nascent RNA


title: Library 4 rep6 WY1866

status: Public on May 20 2025

type: SRA

city: Boston

first: Wei-Chien

last: Yuan

state: MA

address: 1 Blackfan Circle

country: USA

institute: Boston Children's Hospital

library_source: genomic

data_processing:
Barcode sequences were parsed and trimmed from FASTQs using custom python scripts
Paired-end reads were aligned to mm10 using bowtie or STAR.
Duplicate reads were removed using picard.
Peaks were called using MACS2
For the CRISPR screen, reads were trimmed and then mapped to a custom-built index of the library using bowtie 2. The mapped counts were first normalized within each library (total counts = 10E6 reads), averaged across experimental replicates, and then divided by the average normalized reads of the respective sequenced plasmid libraries (BC1-BC4) to calculate the final fold-enrichment for each guide in each mouse.
Genome_build: mm10
Supplementary_files_format_and_content: For RNA-seq, gene count was generted using featurecounts. For bulk ATAC-seq and ChIP-seq, algined reads are converted to bigwig tracks. For scATAC, peak-cell matrix is generated using ChromVAR. For the CRISPR-screening, processed data are tab separated text files for each mouse (biological replicate), showing, for each sgRNA, the fold enrichment over its abundance in the corresponding plasmid library (BC1-BC4).

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
DNA was extracted from GFP+/EPCAM+ sorted cells with DirectPCR lysis buffer (Viagen) and Proteinase K (0.2 mg/ml).
A tenth of the total DNA preparation was used as a template for a PCR using primers targeting the common sgRNA scaffold and containing Illumina TruSeq adapter sequences, with the following parameters: 98ºC 5’, 30 cycles of (98ºC 30’’, 58ºC 30’’, 72ºC 30’’). The number of cycles was optimized by DNA quantification to stop in the middle of the linear amplification phase. Illumina i5 and i7 adapters were added by performing an additional 10-12 PCR cycles with TruSeq adapter primers

tag: tissue

value: hepatocytes

tag: genotype

value: Col:YAP/+, R26:sr/Cas9


title: Sox11_WT_KO_RNA_seq, 1308-TKA, KO56, solvent, biol. replicate 2

city: Freiburg

first: Andreas

last: Hecht

address: Stefan-Meier-Str. 17

country: Germany

institute: Albert-Ludwigs-Universität Freiburg

description:
1308KO56_Solv2
1308-TKA RNA-seq_merge
1308-TKA_RNA-seq_replicate2

library_source: transcriptomic

data_processing:
Adapter sequences and poor quality reads were removed via FastP (Version 0.23.4)
Reads were mapped to the mouse reference genome (mmc10) using STAR aligner (Version 2.7.10b)
Read counts were normalized to the sequencing depths yielding the log2 counts per millions (CPM) as measures for gene expression levels.
Assembly: mm10
Supplementary files format and content: processed data after merging biological replicates: tab-delimited text files listing log2 CPM values per gene across all samples; CPM values of the two biological replicates were averaged and then subjected to log2 transformation; entries with "0" values had no CPM values, i. e. no detectable expression
Supplementary files format and content: processed data for individual biological replicates: tab-delimited text files listing log2 CPM values per gene across all samples; CPM values of each biological replicate were subjected to log2 transformation; entries with "0" values had no CPM values, i. e. no detectable expression

molecule: total RNA

source_name: Small intestine

extract_protocol:
Total RNA was isolated using the PeqGOLD total RNA kit (#732–2871, Peqlab/VWR Life Science, Bruchsal, Germany)
Sequencing libraries were generated using the TruSeq Stranded mRNA Library Prep Kit/TruSeq Stranded mRNA Reference Guide # 1000000040498 v00 (Illumina) and subjected to 2x151 bp paired-end sequencing on a Illumina Novaseq 6000 sequencing device at approximately 50 million reads per library.

value: Small intestine

tag: cell line

tag: cell type

value: Intestinal organoid

value: Sox11 Kockout; Apc-/-, KrasG12D/+, Trp53R172H/+

tag: treatment

value: Solvent


title: 0.3 ug-AgPVP_5

city: Durham

first: Joshua

last: Harrill

address: 109 TW Alexander Dr

institute: US EPA

description:
Library name: GRC371B-17_S15
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-17_S15

data_processing:
Raw data were aligned, trimmed, and normalized using Partek™ Flow™ software(Partek Inc., St. Louis, MO), with pre- and post-alignment quality checks.
Assembly: hg38
Supplementary files format and content: comma-separated .csv file includes normalized counts for each sample

organism: Homo sapiens

source_name: Retina

growth_protocol: ARPE-19 cells were stored in vapor phase liquid nitrogen upon receipt from ATCC. For each of the biological replicates in RNA-seq, one vial of passage 1 cells was thawed to produce all technical replicates. Cells were cultured in sterile DMEM/F12 medium supplemented with 1.5 g/L sodium bicarbonate, 10% FBS, and 100 U/mL penicillin/streptomycin. Sodium hydroxide was added to the media as necessary to attain a pH of 7.4, and all cultures were maintained at 37°C in incubators with 5% CO2

extract_protocol:
Total RNA was extracted from cells using a mirVana™ RNA extraction kit (Life Technologies, Grand361 Island, NY).  RNA purity was assessed by using an RNA 6000 Nano LabChip™ Kit with a 2100 Bioanalyzer (Agilent Technologies,364 Palo Alto, CA). RNA sample concentrations were checked with a Qubit™ RNA BR Assay Kit.
Poly (A) selection done using the Apollo 324™ System (IntegenX Inc., Pleasanton, CA). cDNA library prep was performed using the PrepX™ mRNA 48 366 Protocol on the Apollo 324™ System. PCR amplification took place across 14 cycles with 48 index primers, and the products were run through the Apollo 324™ PrepX™ PCR Cleanup 48 Protocol. The 2100 Bioanalyzer was used with a High Sensitivity DNA Chip to assess product quality and the resultant electropherogram was used to determine average size and concentration. A Qubit™ DNA HS Kit was then used to quantify the collected libraries. Equal amounts of each library were pooled into a total of 4 pools containing a maximum of 24 randomized libraries. The Qubit™ DNA HS Kit was again used to quantify the sequencing samples before they were denatured and diluted to a final concentration of 2.7 pM according to Illumina NextSeq 500 protocols. Samples were then sequenced using the Illumina NextSeq 500 (Illumina, San Diego, CA) with 75 single-read cycles

treatment_protocol: Dosing was performed manually by removing half of the cell culture media from each flask and replacing it with an equivalent volume of 2X concentrated test particle or fresh cell culture media as a negative control. Initial 1 mg/mL AgNP solutions were diluted in media such that the final concentrations applied to cells were 0.3, 1, 3, 10, and 30 μg/mL.

value: Retina

value: 0.3 ug-AgPVP


title: 0.3 ug-AgPVP_4

description:
Library name: GRC371B-16_S12
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-16_S12


title: BrUseq, CFAP20KO, rep2

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

library_source: other

molecule: other

source_name: RPE1 iCas9 p53/puro-dKO CFAP20-KO

growth_protocol: All cell lines were cultured at 37°C with 5% CO2 in DMEM GlutaMAX (Gibco), supplemented with 10% fetal calf serum (Avantor, VWR) and penicillin/streptomycin (Sigma).

value: RPE1 iCas9 p53/puro-dKO CFAP20-KO

tag: genome used_to_map_to


title: Library 4 rep5 WY1952


title: BrUseq, WT, rep3

source_name: RPE1 iCas9 p53/puro-dKO WT

value: RPE1 iCas9 p53/puro-dKO WT


title: 0.3 ug-AgPVP_3

description:
Library name: GRC371B-11_S5
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-11_S5


title: Sox11_WT_KO_RNA_seq, 1308-TKA, KO47, TGF-β1, biol. replicate 2

description:
1308KO47_TGF2
1308-TKA RNA-seq_merge
1308-TKA_RNA-seq_replicate2


title: BrUseq, CFAP20Rescue, rep1

source_name: RPE1 iCas9 p53/puro-dKO CFAP20-KO + CFAP20-GFP


title: 0.3 ug-AgPVP_2

description:
Library name: GRC371-33_S13
column name in Partek_GRC371_Normalized_counts.csv:GRC371-33_S13


title: Sox11_WT_KO_RNA_seq, 1308-TKA, KO47, TGF-β1, biol. replicate 1

description:
1308KO47_TGF1
1308-TKA RNA-seq_merge
1308-TKA_RNA-seq_replicate1


title: Library 4 rep4 WY2080


title: BrUseq, WT, rep2


title: 0.3 ug-AgPVP_1

description:
Library name: GRC371-3_S9
column name in Partek_GRC371_Normalized_counts.csv:GRC371-3_S9


title: Library 4 rep3 WY2082


title: Library 4 rep2 WY2089


title: BrUseq, CFAP20KO, rep1


title: 0.3 ug-AgCitrate_7

description:
Library name: GRC371B-6_S18
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-6_S18

value: 0.3 ug-AgCitrate


title: Library 4 rep1 WY2091


title: BrUseq, WT, rep1


title: 0.3 ug-AgCitrate_6

description:
Library name: GRC371-32_S18
column name in Partek_GRC371_Normalized_counts.csv:GRC371-32_S18


title: Sox11_WT_KO_RNA_seq, 931-TKA, Par, TGF-β1, biol. replicate 2

description:
931_Par_TGF2
931-TKA RNA-seq_merge
931-TKA_RNA-seq_replicate2

value: Sox11 wildtype; Apc-/-, KrasG12D/+, Trp53R172H/+


title: Library 3 rep3 WY1869


title: 0.3 ug-AgCitrate_5

description:
Library name: GRC371B-20_S11
column name in Partek_GRC371_Normalized_counts.csv:GRC371B-20_S11


title: AGS-mimics-3

city: Guangzhou

first: Jide

last: Wang

state: Guangdong

address: 1838 Guangzhou Avenue North

department: Department of Gastroenterology

country: China

institute: Nanfang Hospital, Southern Medical University

data_processing:
StringTie (1.3.3)
The raw data is preprocessed after QC (removing 5' and 3' adaptor sequence and filtering out short fragments ≤ 20 bp) with cutadapt software to obtain trimmed data, which are aligned to the reference genome (GRCh37).
The quantitative analysis of gene expression is divided into two levels: Gene Level and Transcript Level. The software StringTie (1.3.3) was used to compare the results to the known transcriptome to calculate the transcript abundance and then calculated it by Ballgown (2.10.0).
The unit of expression is expressed in FPKM（Fragments Per Kilobase of gene/transcript model per Million mapped fragments）. The expression threshold of genes or transcripts was FPKM ≥ 0.5. The mean FPKM of genes or transcripts in each group exceeded 0.5 were considered to be expressed in the group and subjected to statistical analysis.
Assembly: GRCh37
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample.

source_name: Stomach

growth_protocol: AGS were maintained in DMEM supplemented with 10% fetal bovine serum in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded RNA-Seq Library Prep Kit (Illumina) following manufacturer's protocols.

treatment_protocol: Transient transfected with NC and miR-3648 mimics respectively.

value: Stomach

value: AGS

value: Epithelial Cells

value: AGS cells transfected with miR-3648 mimics

value: transfected with miR-3648 mimics


title: Sox11_WT_KO_RNA_seq, 1308-TKA, KO56, solvent, biol. replicate 1

description:
1308KO56_Solv1
1308-TKA RNA-seq_merge
1308-TKA_RNA-seq_replicate1


title: AGS-mimics-2


title: 0.3 ug-AgCitrate_4

description:
Library name: GRC371-42_S17
column name in Partek_GRC371_Normalized_counts.csv:GRC371-42_S17


title: Library 3 rep2 WY1950

value: hepatocytes


title: Sox11_WT_KO_RNA_seq, 931-TKA, Par, solvent, biol. replicate 2

description:
931_Par_Solv2
931-TKA RNA-seq_merge
931-TKA_RNA-seq_replicate2


title: Sox11_WT_KO_RNA_seq, 931-TKA, Par, solvent, biol. replicate 1

description:
931_Par_Solv1
931-TKA RNA-seq_merge
931-TKA_RNA-seq_replicate1


title: AGS-mimics-1


title: 0.3 ug-AgCitrate_3

description:
Library name: GRC371-31_S12
column name in Partek_GRC371_Normalized_counts.csv:GRC371-31_S12


title: AGS-NC-3

value: AGS cells transfected with NC

value: transfected with NC


title: 0.3 ug-AgCitrate_2

description:
Library name: GRC371-18_S7
column name in Partek_GRC371_Normalized_counts.csv:GRC371-18_S7


title: Library 2 rep5 WY1870

value: Col:YAP/+, R26:sr/Cas9


title: Library 2 rep4 WY2006


title: Sox11_WT_KO_RNA_seq, 931-TKA, NT6, TGF-β1, biol. replicate 2

description:
931_NT6_TGF2
931-TKA RNA-seq_merge
931-TKA_RNA-seq_replicate2

value: Small intestine

value: Intestinal organoid


title: Sox11_WT_KO_RNA_seq, 1308-TKA, KO47, solvent, biol. replicate 2

description:
1308KO47_Solv2
1308-TKA RNA-seq_merge
1308-TKA_RNA-seq_replicate2

value: Sox11 Kockout; Apc-/-, KrasG12D/+, Trp53R172H/+

value: Solvent


title: AGS-NC-2


title: Sox11_WT_KO_RNA_seq, 931-TKA, NT6, TGF-β1, biol. replicate 1

description:
931_NT6_TGF1
931-TKA RNA-seq_merge
931-TKA_RNA-seq_replicate1


title: 0.3 ug-AgCitrate_1

description:
Library name: GRC371-15_S2
column name in Partek_GRC371_Normalized_counts.csv:GRC371-15_S2

value: Retina


title: Library 2 rep3 WY2007


title: 0.3 ug-AgBPEI_5

description:
Library name: GRC371B_41
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_41

value: 0.3 ug-AgBPEI


title: Sox11_WT_KO_RNA_seq, 931-TKA, NT6, solvent, biol. replicate 2

description:
931_NT6_Solv2
931-TKA RNA-seq_merge
931-TKA_RNA-seq_replicate2


title: Sox11_WT_KO_RNA_seq, 1308-TKA, KO47, solvent, biol. replicate 1

description:
1308KO47_Solv1
1308-TKA RNA-seq_merge
1308-TKA_RNA-seq_replicate1


title: AGS-NC-1


title: Sox11_WT_KO_RNA_seq, 931-TKA, Par, TGF-β1, biol. replicate 1

description:
931_Par_TGF1
931-TKA RNA-seq_merge
931-TKA_RNA-seq_replicate1


title: 0.3 ug-AgBPEI_4

description:
Library name: GRC371B_30
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_30


title: TTchemDRBseq, CFAP20-KO, 60min, rep2

data_processing:
*library strategy: nascent RNA-seq
A sequencing quality profile was generated using FastQC (Version 0.11.9). Sequences were trimmed using TrimGalore (Version 0.6.5). Reads were aligned to the Human Genome 38 using STAR (Version 2.7.7a) with genome file GCA_000001405.15_GRCh38 and splice junction file Homo_sapiens.GRCh38.94.correctedContigs.gtf. Duplicate reads were removed using Samtools (Version 1.11) with fixmate -m and markdup -r settings. Bam files were converted into stranded TagDirectories and UCSC genome tracks using HOMER tools (Version 4.8.2). Example genome tracks were generated in IGV (Version 2.4.3).
A list of 49,948 gene-coordinates was obtained from the UCSC genome database selecting the “knownCanonical” table containing the canonical transcription start sites per gene (Karolchik et al., 2004). To prevent contamination of binding profiles, genes were selected to be non-overlapping with at least 2 kb between genes and a minimal size of 3 kb (n=9,944). From this, a set of 3,000 actively transcribed genes was selected by calculating gene size-corrected read-densities of BrU-seq data in WT cells, using the AnnotatePeaks.pl tool of HOMER with default settings. These 3,000 actively transcribed genes were used in downstream analyses, unless stated otherwise. Read-density profiles of transcribed strands around TSS coordinates were defined using the AnnotatePeaks.pl tool of HOMER using the default normalization to 10 million reads. Subsequently, to properly compare the shape of the profiles, the average read-densities at the peak of the profile (average of density at 0.2-1kb after the TSS) was put to 1. Individual datasets were subsequently processed into heatmaps or binding profiles using R (Version 4.0.5) and Rstudio (Version 1.1.423) (Team, 2019).
Assembly: hg38
Supplementary files format and content:
TSScoordinates_InclBrUseqInWTmock.txt: tab-delimited text file containing coordinates of 9,944 TSSs including associated BrUseq signal in WT cells
TTchemDRBseq_ReadDensityAroundTSS_200KbWindow_Above3kb_2kbGap_WT_60m_rep*_DeDup_TranscStrand.txt: tab-delimited text file containing the read-density/10M total reads of the transcribed strand at the indicated distance from the TSS
TTchemDRBseq_ReadDensityAroundTSS_200KbWindow_Above3kb_2kbGap_CFAP20KO_60m_rep*_DeDup_TranscStrand.txt: tab-delimited text file containing the read-density/10M total reads of the transcribed strand at the indicated distance from the TSS
TTchemDRBseq_ReadDensityAroundTSS_200KbWindow_Above3kb_2kbGap_CFAP20resc_60m_rep2_Dedup_FragLength150_TranscStrand.txt: tab-delimited text file containing the read-density/10M total reads of the transcribed strand at the indicated distance from the TSS
TTchemDRBseq_ReadDensityAroundTSS_200KbWindow_Above3kb_2kbGap_CFAP20R100C_60m_rep2_Dedup_FragLength150_TranscStrand.txt: tab-delimited text file containing the read-density/10M total reads of the transcribed strand at the indicated distance from the TSS

extract_protocol:
Immediately after 4SU labeling, cells were washed with PBS and lysed in TRIzol reagent (Invitrogen). Total RNA was isolated by TRIzol/chloroform isolation and ethanol precipitation. 110 μg RNA (in a total volume of 116 μl) was fragmented by adding 4 μl of 5 M NaOH and left on ice for 30 min. Fragmentation was stopped by the addition of 80 μl of 1 M Tris pH 7 and cleaned up twice using the Micro Bio-Spin P-30 Gel Columns (BioRad, 7326223) according to the manufacturer’s instructions. Biotinylation of 4SU-residues was performed in a total volume of 250 μl, containing 10 mM Tris-HCl pH 7.4, 1 mM EDTA and 5 μg of MTSEA biotin-XX linker (Biotium, BT90066) for 30 min at room temperature in the dark. RNA was then purified by phenol-chloroform extraction, denatured by 10 min incubation at 65 °C and added to 150 μl μMACS Streptavidin MicroBeads (Milentyl, 130-074-101). RNA was incubated with beads for 15 min at room temperature and beads were applied to a μColumn in the magnetic field of a μMACS magnetic separator. The beads were washed tree times with 55°C pull-down wash buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween-20). Biotinylated RNA was eluted twice by addition of 100 mM DTT and cleaned up using the RNeasy MinElute kit (Qiagen, 74204) using 1,050 μl ethanol (≥99%) per 200 μl reaction after addition of 700 μl of RLT buffer to precipitate RNA of less than 200 nucleotides.
For WT and CFAP-KO cells, purified 4SU-labelled RNA was then depleted of rRNAs using the QIAseq FastSelect -rRNA depletion kit (Qiagen), followed by library preparation using the TruSeq Stranded Total RNA kit (Illumina, 20020596). The libraries were amplified according to the manufacturer’s instructions, pooled and paired-end sequenced on a DNBSEQ-G400 (BGI) system. For CFAP20-KO cells expressing GFP-CFAP20(WT) or GFP-CFAP20(R100C), no ribodepletion was performed.

treatment_protocol: Cells were exposed to 100 μM DRB (Sigma) for 4 hours. Following removal of DRB, cells were either immediately metabolically labeled with 1 mM 4-thio-uridine (4SU; Glentham Life Sciences) for 30 min, or released in regular medium for 30 min followed by 30 min labeling with 1 mM 4-thio-uridine.

value: RPE1 iCas9 p53/puro-dKO CFAP20-KO

value: DRB treated, 30 min DRB release, followed by 30 min DRB-release + 4SU labeling

value: Streptavidin-Biotin-based pulldown

value: Nascent RNA


title: TTchemDRBseq, CFAP20-KO, 30min, rep2

value: DRB treated, followed by 30 min DRB-release + 4SU labeling


title: TTchemDRBseq, WT, 60min, rep2

value: RPE1 iCas9 p53/puro-dKO WT


title: Library 3 rep1 WY2087


title: 0.3 ug-AgBPEI_3

description:
Library name: GRC371-4_S13
column name in Partek_GRC371_Normalized_counts.csv:GRC371-4_S13


title: Library 1 rep5 WY1949


title: Sox11_WT_KO_RNA_seq, 931-TKA, KO17, TGF-β1, biol. replicate 2

description:
931_KO17_TGF2
931-TKA RNA-seq_merge
931-TKA_RNA-seq_replicate2


title: Library 1 rep6 WY1946


title: Sox11_WT_KO_RNA_seq, 931-TKA, KO17, TGF-β1, biol. replicate 1

description:
931_KO17_TGF1
931-TKA RNA-seq_merge
931-TKA_RNA-seq_replicate1


title: TTchemDRBseq, WT, 30min, rep2


title: Sox11_WT_KO_RNA_seq, 931-TKA, KO17, solvent, biol. replicate 2

description:
931_KO17_Solv2
931-TKA RNA-seq_merge
931-TKA_RNA-seq_replicate2


title: TTchemDRBseq, CFAP20-KO, 60min, rep1


title: Sox11_WT_KO_RNA_seq, 931-TKA, NT6, solvent, biol. replicate 1

description:
931_NT6_Solv1
931-TKA RNA-seq_merge
931-TKA_RNA-seq_replicate1

value: Sox11 wildtype; Apc-/-, KrasG12D/+, Trp53R172H/+


title: 0.3 ug-AgBPEI_1

description:
Library name: GRC371-16_S21
column name in Partek_GRC371_Normalized_counts.csv:GRC371-16_S21


title: 0.0 ug-Negative Control_10

description:
Library name: GRC371B_48
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_48

value: 0.0 ug-Negative Control


title: Library 1 rep3 WY1966

value: hepatocytes


title: Sox11_WT_KO_RNA_seq, 931-TKA, KO3, TGF-β1, biol. replicate 2

description:
931_KO3_TGF2
931-TKA RNA-seq_merge
931-TKA_RNA-seq_replicate2


title: Library 2 rep2 WY2076


title: Library 1 rep2 WY2079


title: 0.0 ug-Negative Control_8

description:
Library name: GRC371-37_S6
column name in Partek_GRC371_Normalized_counts.csv:GRC371-37_S6


title: Library 1 rep4 WY1953


title: 0.3 ug-AgBPEI_2

description:
Library name: GRC371B_29
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_29


title: TTchemDRBseq, WT, 60min, rep1


title: Library 2 rep1 WY2088


title: Sox11_WT_KO_RNA_seq, 931-TKA, KO3, TGF-β1, biol. replicate 1

description:
931_KO3_TGF1
931-TKA RNA-seq_merge
931-TKA_RNA-seq_replicate1


title: Library 1 rep1 WY2081


title: TTchemDRBseq, WT, 30min, rep1


title: 0.0 ug-Negative Control_7

description:
Library name: GRC371-30_S4
column name in Partek_GRC371_Normalized_counts.csv:GRC371-30_S4


title: Sox11_WT_KO_RNA_seq, 931-TKA, KO17, solvent, biol. replicate 1

description:
931_KO17_Solv1
931-TKA RNA-seq_merge
931-TKA_RNA-seq_replicate1


title: ParkinKO_5

city: Epalinges

first: Ping-Chih

last: Ho

address: Ch. des Boveresses 155

country: Switzerland

institute: Ludwig Cancer Institute, UNIL

data_processing:
The reads were mapped to the mm10 using STAR.
The summarizeOverlaps function from the GenomicAlignments package was used to define gene expression level by counting the alignments to exons
Assembly: mm10
Supplementary files format and content: normalized count by DESeq2

source_name: Sorted P14 Cas9 CD8 T cell with parkin gRNA

growth_protocol: Transduced CD8+ T cells were isolated 24 hours post transduction, and 50000 cells of each group were retransferred into time match infected whole body cas9 recipients.

extract_protocol:
500 P14 Cas 9 T cells transduced with either ctrl or Park2-targeting gRNA were directly sorted into lysis buffer at day15 post infection.
Performed by low-input Smart-seq2 mRNA sequencing protocol.

value: Sorted CD8 T cells

value: parkin gRNA


title: Sox11_WT_KO_RNA_seq, 931-TKA, KO3, solvent, biol. replicate 2

description:
931_KO3_Solv2
931-TKA RNA-seq_merge
931-TKA_RNA-seq_replicate2

value: Small intestine


title: Sox11_WT_KO_RNA_seq, 931-TKA, KO3, solvent, biol. replicate 1

description:
931_KO3_Solv1
931-TKA RNA-seq_merge
931-TKA_RNA-seq_replicate1

value: Intestinal organoid


title: ParkinKO_4


title: 0.0 ug-Negative Control_5

description:
Library name: GRC371B_22
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_22


title: RNA-seq-TetO-YAP 5 days rep2

source_name: TetO-YAP S127A

extract_protocol:
RNA was harvested using Trizol reagent.
RNA-seq libraries were generated using TruSeq RNA Sample Prep Kit v2 (Illumina) according to manufacturer’s recommendations.

value: Col:YAP/+, R26:sr/+

value: Dox

tag: time point

value: 5 days


title: 0.0 ug-Negative Control_4

description:
Library name: GRC371-8_S22
column name in Partek_GRC371_Normalized_counts.csv:GRC371-8_S22

value: Retina


title: ParkinKO_3


title: KCOhom_Rep5

city: Berlin

first: Sara

last: Hetzel

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

description: Methylation profiling of whole pancreas from the KCO mouse model.

data_processing:
Raw reads were trimmed (adapter and quality) using cutadapt (version 4.1; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read.
The trimmed reads were aligned to the mouse (mm10) genome using BSMAP (version 2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R).
Duplicates were removed using the ‘MarkDuplicates’ command from GATK (version 4.2.5.0; --VALIDATION_STRINGENCY=LENIENT --REMOVE_DUPLICATES=true).
Methylation rates were called using mcall from the MOABS package (version 1.3.9.6; default parameters).
All analyses were restricted to autosomes and only CpGs covered by at least 10 and at maximum 150 reads were considered for downstream analyses.
Assembly: mm10
Supplementary files format and content: Bigwig file containing methylation rates for CpGs covered by at least 10 and at most 150 reads: <chr> <start> <end> <methylation rate>

source_name: Pancreas

growth_protocol: For studies of pancreatic mouse tumors, we used the previously generated mouse model harboring Kras(LSL-G12D); Pdx1-Cre (KC) for pancreas-specific Kras expression. KC mice were crossed with a genetic model of obesity (Lep(Ob/Ob)) to generate KC; Lep(Ob/+) (KCO(het)) and KC; Lep(Ob/Ob) (KCO) mice. Mouse genotypes were confirmed by PCR using template tail DNA isolated via HotSHOT DNA extraction and GoTaq Green Mastermix (Promega). Mice were fed standard chow for the duration of the study.

extract_protocol:
At 13 weeks of age, mice were euthanized by CO2 asphyxiation and pancreata were rapidly dissected, flash frozen in liquid nitrogen, and stored at -80C. Tumor burden (% area of pancreas comprised of cancerous lesions) was approximately 10% and 60% for KCO(het) and KCO samples, respectively.
Genomic DNA (gDNA) was purified using the DNeasy Blood & Tissue Kit (Qiagen, #69504) following the manufacturer’s instructions. Snap-frozen tissues were cut into small pieces (~25 mg) and digested overnight in Buffer ATL with Proteinase K and collected using the DNeasy Mini spin column. WGBS libraries were then prepared as above using the same kit and protocol. For the KCO samples, we performed target enrichment of previously described PRC2-targeted CGIs using 200 ng of each WGBS library from two KCO(het) and five KCO mice, pooled and mixed with a Twist Custom Methylation Panel specific for targeted CGIs, Universal Blockers (Twist, #100578), and Methylation Enhancer (Twist, #103557), then dried using a SpeedVac system. The dried product was resuspended with fast hybridization mix and enhancer (Twist, #100930), and hybridized at 60°C for 2 hours. Targeted sequences were captured and purified using Streptavidin Binding beads (Twist, #100983), and the final library pool was amplified using 2x Equinox Library Amplification Mix (Twist, #104108) with 11 PCR cycles based on the total length of targeted regions. The final library was purified with DNA Purification Beads (Twist, #100983) and sequenced on a NovaSeq platform (150 bp paired-end reads).

value: Pancreas

tag: tissue type

value: tumor

value: KC; Lep(Ob/Ob)


title: TTchemDRBseq, CFAP20-KO, 30min, rep1

value: RPE1 iCas9 p53/puro-dKO CFAP20-KO

value: Streptavidin-Biotin-based pulldown

value: Nascent RNA


title: ParkinKO_2


title: RNA-seq-TetO-YAP 5 days rep1


title: Ctrl_5

source_name: Sorted P14 Cas9 CD8 T cell with control gRNA

value: control gRNA


title: RNA-seq-TetO-YAP 0 day rep2

value: 0 day


title: ParkinKO_1


title: KCOhom_Rep3


title: KCOhom_Rep2


title: 0.0 ug-Negative Control_1

description:
Library name: GRC371-25_S20
column name in Partek_GRC371_Normalized_counts.csv:GRC371-25_S20

value: 0.0 ug-Negative Control


title: RNA-seq-TetO-YAP 5 days rep4

value: hepatocytes


title: 4186_Diseased Female_AMG

city: Pittsburgh

first: Rehana

middle: K

last: Leak

state: PA

address: 600 Forbes Ave

department: Pharmacology

institute: Duquesne University

description: Library name: X4186_AMG_S10

data_processing:
Transcripts per million (TPM) was calculated by dividing the number of reads mapped to a transcript by the transcript length.
Assembly: RNAseq reads were aligned to the Human genome using STAR (v2.7.9a) (Dobin et al., 2013) based on Ensembl release GRCh38 gene annotations. Gene expression quantification was done using featureCounts (Liao et al., 2014) and low-expression genes were filtered out. Using the count data, differential expression analysis was done using the R package DESeq2 (Love et al., 2014), with a false discovery rate (FDR) at the 5% threshold and ± 1.5 log2fold change.
Supplementary files format and content: TPM Data for all samples is in the "TPM Data" .xlsx file with the sample IDs across the collumns and the TPM values for each gene/transcript down the rows.

source_name: Amygdala

extract_protocol:
Qiagen RNeasy Plus Micro Kit (74034, Qiagen, Germantown, MD)
Transcriptome libraries were generated using the Takara SMART-Seq kit (634447, Takara Bio USA, Inc, Mountain View, CA) according to manufacturer recommendations. Library assessment and quantification were performed with Qubit 1X dsDNA (Q33231, Invitrogen, Waltham, MA) using Invitrogen’s Qubit 4 fluorometer and high-sensitivity NGS Fragment kit (DNF-474-1000, Agilent, Santa Clara,  CA) on an Agilent 5300 Fragment Analyzer. Libraries were sequenced on an illumina NextSeq 500 with a loading concentration of 2.0 pM, generating an average of ~23 million reads per sample, 2x75 bp. Sequence read quality was evaluated via FastQC (v0.11.9). The sequences were trimmed for quality using TrimGalore (v0.6.5).

value: Amygdala


title: KCOhom_Rep1


title: Ctrl_4

value: Sorted CD8 T cells


title: RNA-seq-TetO-YAP 0 day rep1


title: 0.0 ug-Negative Control_6

description:
Library name: GRC371-26_S7
column name in Partek_GRC371_Normalized_counts.csv:GRC371-26_S7


title: KCOhet_Rep2

value: KC; Lep(Ob/+)


title: RNA-seq-TetO-YAP 5 days rep3

value: Col:YAP/+, R26:sr/+


title: Ctrl_3


title: 0.0 ug-Negative Control_9

description:
Library name: GRC371-43_S20
column name in Partek_GRC371_Normalized_counts.csv:GRC371-43_S20


title: 4155_Diseased Female_AMG

description: Library name: X4155_AMG_S4


title: 0.0 ug-Negative Control_3

description:
Library name: GRC371-5_S23
column name in Partek_GRC371_Normalized_counts.csv:GRC371-5_S23


title: RNA-seq-TetO-YAP 0 day rep3

value: Dox


title: Ctrl_2


title: scATAC-seq-Hepatocyte-BEC

extract_protocol:
hepatocytes were isolated, fixed in 0.1% formaldehyde, and resuspended in PBS.
Tn5 transposase produced in-house was loaded with barcoded oligo adapters for a total of 96 different combinations. Fixed cells were transposed by each barcoded Tn5 complex in a 96-well plate at 37°C for 30 minutes before quenching the reaction with EDTA. Cells were pooled and redistributed into another 96-well plate where they underwent reverse crosslinking and PCR with uniquely barcoded primers.

value: Col:YAP/+, R26:sr/Tom


title: 0.0 ug-Negative Control_2

description:
Library name: GRC371B_37
column name in Partek_GRC371_Normalized_counts.csv:GRC371B_37

value: Retina


title: RRBS_Apc_Kras_G13D_tumor_Rep2

description: Methylation profiling of tumor tissue from the Apc/Kras mouse model (different activating Kras mutations).

data_processing:
Raw reads were subjected to adapter and quality trimming using cutadapt (version 4.1; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter), followed by NuGEN diversity adapter trimming (https://github.com/nugentechnologies/NuMetRRBS).
The trimmed reads were aligned to the mouse genome (mm10) using BSMAP (version 2.90; parameters: -v 0.1 -s 12 -q 20 -w 100 -S 1 -u -R -D C-CGG).
Aligned reads were deduplicated based on unique molecular identifiers (UMIs) using NuDup (https://github.com/nugentechnologies/nudup; parameters: --start 6 --length 6).
Methylation rates were called using mcall from the MOABS package (version 1.3.9.6; default parameters).
All analyses were restricted to autosomes and only CpGs covered by at least 5 and at maximum 150 reads were considered for downstream analyses.
Assembly: mm10
Supplementary files format and content: Bigwig file containing methylation rates for CpGs covered by at least 5 and at most 150 reads: <chr> <start> <end> <methylation rate>

source_name: Colon

growth_protocol: Mouse colon tumors expressing mutationally activated K-Ras were derived from Fabp1-Cre; Apc(2lox14/+); Kras(LSL-G12D/+) (or Kras(LSL-G13D/+) or Kras(LSL-A146T/+)) animals.

extract_protocol:
Tumors were isolated during necropsy of moribund animals and immediately snap frozen in liquid nitrogen. The animal procedures were performed under protocol approved by the Beth Israel Deaconess Medical Center IACUC.
Concentration of genomic DNA (gDNA) was quantified using a Qubit 3.0 Fluorometer. RRBS was performed on 100 ng gDNA of each sample using the NuGen Ovation RRBS Methyl-Seq System (Tecan, #0353) following the manufacturer’s recommendationswith the following modifications:After the final repair step, thebisulfite conversion of DNA was conducted using theQiagen EpiTect Fast Bisulfite Conversion kit(Qiagen, #59824) following the manufacturer’s recommendations, eluting the bisulfite converted DNA in 23 µl EB. Libraries were amplified with 12 cycles of PCR. Amplified library purificationwith Agencourt RNAclean XP beads (Beckman Coulter, #A63987)was performed twice (1X). The purified libraries were sequencedfor 76 bp single-end readson a NovaSeq 6000 platform (Illumina).

value: Colon


title: 4150_Diseased Female_AMG

description: Library name: X4150_AMG_S9


title: KCOhom_Rep4

value: Pancreas

value: tumor


title: 4365_Diseased Male_AMG

description: Library name: X4365_AMG_S5


title: Ctrl_1


title: 4220_Diseased Male_AMG

description: Library name: X4220_AMG_S3


title: Biological replicate 6, shoot, P33G treatment, day10

city: Singapore

first: Beng-Soon

last: Teh

address: 14 Science Drive 4

department: Biological Sciences

country: Singapore

institute: National University of Singapore

description:
Library name: D10ApP33G_St_R6
Column name in raw_counts_all_samples.xlsx: D10Ap33GS_R6

data_processing:
Raw data containing adapter, poly-N and low quality reads were removed using fastp
Clean reads were mapped to the reference genome of Brassica Rapa subsp. Chinensis (GCF_000309985_2) using Hisat2 (v2.0.5)
The mapped reads were assembled using StringTie (v1.3.3b)
The number of reads mapped to each gene was counted by featureCounts (v1.5.0-p3)
Differential expression analysis was carried out using DESeq2 (v1.20.0)
Assembly: GCF_000309985_2
Supplementary files format and content: Microsoft Excel Worksheet includes raw counts for each sample
Supplementary files format and content: Microsoft Excel Worksheet includes FPKM values for each sample

organism: Brassica rapa

source_name: shoot

growth_protocol: A single bacterial strain was inoculated through plant seeds for treated plants. Untreated (no bacteria) and bacterial-treated Brassica rapa plants were grown for two weeks until seedlings emerged.

extract_protocol:
Plant roots and leaves for bacterial-treated and untreated were harvested. RNA was extracted using RNeasy Plant Mini Kit (QIAGEN). The extracetd RNA was sent for sequencing.
RNA libraries were prepared using  strand -specific mRNA library preparation

treatment_protocol: A total of 10 aphids were placed on bacterial-treated and untreated (no bacteria) two-week old plants. A total of 6 replicates each of bacterial-treated and non-treated were prepared for two time points (day 5 and day 10) (n=24). Aphids were allowed to infest plants until day 5 and  day 10. Thereafter, aphids were removed from plants.

value: shoot

value: Bacterial treatment

tag: time

value: Day 10


title: RRBS_Apc_Kras_G12D_tumor_Rep2


title: RRBS_Apc_Kras_G13D_tumor_Rep1


title: Biological replicate 5, shoot, P33G treatment, day10

description:
Library name: D10ApP33G_St_R5
Column name in raw_counts_all_samples.xlsx: D10Ap33GS_R5


title: RRBS_Apc_Kras_G12D_tumor_Rep1


title: RRBS_Apc_Kras_A146T_tumor_Rep2


title: Biological replicate 4, shoot, P33G treatment, day10

description:
Library name: D10ApP33G_St_R4
Column name in raw_counts_all_samples.xlsx: D10Ap33GS_R4


title: 4002_Diseased Male_AMG

description: Library name: X4002_AMG_S17


title: 3924_Control Female_AMG

description: Library name: X3924_AMG_S1


title: Biological replicate 3, shoot, P33G treatment, day10

description:
Library name: D10ApP33G_St_R3
Column name in raw_counts_all_samples.xlsx: D10Ap33GS_R3


title: Non-epilepsy control, MazF-UnDigested 10

type: RNA

city: Dublin

first: Gary

middle: P

last: Brennan

state: Dublin

address: UCD Conway Institute, Stillorgan Road

department: School of Biomolecular and Biomedical Sciences

country: Ireland

institute: UCD

description:
C10.txt
C10(MazF-UnDigested,Normalized)

hyb_protocol: The sample preparation and microarray hybridization were performed based on Arraystar’s standard protocols. Briefly, the total RNA was divided into two fractions. One fraction denoted as “MazF-Digested” was treated with RNA endoribonuclease MazF to cleave the unmodified m6A sites; the other fraction denoted as “MazF-Undigested” was untreated with MazF for both modified and unmodified sites.

scan_protocol: After washing the slides, the arrays were scanned in two-color channels by an Agilent Scanner G2505C.

data_processing:
Raw intensities of MazF-Digested (Cy5-labelled) and MazF-Undigested (Cy3-labelled) were normalized with the average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 7 out of 24 samples were retained for further “m6A site methylation stoichiometry” and “m6A site abundance” analyses. The “m6A site methylation stoichiometry” was calculated for the percentage of modification for each site, “m6A site abundance” was calculated for the m6A site methylation amount.
Differentially m6A-methylated sites between two comparison groups were compiled by the fold change and statistical significance (p-value) thresholds. Hierarchical Clustering was performed to display m6A-methylation pattern among samples.

source_name: Autopsy control human brain tissue

label_protocol: The “MazF-Digested” and “MazF-Undigested” RNAs were separately labeled with Cy5 and Cy3 as cRNAs using Arraystar Super RNA Labeling Kit. The “MazF-Digested” and “MazF-Undigested” cRNAs were combined together and hybridized onto Arraystar Human m6A Single Nucleotide Array (8x15K, Arraystar).

extract_protocol: Total RNA was extracted from ~30 mg of each human hippocampus tissue sample via a standardised phenol extraction protocol using TRIzol® Reagent (Invitrogen/Thermo Fisher, USA). All work was carried out on ice and in a fume hood except where otherwise indicated. Briefly, 800 μl of TRIzol® was added to each sample in a 2 ml microcentrifuge (Eppendorf, USA) tube and the tissue homogenised using a TissueRuptor II handheld rotor–stator homogenizer (Qiagen). Homogenised samples were centrifuged for 10 min at 12 000 ×g at 4 ° C and then transferred to sterile, nuclease free 1.5 ml microcentrifuge tubes. The samples were incubated at room temperature (RT) for 5 min. A volume of 160 μl chloroform was added to each tube, immediately, shaking the tubes by hand after addition, for 15 s to mix. They were incubated for 3 min at RT before being centrifuged for 15 min at 12 000 ×g at 4 ° C. The upper aqueous phase was transferred from each tube into new, labelled, sterile tubes. A volume of 400 μl of isopropanol was added to each sample along with 1.5 μl of Glycoblue (Invitrogen, USA) co-precipitant, and they were placed in the freezer overnight at -20 ° C. The following day samples were then centrifuged for 15 mins at 12 000 ×g at 4 ° C. The supernatants were discarded, and the pellets were washed in 500 μl ice-cold 75% RNase free ethanol (EtOH). All samples were centrifuged at 12 000 ×g for 10 min at 4 ° C and the wash / centrifugation step was then repeated. The RNA pellets were left to air dry at RT before resuspension in 25 μl RNase free water. The quantity and purity of the extracted RNA was determined via nanodrop spectrophotometry (Nanodrop 2000C, Thermo Fisher Scientific) and the total extracted RNA stored at -80 ° C.

value: Non-epilepsy control

value: MazF-UnDigested

tag: sample group

value: Control


title: KCOhet_Rep1


title: 3795_Control Female_AMG

description: Library name: X3795_AMG_S12


title: RRBS_Apc_Kras_A146T_tumor_Rep1


title: Non-epilepsy control, MazF-UnDigested 9

description:
C9.txt
C9(MazF-UnDigested,Normalized)


title: Biological replicate 2, shoot, P33g treatment, day10

description:
Library name: D10ApP33G_St_R2
Column name in raw_counts_all_samples.xlsx: D10Ap33GS_R2


title: Cep83 +/+FL1KOFL3lx/+ control replicate2

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
Transcriptome and barcode libraries were sequenced either on an Illumina NextSeq 500 and NovaSeq 6000 at the Next Generation Sequencing Facility of the Max Planck Institute of Biochemistry. Then, the sequencing data was processed with cellranger (version 7.0.1, reference 'refdata-gex-mm10-2020').
Assembly: mm10
Supplementary files format and content: filtered feature barcode matrix output of cellranger, zipped

source_name: neocortex

extract_protocol:
E15.5 of mutant embryos were removed from the uterus of mutant females, and stored in ice-cold in Leibowitz medium with 5% FBS. Brains were isolated and cut in 300 μm using a vibratome (Leica VT1000S, Germany) in cutting buffer, Leibowitz medium with 5% FBS. Then, brain sections were manually dissected for both hemisphere of cortical primordium of cortex. Meanwhile, genotyping was performed. Then, collected tissues were transferred into a dissociation Buffer, EBSS. Dissociation was performed with Worthington Kit and manually Papain dissociation system was carried out according to the recommended protocol (Worthington, #LK003163).
For experiments utilizing the 10x Genomics platform, the following reagents were used Chromium Single Cell Next GEM Single Cell 3’ GEM kit v3.1 (PN-1000130), Library Construction Kit (PN-1000196), Chromium Next GEM Single Cell 3′ Gel Bead Kit v3.1 (PN-1000129) and Single Index Kit T Set A (PN-1000213) and Dual Index Kit TT Set A (PN-1000215) were used according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagents Kits v3.1 User Guide.

value: neocortex

value: Cortical neurons

tag: chemistry

value: Dual Index Kit TT


title: Fgf10/Flrt1/3 TKO replicate3

description: 10x genomics


title: Non-epilepsy control, MazF-UnDigested 7

description:
C7.txt
C7(MazF-UnDigested,Normalized)


title: Biological replicate 6, shoot, control, day10

description:
Library name: D10ApUT_St_R6
Column name in raw_counts_all_samples.xlsx: D10AphUTS_R6


title: Non-epilepsy control, MazF-UnDigested 5

description:
C5.txt
C5(MazF-UnDigested,Normalized)


title: Non-epilepsy control, MazF-UnDigested 6

description:
C6.txt
C6(MazF-UnDigested,Normalized)


title: 3336_Control Male_AMG

description: Library name: X3336_AMG_S16

value: Amygdala


title: Cep83/Flrt1/3 TKO replicate3

description: 10x genomics


title: 3298_Control Male_AMG

description: Library name: X3298_AMG_S2


title: Biological replicate 5, shoot, control, day10

description:
Library name: D10ApUT_St_R5
Column name in raw_counts_all_samples.xlsx: D10AphUTS_R5


title: Cep83 +/+FL1KOFL3lx/+ control replicate1

description: 10x genomics


title: 4186_Diseased Female_OB

description: Library name: X4186_OB_S20

source_name: Olfactory Bulb

value: Olfactory Bulb


title: Cep83/Flrt1/3 TKO replicate2

description: 10x genomics


title: Non-epilepsy control, MazF-UnDigested 3

description:
C3.txt
C3(MazF-UnDigested,Normalized)


title: Biological replicate 4, shoot, control, day10

description:
Library name: D10ApUT_St_R4
Column name in raw_counts_all_samples.xlsx: D10AphUTS_R4


title: Non-epilepsy control, MazF-UnDigested 2

description:
C2.txt
C2(MazF-UnDigested,Normalized)


title: Non-epilepsy control, MazF-UnDigested 1

description:
C1.txt
C1(MazF-UnDigested,Normalized)


title: Biological replicate 3, shoot, control, day10

description:
Library name: D10ApUT_St_R3
Column name in raw_counts_all_samples.xlsx: D10AphUTS_R3


title: Fgf10 +/+FL1KOFL3lx/+ control replicate2

description: 10x genomics


title: 3345_Control Female_AMG

description: Library name: X3345_AMG_S22


title: 3401_Control Male_AMG

description: Library name: X3401_AMG_S24


title: Non-epilepsy control, MazF-UnDigested 4

description:
C4.txt
C4(MazF-UnDigested,Normalized)


title: Biological replicate 1, shoot, P33G treatment, day10

description:
Library name: D10ApP33G_St_R1
Column name in raw_counts_all_samples.xlsx: D10Ap33GS_R1


title: Sclerotic TLE sample, MazF-UnDigested 7

description:
B7.txt
B7(MazF-UnDigested,Normalized)

source_name: Resected human hippocampus tissue

value: Sclerotic hippocampus

value: Disease


title: Fgf10/Flrt1/3 TKO replicate2

description: 10x genomics


title: Biological replicate 2, shoot, control, day10

description:
Library name: D10ApUT_St_R2
Column name in raw_counts_all_samples.xlsx: D10AphUTS_R2


title: 4150_Diseased Female_OB

description: Library name: X4150_OB_S18


title: 4155_Diseased Female_OB

description: Library name: X4155_OB_S19


title: 4220_Diseased Male_OB

description: Library name: X4220_OB_S6


title: Biological replicate 6, root, P33G treatment, day10

description:
Library name: D10ApP33G_Rt_R6
Column name in raw_counts_all_samples.xlsx: D10Ap33GR_R6

source_name: root

value: root


title: Biological replicate 1, shoot, control, day10

description:
Library name: D10ApUT_St_R1
Column name in raw_counts_all_samples.xlsx: D10AphUTS_R1


title: Fgf10/Flrt1/3 TKO replicate1

description: 10x genomics

value: Single Index Kit T


title: Sclerotic TLE sample, MazF-UnDigested 5

description:
B5.txt
B5(MazF-UnDigested,Normalized)


title: Biological replicate 5, root, P33G treatment, day10

description:
Library name: D10ApP33G_Rt_R5
Column name in raw_counts_all_samples.xlsx: D10Ap33GR_R5


title: Biological replicate 4, root, P33G treatment, day10

description:
Library name: D10ApP33G_Rt_R4
Column name in raw_counts_all_samples.xlsx: D10Ap33GR_R4


title: BMDMs, conditional knockout, rep3

city: Daejeon

first: Taylor

last: Roh

address: 266, Munhwa-ro

department: Microbiology

country: South Korea

institute: Chungnam National University

data_processing:
Paired-end sequencing reads were generated on the Illumina sequencing NovaSeq platform. Before starting analysis, Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality. The cleaned reads were aligned to the Mus musculus (mm10) using HISAT v2.1.0 (KIM et al, 2015), based on the HISAT and Bowtie2 implementations. The reference genome sequence and gene annotation data were downloaded from NCBI Genome assembly and NCBI RefSeq database respectively. Aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9. After alignment, the transcripts were assembled and quantified using StringTie v2.1.3b (Pertea, Mihaela, et al., 2015, 2016). Gene-level and Transcript-level quantification were calculated as raw read count, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Million).
Assembly: genome used for mapping: mm10
Supplementary files format and content: fastq

source_name: BMDMs

extract_protocol:
Total RNA concentration was calculated by Quant-IT RiboGreen (Invitrogen). To determine the DV200 (% of RNA fragments >200 bp) value, samples are run on the TapeStation RNA screentape (Agilent).
A total of 100 ng of total RNA was subjected to a sequencing library construction using the Agilent SureSelect RNA Direct kit according to the manufacturer's protocol.

value: BMDMs

value: Macrophages

tag: strain background

value: cKO


title: 4002_Diseased Male_OB

description: Library name: X4002_OB_S7


title: Sclerotic TLE sample, MazF-UnDigested 4

description:
B4.txt
B4(MazF-UnDigested,Normalized)


title: 3924_Control Female_OB

description: Library name: X3924_OB_S13


title: BMDMs, conditional knockout, rep2


title: Sclerotic TLE sample, MazF-UnDigested 2

description:
B2.txt
B2(MazF-UnDigested,Normalized)


title: Sclerotic TLE sample, MazF-UnDigested 6

description:
B6.txt
B6(MazF-UnDigested,Normalized)


title: Biological replicate 3, root, P33G treatment, day10

description:
Library name: D10ApP33G_Rt_R3
Column name in raw_counts_all_samples.xlsx: D10Ap33GR_R3

value: Bacterial treatment


title: 3795_Control Female_OB

description: Library name: X3795_OB_S11


title: 4365_Diseased Male_OB

description: Library name: X4365_OB_S8


title: Biological replicate 2, root, P33g treatment, day10

description:
Library name: D10ApP33G_Rt_R2
Column name in raw_counts_all_samples.xlsx: D10Ap33GR_R2

value: Day 10


title: BMDMs, conditional knockout, rep1


title: Fgf10 +/+FL1KOFL3lx/+ control replicate1

description: 10x genomics


title: 3345_Control Female_OB

description: Library name: X3345_OB_S21


title: 3401_Control Male_OB

description: Library name: X3401_OB_S23


title: Non-sclerotic TLE sample, MazF-UnDigested 7

description:
A7.txt
A7(MazF-UnDigested,Normalized)

value: Non-sclerotic hippocampus


title: Non-epilepsy control, MazF-UnDigested 8

description:
C8.txt
C8(MazF-UnDigested,Normalized)

value: Non-epilepsy control

value: MazF-UnDigested


title: Sclerotic TLE sample, MazF-UnDigested 1

description:
B1.txt
B1(MazF-UnDigested,Normalized)


title: Biological replicate 1, root, P33G treatment, day10

description:
Library name: D10ApP33G_Rt_R1
Column name in raw_counts_all_samples.xlsx: D10Ap33GR_R1


title: BMDMs, floxed, rep2

value: WT


title: Sclerotic TLE sample, MazF-UnDigested 3

description:
B3.txt
B3(MazF-UnDigested,Normalized)


title: 3336_Control Male_OB

description: Library name: X3336_OB_S15


title: Non-sclerotic TLE sample, MazF-UnDigested 6

description:
A6.txt
A6(MazF-UnDigested,Normalized)


title: Biological replicate 6, root, control, day10

description:
Library name: D10ApUT_Rt_R6
Column name in raw_counts_all_samples.xlsx: D10ApUTRt_R6

value: Control


title: Non-sclerotic TLE sample, MazF-UnDigested 5

description:
A5.txt
A5(MazF-UnDigested,Normalized)


title: 3298_Control Male_OB

description: Library name: X3298_OB_S14


title: Non-sclerotic TLE sample, MazF-UnDigested 4

description:
A4.txt
A4(MazF-UnDigested,Normalized)


title: mPFC_male, scRNAseq

city: Beijing

first: Kun

last: Li

address: HaiDian

institute: Tsinghua University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: medial prefrontal cortex

extract_protocol:
The mPFC tissues were extracted using a brain matrix from two estrous female mice, two diestrous female mice, and two male mice. The dissected tissue was then cut into small pieces and transferred to a 15 ml tube containing 20 U/mL pre-activated papain (Worthington, LK003178, 37°C for 30 min) and 0.1 U/uL recombinant RNase inhibitor (Takara, 2313A). Papain digestion was performed at 34℃ for 20 min. Following digestion, the papain solution was replaced with ice-cold, carbogen-bubbled ACSF (pH 7.2-7.4, 125 mM NaCl, 2.5 mM KCl, 25 mM NaHCO3, 1.25 mM NaH2PO4, 25 mM glucose, 1 mM MgCl2, and 1 mM CaCl2, oxygenated with 95% O2 and 5% CO2) containing 1% fetal bovine serum (FBS) and 0.1 U/μL recombinant RNase inhibitor. The tissue pieces were dissociated using gentle pipetting through 1000μL and 200μL tips, to obtain single-cell suspensions. Subsequently, the suspensions were filtered through a 35μm cell strainer (Corning, 352235) to remove debris, and then layered onto 30% Percoll (Sigma, P4937, diluted by ACSF containing 1% FBS and 0.1 U/μL recombinant RNase inhibitor), followed by centrifugation at 700g for 10 minutes at 4℃. After two washes, the cells were resuspended in 1X PBS with 0.02% BSA and 0.1 U/μL recombinant RNase inhibitor. The cell viability and concentration were determined, and 15000 single cells per sample were uploaded onto 10 × Genomics 3′ library chips, using the Single Cell 3′ Library & Gel Bead kit (v.3.1), as per the manufacturer's instructions.
The cell viability and concentration were determined, and 15000 single cells per sample were uploaded onto 10 × Genomics 3′ library chips, using the Single Cell 3′ Library & Gel Bead kit (v.3.1), as per the manufacturer's instructions.The resulting libraries were sequenced on an Illumina NovaSeq 6000.

value: medial prefrontal cortex

value: total mPFC neurons

tag: Stage

value: male


title: Non-sclerotic TLE sample, MazF-UnDigested 3

description:
A3.txt
A3(MazF-UnDigested,Normalized)


title: EFF_121-D77_MAIT

city: silver spring

first: Dohoon

last: Kim

address: 503 BLDG, Walter Reed Army institute of research

institute: Henry M Jackson Foundation

data_processing:
Quality control was performed on raw FASTQ files using FastQC to assess the quality of the sequencing data and checked with RIN(RNA Integrity Numbers)
Adapters and low-quality bases were trimmed using Trimmomatic.
Cleaned reads were aligned to the reference genome using STAR aligner(ver. 2.6.1d) with default parameters.
Aligned reads were quantified to gene-level expression using RSEM(ver. 1.3.1).
Raw read counts and TPM (Transcripts Per Million) were generated for each sample.
Differential expression analysis was carried out using edgeR.
Assembly: hg38
Supplementary files format and content: The processed data files are in tab-delimited text format and include gene expression matrices (TPM and raw counts) and differential expression results (gene IDs, log2 fold changes, p-values, and FDR).

source_name: PBMC

growth_protocol: Twenty naïve study participants from 2 previously described ETEC challenges were included.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen), and RNA quality and concentration were assessed with the Agilent 2100 Bioanalyzer Pico Chip.
RNA-seq libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) according to the manufacturer’s instructions. Amplified material was purified using Agencourt AMPure XP beads (Beckman). cDNA quantity was assessed on a Qubit 3.0 (ThermoFisher) and fragment size was evaluated on a 2100 BioAnalyzer (Agilent).

treatment_protocol: To study the immune response to enteric bacterial pathogen, healthy consenting adults were orally challenged with an infectious dose of either the B7A or H10407 strain of ETEC, causing moderate to severe diarrhea (MSD)

value: PBMC

value: bulk sorted MAIT cells

value: post ETEC challenge


title: mPFC_diestrus, scRNAseq

description: 10x Genomics

value: diestrus


title: BMDMs, floxed, rep3

value: BMDMs


title: EFF_121-D69_MAIT

value: Baseline


title: Biological replicate 3, root, control, day10

description:
Library name: D10ApUT_Rt_R3
Column name in raw_counts_all_samples.xlsx: D10ApUTRt_R3

value: root


title: mPFC_estrus, scRNAseq

description: 10x Genomics

value: estrus


title: Biological replicate 2, root, control, day10

description:
Library name: D10ApUT_Rt_R2
Column name in raw_counts_all_samples.xlsx: D10ApUTRt_R2

value: Day 10


title: Biological replicate 1, root, control, day10

description:
Library name: D10ApUT_Rt_R1
Column name in raw_counts_all_samples.xlsx: D10ApUTRt_R1


title: triple negative breast cancer, palbociclib+OPG_Fc, rep3

city: Lisbon

first: Sandra

last: Casimiro

address: Av. Prof. Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

description:
55_5 Expression
Palbo+OPG_Fc_3

data_processing:
mapping to reference genome (GCF_000001405.38_GRCh38.p12) was performed with HISAT
mapping to the reference genes with Bowtie2
Expression levels in fragments per kilobase million (FPKM) for each sample were calculated with RSEM
Differential expressed genes (DEGs) were detected with PossionDis
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: breast

growth_protocol: MDA-MB-231 cells were harvested at the exponential phase of growth and resuspended at 10^5 cells/ml in 50% phenol-free matrigel solution (#356237, Corning). Mice were injected subcutaneously and bilaterally with 100 µl of cell suspension, directly into the flanks. Tumor growth was monitored every three days with a caliper and tumor volume calculated using the formula Tvol= 1/2(lengthxwidth2). When tumors reached approximately 100mm3.

extract_protocol:
Total RNA was extracted using the NZY Total RNA Isolation kit (#MB13402, Nzytech), according to manufacturer’s instructions. Tumor tissues preserved in RNA later (#AM7021, Thermo Fisher Scientific) at necropsy were transferred to lysis buffer with silica beads (#110791102; Biospec Products), and disrupted in a Minibeadbeater (Biospec Products) for 1-2 min.
DNBSEQ Eukaryotic Strand-specific mRNA library

treatment_protocol: OPG-Fc 10mg/kg i.p. 3x/week (#461130, Amgen, Inc.); Palbociclib (Palbo) 30mg/Kg/day p.o. (#PZ0199, Sigma-Aldrich); Palbo+OPG-Fc 10mg/kg i.p. 3x/week (#461130, Amgen, Inc.); or vehicle (0,05 M Na Lactate (#L7900, Sigma-Aldrich) plus 95% corn oil (#C8267, Sigma-Aldrich) in 5% DMSO (#D8418-50ML, Sigma-Aldrich)

value: breast

value: epithelial


title: Non-sclerotic TLE sample, MazF-UnDigested 1

description:
A1.txt
A1(MazF-UnDigested,Normalized)

value: Non-sclerotic hippocampus

value: MazF-UnDigested

value: Disease


title: BMDMs, floxed, rep1

value: Macrophages

value: WT


title: EFF_120-D77_MAIT


title: Biological replicate 6, shoot, P33G treatment, day5

description:
Library name: D5ApP33G_St_R6
Column name in raw_counts_all_samples.xlsx: D5Ap33GSt_R6

value: shoot

value: Bacterial treatment

value: Day 5


title: EFF_117-D77_MAIT

value: PBMC

value: bulk sorted MAIT cells

value: post ETEC challenge


title: triple negative breast cancer, palbociclib+OPG_Fc, rep1

description:
55_2 Expression
Palbo+OPG_Fc_1


title: Biological replicate 5, shoot, P33G treatment, day5

description:
Library name: D5ApP33G_St_R5
Column name in raw_counts_all_samples.xlsx: D5Ap33GSt_R5


title: Non-epilepsy control, MazF-Digested 10

value: Non-epilepsy control

value: MazF-Digested

value: Control


title: Non-sclerotic TLE sample, MazF-UnDigested 2

description:
A2.txt
A2(MazF-UnDigested,Normalized)


title: Biological replicate 5, root, control, day10

description:
Library name: D10ApUT_Rt_R5
Column name in raw_counts_all_samples.xlsx: D10ApUTRt_R5

value: root

value: Day 10


title: Biological replicate 4, root, control, day10

description:
Library name: D10ApUT_Rt_R4
Column name in raw_counts_all_samples.xlsx: D10ApUTRt_R4


title: EFF_117-D69_MAIT

value: Baseline


title: triple negative breast cancer, palbociclib, rep2

description:
54_5 Expression
Palbo_2

value: breast

value: epithelial

value: Palbociclib


title: Biological replicate 4, shoot, P33G treatment, day5

description:
Library name: D5ApP33G_St_R4
Column name in raw_counts_all_samples.xlsx: D5Ap33GSt_R4


title: Non-epilepsy control, MazF-Digested 9


title: EFF_070-D77_MAIT


title: Biological replicate 3, shoot, P33G treatment, day5

description:
Library name: D5ApP33G_St_R3
Column name in raw_counts_all_samples.xlsx: D5Ap33GSt_R3


title: Non-epilepsy control, MazF-Digested 8


title: triple negative breast cancer, OPG_Fc rep2

description:
53_3 Expression
OPG_Fc_2


title: Non-epilepsy control, MazF-Digested 7


title: EFF_070-D69_MAIT


title: EFF_120-D69_MAIT


title: Biological replicate 1, shoot, P33G treatment, day5

description:
Library name: D5ApP33G_St_R1
Column name in raw_counts_all_samples.xlsx: D5Ap33GSt_R1


title: Non-epilepsy control, MazF-Digested 5


title: Biological replicate 2, shoot, P33g treatment, day5

description:
Library name: D5ApP33G_St_R2
Column name in raw_counts_all_samples.xlsx: D5Ap33GSt_R2


title: Biological replicate 6, shoot, control, day5

description:
Library name: D5ApUT_St_R6
Column name in raw_counts_all_samples.xlsx: D5ApUTSt_R6


title: Non-epilepsy control, MazF-Digested 4


title: Non-epilepsy control, MazF-Digested 6


title: triple negative breast cancer, untreated, rep2

description:
52_1b Expression
VEH_2

value: vehicle


title: EFF_067-D77_MAIT


title: EFF_067-D69_MAIT


title: EFF_063-D69_MAIT


title: triple negative breast cancer, untreated, rep3

description:
52_5 Expression
VEH_3

value: WT


title: EFF_063-D77_MAIT


title: triple negative breast cancer, untreated, rep1

description:
52_1a Expression
VEH_1


title: Biological replicate 5, shoot, control, day5

description:
Library name: D5ApUT_St_R5
Column name in raw_counts_all_samples.xlsx: D5ApUTSt_R5

value: shoot


title: Biological replicate 4, shoot, control, day5

description:
Library name: D5ApUT_St_R4
Column name in raw_counts_all_samples.xlsx: D5ApUTSt_R4


title: triple negative breast cancer, palbociclib+OPG_Fc, rep2

description:
55_4 Expression
Palbo+OPG_Fc_2


title: EFF_031-D77_MAIT


title: triple negative breast cancer, palbociclib, rep1

description:
54_1 Expression
Palbo_1


title: R11

city: Shanghai

first: Ye

last: Zhou

address: Xiangyin Road

department: National Key Laboratory of Immunity & Inflammation

institute: Naval Medical University

description: Library name: Sample 23

data_processing:
The data were first cleaned by trimming adapters, removing low-quality sequences, and removing host reads, and the clean reads of each sample were mapped to reference sequence that was spliced by Megahits v1.2.8 (Hong Kong, China).
Host reads were aligned to GRCm39 using the STAR v2.7.11b (Princeton, NJ).
Raw Count is the number of reads directly mapped to a gene/transcript with the purpose of identifying specific viral species in this article.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files include reads count for each sample.

source_name: nasal mucosa

extract_protocol:
Total RNA was extracted from nasal mucosa using Trizol, and the RNA integrity and quantity were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.
Upon confirming the RNA quality standards (total RNA ≥ 500ng, RNA integrity number ≥ 5.8), the RNA library for meta-transcriptome sequencing was prepared by depleting ribosomal RNA using an rRNA Removal Kit, fragmenting the RNA into 250-300 bp pieces, and reverse-transcribing these into cDNA. Subsequent steps included end repair, adenylation, and adaptor ligation. The library was then size-selected, amplified, and its concentration and insert size were validated using Qubit® fluorometer, Agilent 2100 Bioanalyzer, and qPCR before sequencing.

value: nasal mucosa

value: HDM+Ribavirin


title: Non-epilepsy control, MazF-Digested 3


title: triple negative breast cancer, OPG_Fc rep1

description:
53_1 Expression
OPG_Fc_1


title: Biological replicate 3, shoot, control, day5

description:
Library name: D5ApUT_St_R3
Column name in raw_counts_all_samples.xlsx: D5ApUTSt_R3

value: Day 5


title: Non-epilepsy control, MazF-Digested 2


title: EFF_031-D69_MAIT

value: PBMC

value: bulk sorted MAIT cells


title: Biological replicate 2, shoot, control, day5

description:
Library name: D5ApUT_St_R2
Column name in raw_counts_all_samples.xlsx: D5ApUTSt_R2


title: R12

description: Library name: Sample 24


title: EFF_022-D69_MAIT


title: V12

description: Library name: Sample 21

value: HDM+Vehicle


title: R10

description: Library name: Sample 22


title: Sclerotic TLE sample, MazF-Digested 7

value: Sclerotic hippocampus

value: MazF-Digested

value: Disease


title: Sclerotic TLE sample, MazF-Digested 5


title: Biological replicate 1, shoot, control, day5

description:
Library name: D5ApUT_St_R1
Column name in raw_counts_all_samples.xlsx: D5ApUTSt_R1

value: Control


title: Sclerotic TLE sample, MazF-Digested 6


title: B7A_040-D7_MAIT

value: post ETEC challenge


title: Non-epilepsy control, MazF-Digested 1

value: Non-epilepsy control


title: EFF_022-D77_MAIT


title: V10

description: Library name: Sample 19


title: V11

description: Library name: Sample 20


title: B7A_040-D1_MAIT

value: Baseline


title: Biological replicate 4, root, P33G treatment, day5

description:
Library name: D5ApP33G_Rt_R4
Column name in raw_counts_all_samples.xlsx: D5Ap33GRt_R4

value: root

value: Bacterial treatment


title: Sclerotic TLE sample, MazF-Digested 4


title: B7A_039-D7_MAIT


title: Sclerotic TLE sample, MazF-Digested 3


title: R09

description: Library name: Sample 18

value: WT

value: PBS+Ribavirin


title: Sclerotic TLE sample, MazF-Digested 2


title: Sclerotic TLE sample, MazF-Digested 1


title: Biological replicate 3, root, P33G treatment, day5

description:
Library name: D5ApP33G_Rt_R3
Column name in raw_counts_all_samples.xlsx: D5Ap33GRt_R3


title: Non-sclerotic TLE sample, MazF-Digested 7

value: Non-sclerotic hippocampus


title: B7A_028-D1_MAIT


title: B7A_021-D7_MAIT


title: V08

description: Library name: Sample 14

value: nasal mucosa

value: PBS+Vehicle


title: B7A_028-D7_MAIT

value: PBMC


title: Biological replicate 1, root, P33G treatment, day5

description:
Library name: D5ApP33G_Rt_R1
Column name in raw_counts_all_samples.xlsx: D5Ap33GRt_R1

value: Day 5


title: Biological replicate 5, root, control, day5

description:
Library name: D5ApUT_Rt_R5
Column name in raw_counts_all_samples.xlsx: D5ApUTRt_R5


title: R07

description: Library name: Sample 16


title: Biological replicate 2, root, P33g treatment, day5

description:
Library name: D5ApP33G_Rt_R2
Column name in raw_counts_all_samples.xlsx: D5Ap33GRt_R2


title: B7A_039-D1_MAIT

value: bulk sorted MAIT cells


title: B7A_021-D1_MAIT


title: B7A_013-D7_MAIT


title: Biological replicate 6, root, control, day5

description:
Library name: D5ApUT_Rt_R6
Column name in raw_counts_all_samples.xlsx: D5ApUTRt_R6


title: Biological replicate 4, root, control, day5

description:
Library name: D5ApUT_Rt_R4
Column name in raw_counts_all_samples.xlsx: D5ApUTRt_R4


title: R06

description: Library name: Sample 12

value: OVA+Ribavirin


title: V09

description: Library name: Sample 15


title: Biological replicate 5, root, P33G treatment, day5

description:
Library name: D5ApP33G_Rt_R5
Column name in raw_counts_all_samples.xlsx: D5Ap33GRt_R5


title: Biological replicate 6, root, P33G treatment, day5

description:
Library name: D5ApP33G_Rt_R6
Column name in raw_counts_all_samples.xlsx: D5Ap33GRt_R6


title: Non-sclerotic TLE sample, MazF-Digested 3

value: MazF-Digested


title: R08

description: Library name: Sample 17


title: Biological replicate 3, root, control, day5

description:
Library name: D5ApUT_Rt_R3
Column name in raw_counts_all_samples.xlsx: D5ApUTRt_R3


title: B7A_013-D1_MAIT


title: Non-sclerotic TLE sample, MazF-Digested 4

value: Disease


title: V07

description: Library name: Sample 13


title: Non-sclerotic TLE sample, MazF-Digested 5


title: R05

description: Library name: Sample 11


title: Non-sclerotic TLE sample, MazF-Digested 2


title: Non-sclerotic TLE sample, MazF-Digested 1


title: Non-sclerotic TLE sample, MazF-Digested 6


title: triple negative breast cancer, palbociclib+OPG_Fc, rep3

description: COMB_127_1 FPKM

data_processing:
mapping to reference genome (Mus_musculus_10090.NCBI.GCF_000001635.27_GRCm39.v2201) was performed with HISAT
mapping to the reference genes with Bowtie2
Expression levels in fragments per kilobase million (FPKM) for each sample were calculated with RSEM
Differential expressed genes (DEGs) were detected with PossionDis
Assembly: mm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: 4T1 cells were harvested at the exponential phase of growth and resuspended at 10^5 cells/ml in 50% phenol-free matrigel solution (#356237, Corning). Mice were injected subcutaneously and bilaterally with 100 µl of cell suspension, directly into the flanks. Tumor growth was monitored every three days with a caliper and tumor volume calculated using the formula Tvol= 1/2(lengthxwidth2). When tumors reached approximately 100mm3.

extract_protocol:
Total RNA was extracted using the NZY Total RNA Isolation kit (#MB13402, Nzytech), according to manufacturer’s instructions. Tumor tissues preserved in RNA later (#AM7021, Thermo Fisher Scientific) at necropsy were transferred to lysis buffer with silica beads (#110791102; Biospec Products), and disrupted in a Minibeadbeater (Biospec Products) for 1-2 min.
mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control.

value: breast

value: epithelial


title: B7A_012-D7_MAIT

value: post ETEC challenge


title: Biological replicate 2, root, control, day5

description:
Library name: D5ApUT_Rt_R2
Column name in raw_counts_all_samples.xlsx: D5ApUTRt_R2

value: Control


title: R04

description: Library name: Sample 10


title: triple negative breast cancer, palbociclib+OPG_Fc, rep2

description: COMB_125_2 FPKM


title: Biological replicate 1, root, control, day5

description:
Library name: D5ApUT_Rt_R1
Column name in raw_counts_all_samples.xlsx: D5ApUTRt_R1

value: root


title: B7A_012-D1_MAIT

value: Baseline


title: V06

description: Library name: Sample 9

value: WT

value: OVA+Vehicle


title: triple negative breast cancer, palbociclib+OPG_Fc, rep1

description: COMB_125_1 FPKM


title: DRIPseq, CFAP20KO, RNAseH, rep2

data_processing:
For all sequencing data, a sequencing quality profile was generated using FastQC (Version 0.11.9). Sequences were trimmed using TrimGalore (Version 0.6.5). Reads were aligned to the Human Genome 38 using bwa-mem tools (BWA (Version 0.7.17) and reference genome GCA_000001405.15_GRCh38 (Li, 2013). Only uniquely mapping and high-quality reads (> q30) were included in the analyses. Bam files were converted into stranded TagDirectories and UCSC genome tracks using HOMER tools (Version 4.8.2). Example genome tracks were generated in IGV (Version 2.4.3).
OK-seq data in untreated RPE1 cells was downloaded from Chen et al. 2019 (datasets GSM3130725 and GSM3130726). Sequences were trimmed using TrimGalore (Version 0.6.5), and aligned to the Human Genome 38 using STAR (Version 2.7.7a) with genome file GCA_000001405.15_GRCh38. Duplicate reads were removed using Samtools (Version 1.11) with fixmate -m and markdup -r settings. Replication initiation zones were subsequently defined using the replication fork directionality analysis R toolkit (OKseqHMM; available on https://github.com/CL-CHEN-Lab/OK-Seq), with read coverage threshold 6 for GSM3130725 and 1 for GSM3130726, and smoothing window size 15 kb. Initiation zones present in both datasets were identified using mergePeaks of HOMER tools (Version 4.8.2), with -d given. Origins were defined as the center of initiation zones. For all origins, their nearest TSS was defined using annotatePeaks of HOMER tools, together with the distance between the TSS and the origin. Here, a negative distance represents an origin upstream of the TSS (co-directional transcription relative to replication), while a positive distance represents an origin downstream of a TSS (head-on transcription relative to replication). To allow for clean transcription versus replication analyses, we further selected only origins for which their nearest TSS was not preceded by another gene within 5kb upstream of the TSS. This resulted in a list of 2,040 origins.
A list of 49,948 gene-coordinates was obtained from the UCSC genome database selecting the knownCanonical table containing the canonical transcription start sites per gene (Karolchik et al., 2004). To prevent contamination of binding profiles, genes were selected to be non-overlapping with at least 2 kb between genes and a minimal size of 3 kb (n=9,944). From this, a set of 3,000 actively transcribed genes was selected by calculating gene size-corrected read-densities of BrU-seq data in WT cells, using the AnnotatePeaks.pl tool of HOMER with default settings.
Read-density profiles around origin or TSS/TTS coordinates were defined using the AnnotatePeaks.pl tool of HOMER, using the default normalization to 10 million reads. Individual datasets were subsequently processed into heatmaps or binding profiles using R (Version 4.0.5) and Rstudio (Version 1.1.423) (Team, 2019).
Assembly: hg38
Supplementary files format and content:
DRIPseq_ReadDensityAroundOKseqOrigins_200KbWindow_CFAP20KO_mock_rep*_NoDedup.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from a set of origins
DRIPseq_ReadDensityAroundOKseqOrigins_200KbWindow_CFAP20KO_RNaseH_rep*_NoDedup.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from a set of origins
DRIPseq_ReadDensityAroundOKseqOrigins_200KbWindow_WT_mock_rep*_NoDedup.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from a set of origins
DRIPseq_ReadDensityAroundOKseqOrigins_Hg38_200KbWindow_WT_RNaseH_rep1_NoDedup.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from a set of origins
DRIPseq_ReadDensityAroundTSS_Hg38_200kbWindow_CFAP20KO_mock_rep*.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TSS of ~9944 non-overlapping genes with a minimal size of 3 kb.
DRIPseq_ReadDensityAroundTSS_Hg38_200kbWindow_CFAP20KO_RNAseH_rep*.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TSS of ~9944 non-overlapping genes with a minimal size of 3 kb.
DRIPseq_ReadDensityAroundTSS_Hg38_200kbWindow_WT_mock_rep*.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TSS of ~9944 non-overlapping genes with a minimal size of 3 kb.
DRIPseq_ReadDensityAroundTSS_Hg38_200kbWindow_WT_RNAseH_rep1.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TSS of ~9944 non-overlapping genes with a minimal size of 3 kb.
DRIPseq_ReadDensityAroundTTS_Hg38_200kbWindow_CFAP20KO_mock_rep*.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TTS of ~9944 non-overlapping genes with a minimal size of 3 kb.
DRIPseq_ReadDensityAroundTTS_Hg38_200kbWindow_CFAP20KO_RNAseH_rep*.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TTS of ~9944 non-overlapping genes with a minimal size of 3 kb.
DRIPseq_ReadDensityAroundTTS_Hg38_200kbWindow_WT_mock_rep*.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TTS of ~9944 non-overlapping genes with a minimal size of 3 kb.
DRIPseq_ReadDensityAroundTTS_Hg38_200kbWindow_WT_RNAseH_rep1.txt: tab-delimited text file containing the read-density/10M total reads at the indicated distance from the TTS of ~9944 non-overlapping genes with a minimal size of 3 kb.
OriginCenter_OKseq_Select5kbUpstreamTSSempty.txt: tab-delimited text file containing coordinates of origins identified as described.
TSScoordinates_InclBrUseqInWTmock.txt: tab-delimited text file containing coordinates of 9,944 TSSs including associated BrU-seq signal in WT cells

source_name: RPE1 iCas9 p53/puro-dKO CFAP20-KO

extract_protocol:
After trypsinization, pellets were lysed in TE buffer 0.2% SDS supplemented with 0.04 mg/mL Proteinase K (life technologies, EO0491) at 37°C overnight. Samples were centrifuged and DNA was extracted from the lysates with phenol chloroform isoamyl alcohol (25:24:1, Thermo Fisher, 10103971). The extracted DNA was then precipitated with 1/10 volume 3M Sodium Acetate pH 5.2 and 2.5 volume ethanol. White DNA particles were rescued with a cut 1 mL tip and washed 3 times with 80% ethanol. Dried DNA was restituted by incubation in TE buffer at 4° overnight. For enzyme digestion, samples were incubated with HindIII-HF, EcoRI-HF, BsrGI-HF, SspI-HF and XbaI (NEB, R3104, R3101, R3575, R3132, R0145 respectively) 30 U each in NEB buffer 2.1 with 0.2 mg/mL BSA (NEB, B9000) overnight at 37°C. Digested DNA was then extracted by adding 0.4 volume water and 1 volume phenol chloroform isoamyl alcohol (25:24:1). The aqueous phase after extraction was incubated with 33 μg/mL glycogen (Thermo Scientific, R0561), 1/10 volume 3M Sodium Acetate pH 5.2 and 2.5 volumes ethanol overnight at -20°C to precipitate the DNA. Samples were centrifuged at 16000 g for 35 min at 4ºC and the supernatant was discarded. After air drying, pellets were resuspended in TE buffer for 1 h on ice. For RNaseH1 control, 10 μg of sample was collected in pre-lubricated tubes and treated with 3 μl RNaseH1 (NEB, M0297) and 6 μl RNaseH1 reaction buffer (NEB, B0297) in a total volume of 50 μl in TE buffer overnight at 37°C. 8 μg DNA was dissolved in a total volume of 500 μl TE buffer and from this, 50 μl input sample was collected. For the R-loop immunoprecipitation 10 μl DNA-RNA Hybrid [S9.6] Antibody was added to 8 μg DNA in pre-lubricated tubes in a total volume of 50 μl in 10x binding buffer (100 mM sodium phosphate pH 7, 1.4 M sodium chloride, 0.5% Triton X-100) and incubated overnight at 4°C in a rotating shaker (11rpm). Per sample, 100 μl Dynabeads™ Protein A (Themo Fisher, 10001D) were washed twice with 1x binding buffer (10x binding buffer diluted in TE buffer) for 10 min at RT. The beads were then added to the DNA and incubated at 4°C in a rotating shaker (11rpm) for 2 h. By using a rotator at RT, the beads were washed twice in 1x binding buffer for 15 min. To elute the DNA, the beads were incubated in 300 μl DRIP elution buffer (50 mM Tris pH 8.0, 10 mM EDTA pH 8.0, 0.5% SDS) supplemented with 7 μl Proteinase K at 56°C on a rotator for 45 min. The eluted DNA was then first purified with 1 volume phenol chloroform isoamyl alcohol (25:24:1) followed by a cleanup with 33 μg/mL glycogen, 1/10 volume 3M sodium acetate pH 5.2 and 2.5 volumes ethanol. The aqueous phase was then incubated overnight at -20°C to precipitate the DNA. Samples were centrifuged at 16000 g for 35 min at 4°C and the precipitates were cleaned with 80% ethanol at RT. After air drying, pellets were gently resuspended in 200 μl TE buffer and left on ice for a few hours. The samples were sonicated by using the Bioruptor Pico (Diagenode), 6 cycles of 15s ON/60 s OFF in a 4°C water bath. The final sample was purified using a Qiagen MinElute kit (Quiagen, 28004) and concentrations were measured on the Qubit 2.0 (Invitrogen) with the use of the Qubit 1x dsDNA HS assay kit (Thermo Fisher, Q33230).
Sample libraries were prepared using Hifi Kapa sample prep kit and A-T mediated ligation of Nextflex adapters or xGen UDI-UMI adapters. Samples were sequenced using an Illumina NextSeq500 or HiSeq X, using paired-end sequencing with 42 or 151 bp from each end.

treatment_protocol: Cells were grown to ~80% confluency

value: RPE1 iCas9 p53/puro-dKO CFAP20-KO

value: RNAseH1-treated prior to R-loop pulldown (neg control)

value: DNA-RNA Hybrid [S9.6] Antibody

value: R-loop associated DNA


title: triple negative breast cancer, palbociclib, rep3

description: PAL_134_5 FPKM

value: Palbociclib


title: triple negative breast cancer, palbociclib, rep2

description: PAL_132_4 FPKM


title: DRIPseq, WT, mock, rep2

source_name: RPE1 iCas9 p53/puro-dKO WT

value: RPE1 iCas9 p53/puro-dKO WT

value: Untreated


title: V04

description: Library name: Sample 7

value: nasal mucosa


title: R03

description: Library name: Sample 6

value: PBS+Ribavirin


title: triple negative breast cancer, OPG_Fc rep3

description: OPG_130_5 FPKM

value: breast


title: DRIPseq, CFAP20KO, mock, rep2


title: R02

description: Library name: Sample 5


title: Pseudogymnoascus destructans, Cu-sulfate5

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

description:
Library name: Cu5
Column names in 3.7.23.counttable.csv: Cu5

data_processing:
Sequencing reads trim using fastq_quality_trimmer (-t 30, -l 35); reads filter using fastq_quality_filter (-q30, -p 80); Genome mapping using Tophat2 (2.0.13); Read counting using subread (1.4.6)
Assembly: GCF_001641265.1_ASM164126v1_genomic
Supplementary files format and content: Read count per genome feature (gene); csv format; Each row is a gene, each column is a sample

organism: Pseudogymnoascus destructans

growth_protocol: The Pseudogymnoascus destructans (Pd) strain (MYA4855) was purchased from the American tissue culture collection (ATCC strain number 20631-21) and used for all experiments. The long-term propagation of Pd was carried out using solid Yeast extract-peptone and glucose (YPD) plates at 15ºC and consisted of 10 g/L of yeast extract, 20 g/L of peptone, 20 g/L glucose, and 15 g/L of agar. Metal growth studies were performed using chemically defined growth plates (SC-Ura) which were made using Milli-Q water and 1.8 g/L of yeast nitrogen base, 5g/L ammonium sulfate (NH4SO4), 20 g/L glucose, 100 mg/L histidine, 1.7 g/L of the SC-Ura-His amino acid supplement mixture, and 15 g/L agar

extract_protocol:
Transcriptomic studies were performed on Pd fungi grown for 10 days at 15 ºC on SC-Ura plates alone or supplemented with either copper chelator BCS (800 µM) or CuSO4 (500 µM). Fungal cells, including conidia and mycelium, were suspended in 2 ml of TE buffer by gently rubbing the mycelium mass with a sterile inoculating loop. The resulting cell suspension was transferred to a 2 mL microcentrifuge tube and pelleted for 5 minutes at 16,000 X g. The cells were washed twice with 1 ml of TE buffer. The resulting cell pellet was snap-frozen in dry ice and stored in – 80 C for later use. Total RNA was extracted from Pd cells using TRIZOL reagents using the manufacturer’s recommended procedure (Ref). Briefly, 1 ml of TIRZOL reagent was added to Pd cells along with approximately 100 μL of 0.5 μM zirconium beads (ZB-05; Next. Advanced) and homogenized at 4C in a bullet blender (SpeedXXX for 5 minutes). The resulting cell lysate was incubated on ice for 5 minutes. The cell lysates were then thoroughly mixed with 0.2 ml chloroform and incubated for 2 to 3 minutes before centrifugation at 12,000 X g for 15 minutes. The upper aqueous layer was transferred to a new microcentrifuge tube and 500 μL of isopropanol was added to the tube. After mixing, the solution was incubated on ice for 10 minutes and centrifuged at 12,000 X g at 4 °C. The supernatant was discarded, and 1 ml of 75% ethanol was added, vortex and centrifuged at 7,500 X g for 5 minutes at 4 ºC. The supernatant was discarded, and the white pellet was air-dried for 5–10 minutes. The RNA (pellet) was resuspended in 50 µl of 1X TE buffer and incubated for 15 minutes at 55 °C in a hot water bath. Finally, the concentration of the RNA was determined using nanodrop and analyzed using an Agilent bioanalyzer. Then RNA was stored at -80 ºC. All RNA samples were sent to Innomics, Inc, (Sunnyvale, CA) for the polyA mRNA enrichment, sequencing library construction, indexing and RNA sequencing.
polyA capture

treatment_protocol: Prior to autoclaving 1 pellet (~200 mg) of NaOH was added to the SC-Ura media prior to autoclave sterilization. The addition of sterile Cu-sulfate and Bathocuproine sulfonic acid sodium salt (BCS) was added to the SC-URA growth media using a 125 mM stock solution after autoclave sterilization at a temperature of approximately 50 ºC.

value: Cu-sulfate

tag: batch


title: V05

description: Library name: Sample 8


title: Pseudogymnoascus destructans, Cu-sulfate6

description:
Library name: Cu6
Column names in 3.7.23.counttable.csv: Cu6

source_name: Pseudogymnoascus destructans (Pd) strain (MYA4855)


title: Pseudogymnoascus destructans, Cu-sulfate7

description:
Library name: Cu7
Column names in 3.7.23.counttable.csv: Cu7

value: Pseudogymnoascus destructans (Pd) strain (MYA4855)


title: triple negative breast cancer, palbociclib, rep1

description: PAL_124_1 FPKM

value: epithelial


title: Pseudogymnoascus destructans, Cu-sulfate4

description:
Library name: Cu4
Column names in 3.7.23.counttable.csv: Cu4


title: Pseudogymnoascus destructans, Cu-sulfate8

description:
Library name: Cu8
Column names in 3.7.23.counttable.csv: Cu8


title: R01

description: Library name: Sample 4


title: Pseudogymnoascus destructans, Cu-sulfate3

description:
Library name: Cu3
Column names in 3.7.23.counttable.csv: Cu3


title: Pseudogymnoascus destructans, Cu-sulfate2

description:
Library name: Cu2
Column names in 3.7.23.counttable.csv: Cu2


title: triple negative breast cancer, OPG_Fc rep2

description: OPG_130_4 FPKM


title: V03

description: Library name: Sample 3

value: PBS+Vehicle


title: V02

description: Library name: Sample 2


title: triple negative breast cancer, OPG_Fc rep1

description: OPG_129_3 FPKM


title: Pseudogymnoascus destructans, Cu-sulfate1

description:
Library name: Cu1
Column names in 3.7.23.counttable.csv: Cu1


title: DRIPseq, WT, RNAseH, rep1


title: triple negative breast cancer, untreated, rep2

description: VEH_128_2 FPKM

value: vehicle


title: DRIPseq, CFAP20KO, RNAseH, rep1


title: V01

description: Library name: Sample 1

value: WT


title: Sample_2915_WT

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Base calling and de-multiplexing was performed using CASAVA v1.8.2 and fastQC was used for quality control.
Subsequently, the reads were aligned to the mm10-based mouse Gencode reference transcriptome vM16 and quantified on gene level using star v2.7.1a. (Dobin et al., 2013).
Gene expression quantifications were imported to R 3.5.3 (2019-03-11) and DESeq2 v1.22.2 was used for downstream analyses (Love et al., 2014).
Lowly expressed genes (rowSums > 10) were filtered and variance stabilizing transformation was performed.
Subsequently, principal component analysis was conducted on all present genes using the prcomp function (R/stats 3.5.3).
Differential expression analysis was performed comparing WT and KO samples without pre-defined fold change threshold and using independent hypothesis weighting (IHW, v1.10.1) (Ignatiadis et al., 2016) as the multiple testing procedure.
Genes with an adjusted p-value < 0.05 and a fold change >1.5 were determined as significantly differentially expressed.
Functional enrichment analysis using the MSigDB data base (Liberzon et al., 2015) was performed on the DE gene sets using the R package ClusterProfiler v3.10.1 (Yu et al., 2012)).
Assembly: mm10 gencode vM16
Supplementary files format and content: rawexpression_unfiltered_231213.csv: comma separated file holding unfiltered quantifications of sequencing reads across all genes over all samples
Supplementary files format and content: normalized_expression_filtered_231213.csv: comma separated file holding filtered quantifications of sequencing reads across genes with at least 10 reads quantified over all samples

molecule: polyA RNA

source_name: Spleen and lymph node

extract_protocol:
Total RNA was isolated from splenic CD4+ T naive cells lysed in QIAzol Lysis Reagent (Qiagen) using the miRNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
RNA quality and concentration was measured on the Agilent Tapestation 2200 (Agilent) using RNA screen tapes (Agilent) and further processed for barcoding, multiplexing and cDNA library construction using the TruSeq RNA Sample Preparation Kit v2 (Illumina). For indexing, barcoding indexes of Set A were used. cDNA library was measured in quality and quantity on Agilent Tapestation 2200 (Agilent) using High sensitivity Screen Tape (Agilent) and sequencing (single read, 75 bp) was performed on an Illumina HiSeq 1500 platform using the TruSeq SBS Kit v3 (Illumina) and TruSeq SR Cluster Kit v2 (Illumina) according to the manufacturer’s instruction.

value: Spleen and lymph node

value: naive CD3+CD4+CD25-CD44low/-CD62L+ T cells

value: Satb1fl/fl x CD4-CreERT2wt/+


title: Ewing1_GEX

first: Anthony

middle: Richard

last: Cillo

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

data_processing:
Demultiplexing was performed using bcl2fastq v2.20.0.
Gene expression libraries were aligned to GRCh38 using CellRanger v7.0.1.
Assembly: GRCh38
Supplementary files format and content: Gzipped tar archive file containing tab-delimited barcodes, features, and matrix files.

source_name: tumor

extract_protocol:
Freshly resected Ewing sarcoma tumors were mechanically disrupted/ Single-cell RNAseq was performed using 10X Genomics and libraries were sequenced on an Illumina NovaSeq500 instrument.
The library generation strategy was as per the manufacturer's instructions for 10X Genomics 5' based chemistries.

value: tumor

tag: disease state

value: Ewing sarcoma


title: DRIPseq, WT, mock, rep1

tag: pulldown antibody

value: DNA-RNA Hybrid [S9.6] Antibody

value: R-loop associated DNA


title: triple negative breast cancer, untreated, rep1

description: VEH_123_2 FPKM


title: Pseudogymnoascus destructans, Control6

description:
Library name: C6
Column names in 3.7.23.counttable.csv: C6


title: Pseudogymnoascus destructans, Control5

description:
Library name: C5
Column names in 3.7.23.counttable.csv: C5


title: Sample_2911_WT


title: Pseudogymnoascus destructans, Control7

description:
Library name: C7
Column names in 3.7.23.counttable.csv: C7


title: DRIPseq, CFAP20KO, mock, rep1

value: RPE1 iCas9 p53/puro-dKO CFAP20-KO

value: Untreated

tag: type of_material


title: Sample_2913_WT

tag: tissue


title: PA14 ptsP and ptsN deleted cells, SCFM-2, biol rep 4

city: Stillwater

first: Matthew

last: Cabeen

state: Oklahoma

address: 307 Life Science East

department: Microbiology and Molecular Genetics

institute: Oklahoma State University

description: Library name: V4_S107

data_processing:
Sequence reads were processed and trimmed using FastQC and Cutadapt
Sequence reads were aligned to genome using Bowtie 2.
Differential gene expression analysis was processed using EdgeR.
All software was set using default parameters.
Assembly: NC_008463
Supplementary files format and content: Excel file includes gene list with log2 fold changes, P values, false discovery rate (FDR) P-values, log2 of read counts per million (CPM), and F-statistic.

organism: Pseudomonas aeruginosa

source_name: whole cells

growth_protocol: P. aeruginosa strains as noted were grown overnight in LB, washed 2X with PBS, then inoculated 1:1000 into liquid SCFM2 and grown at 37°C with shaking to an OD600 of 0.3 before extraction

extract_protocol:
Total RNA was extracted using the NEB Monarch total RNA extraction kit according to the manufacturer's protocol for gram-negative bacteria. Ribosomal RNA was removed using the Ribo-Zero kit.
Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero plus kit was used according to the manufacturer's protocol

value: whole cells

tag: genotype

value: DptsP DptsN


title: Sample_2914_WT


title: PA14 ptsP and ptsN deleted cells, SCFM-2, biol rep 5

description: Library name: V5_S108


title: PA14 ptsP and ptsN deleted cells, SCFM-2, biol rep 3

description: Library name: V3_S106