title: LoVo METTL3 K513R 3

city: Wuhan

first: Haijie

last: Li

address: no.1095 Jiefang Avenue

department: Tongji Hospital

institute: Huazhong University of Science and Technology

description:
Library name: Sample18
K513R_3
All_reads_counts.txt

data_processing:
[MeRIP-Seq]  Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
[MeRIP-Seq]  Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster.
[MeRIP-Seq]  After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters.
[MeRIP-Seq]  After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated
[MeRIP-Seq]   The exomePeak（Version 3.8）software was used for peak calling. The m6A peaks were annotated using bedtools（Version 2.25.0）. The deepTools（version 2.4.1）was used for peak distribution analysis. The differentially m6A peaks were identified by a python script，using fisher test.
Assembly: [MeRIP-Seq]  GRCh38_release110
Supplementary files format and content: [MeRIP-Seq]  tab-delimited text file includes raw counts for each Sample
[RNA-Seq]  Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
[RNA-Seq]  Clean Reads were mapped to the reference genome of Homo sapiens (Homo_sapiens.GRCh38;ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/） using STRA software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
[RNA-Seq]  Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
[RNA-Seq]  Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a p-value cutoff of 0.05 to judge statistically significant enrichment.
[RNA-Seq]   Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Assembly: [RNA-Seq]  GRCh38_release110
Supplementary files format and content: [RNA-Seq]  tab-delimited text file includes raw counts for each Sample

source_name: LoVo

extract_protocol:
[MeRIP-Seq]  50 μg total RNAs were used for polyadenylated RNA enrichment by VAHTS mRNA Capture Beads. 20mM ZnCl2 was added to mRNA and incubated at 95℃ for 5min-10min until the RNA fragments were mainly distributed in 100-200 nt. Then 10% RNA fragments was saved as Input and the rest was used for m6A immunoprecipitation（IP）.The specific anti-m6A antibody (Synaptic Systems, 202203) was applied for m6A immunoprecipitation. RNA samples of both input and IP were prepared using TRIzol reagent.
[MeRIP-Seq]   The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina(Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer's instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.
[RNA-Seq]  2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Catalog NO. MRZG12324, Illumina)
[RNA-Seq]   Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

value: LoVo

tag: cell type

value: colorectal cancer cells

value: METTL3 K513R


title: 50-ko-alpha3

status: Public on Dec 01 2025

type: SRA

city: Rehovot

first: Mike

last: Fainzilber

address: Dept. of Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

description:
counts.txt
norm_counts.txt

library_source: transcriptomic

data_processing:
fastq files were generated by the usage bcl2fastq-v2.17.1.14 (basecalling)
Reads were trimmed using cutadapt
Reads were aligned to the mouse genome build mm10 using, Tophat (v2.0.10).
Counting reads on Refseq realese mm10  genes, was done with HTSeq-count (version 0.6.1p1)
Differential analysis was carried out using DESeq2 (1.6.3)
Genome_build: mm10
Supplementary_files_format_and_content: txt file includes the raw counts, genereted by HTSeq-count
Supplementary_files_format_and_content: txt file includes the normalized counts (DESeq2 Normalization)

molecule: total RNA

organism: Mus musculus

source_name: embryonic DRG tissue

extract_protocol:
isolation of lumbar DRG tissue from E13.5 embryos
Inhouse polyA based RNA seq

tag: developmental stage

value: Embryo 13.5

tag: strain

tag: genotype

tag: tissue

value: embryonic DRG tissue


title: PBS-treated 4T1 cells replicate 1

city: xiamen

first: Zhiyuan

last: Chen

address: Xiamen, Fujian Province, China, 361000

country: China

institute: Xiamen University

description: Library name: T1-1

data_processing:
Clean reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR.
Clean reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR.
Gene-level read counts were generated using featureCounts.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited gene expression matrix containing gene symbols and TPM values for each sample

extract_protocol:
Total RNA was extracted using TRIzol reagent. RNA integrity was confirmed using an Agilent 2100 Bioanalyzer.
Sequencing libraries were prepared following the standard BGI mRNA library prep protocol, which includes mRNA enrichment, fragmentation, cDNA synthesis, adapter ligation, and PCR amplification.

treatment_protocol: Cells were treated with either: 1. Experimental group: CM-PEG-PLGA@DOX/R848 nanoparticles at a dose equivalent to 2μg/mL DOX. 2. Control group: Phosphate Buffered Saline (PBS). Treatment duration was 24 hours.

tag: cell line

tag: treatment

value: PBS


title: LoVo METTL3 K513R 2

description:
Library name: Sample17
K513R_2
All_reads_counts.txt

organism: Homo sapiens


title: PBS-treated 4T1 cells replicate 3

description: Library name: T1-3


title: 42-ko-alpha3

description:
counts.txt
norm_counts.txt


title: acRIP-seq of WT lin- IP, rep2

city: GuangZhou,GuangDong Province

first: Feng

last: Huang

state: China

institute: Guangzhou Laboratory

description:
Library name: sample4
acRIP-seq WT lin- IP, rep2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by cutadapt with parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q 20,20 --max-n 0.25 --trim-n.
The clean reads were then mapped to the mouse genome (mm39) with HISAT2 with “--rna-strandness RF” parameters, and supplying the GENCODE Release VM30 gene annotation. A post-alignment filter was preformed to remove alignments to ribosomal RNA (rRNA), secondary alignment and non-concordant mate pairs.
Ac4C peaks on each transcripts of gene were called using homemade Perl scripts according to the strand, separated by “-f 83 (and 163)” or “-f 99 (and 147) with SAMtools.
Peaks were identified as regions concentrated with significantly more normalized reads (fold change > 1.5 and adjusted P-value < 0.05) in IP than their corresponding input samples.
Assembly: mm39
Supplementary files format and content: bigwig files were generated by deepTools. BedWig files can be uploaded to UCSC Genome Browser for visualization.

source_name: Bone marrow

extract_protocol:
Total RNA was isolated using the TRIzol reagent.
After acRIP, input samples and IP products were used to construct NGS libraries using Smarter® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian following manufacturer’s protocol.

treatment_protocol: For Lin- cell isolation, bone marrow cells were incubated with biotin-labeled lineage antibody cocktail and enriched using the Lineage Cell Depletion Kit (Miltenyi, Cat# 130-090-858) according to manufacturer’s instruction. After washing, cells were stained with the antibodies and sorted in BD FACSAria Fusion.

value: Bone marrow

value: Bone marrow cells

value: WT lin-

value: IP


title: 75-ko-alpha3

description:
counts.txt
norm_counts.txt


title: LoVo METTL3 K513R 1

description:
Library name: Sample16
K513R_1
All_reads_counts.txt


title: Vulva_S14

type: RNA

city: Leiden

first: Roderick

last: Slieker

address: PO Box 9600

department: Medical Oncology

country: Netherlands

institute: Leiden University Medical Center

description: 1K plex

hyb_protocol: not provided

scan_protocol: CosMx SMI

data_processing:
AtoMx
Counts

source_name: Vulva

label_protocol: not provided

extract_protocol: not provided

tag: timepoint

value: Pre

tag: group

value: NR


title: acRIP-seq of WT lin- IP, rep1

description:
Library name: sample3
acRIP-seq WT lin- IP, rep1


title: acRIP-seq of WT lin- Input, rep2

description:
Library name: sample2
acRIP-seq WT lin- Input, rep2

value: Input


title: LoVo METTL3 WT 3

description:
Library name: Sample15
WT_3
All_reads_counts.txt

value: METTL3 WT


title: acRIP-seq of WT lin- Input, rep1

description:
Library name: sample1
acRIP-seq WT lin- Input, rep1


title: Vulva_S9

description: 1K plex

value: PR


title: Vulva_S10

description: 1K plex

value: CR


title: LoVo METTL3 WT 2

description:
Library name: Sample14
WT_2
All_reads_counts.txt


title: LoVo METTL3 WT 1

description:
Library name: Sample13
WT_1
All_reads_counts.txt


title: Vulva_S8

description: 1K plex


title: BM, rep3

description:
Library name: sample33
Mouse BM total RNA

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by by cutadapt with parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q 20,20 --max-n 0.25 --trim-n.
The clean reads were then mapped to the mouse genome (mm39) with HISAT2  with default parameters, and supplying the GENCODE Release VM30 gene annotation. A post-alignment filter was preformed to remove alignments to ribosomal RNA (rRNA), secondary alignment and non-concordant mate pairs.
Read counts on genes were calculated by HTSeq against the GENCODE Release VM30 gene annotation. Differentially expressed genes were calculated by DESeq2 with fold change > 1.5 and adjusted P-value < 0.05.
Assembly: mm39
Supplementary files format and content: Raw read count of genes calculated by HTSeq.

molecule: polyA RNA

extract_protocol:
Total RNA was isolated using the TRIzol reagent.
Libraries for RNA-seq were constructed using TruePrep® DNA Library Prep Kit V2 for Illumina following manufacturer’s protocol.

treatment_protocol: For stem/progenitor cell isolation, bone marrow cells were incubated with biotin-labeled lineage antibody cocktail and enriched using the Lineage Cell Depletion Kit (Miltenyi, Cat# 130-090-858) according to manufacturer’s instruction. After washing, cells were stained with the antibodies, and sorted in BD FACSAria Fusion. For mature cells, cells were stained with the antibodies, and sorted in BD FACSAria Fusion.

value: BM


title: BM, rep2

description:
Library name: sample32
Mouse BM total RNA


title: LoVo METTL3 K513R_3_IP

description:
Library name: Sample12
K513R_3_IP
all_peaks.txt

value: LoVo


title: Vulva_S6

description: 1K plex


title: Vulva_S7

description: 1K plex


title: BM, rep1

description:
Library name: sample31
Mouse BM total RNA


title: Vulva_S15

description: 1K plex


title: untreated macrophage THP1, replicate 4

city: Belfast

first: Shania

middle: M

last: Corry

address: Queen's University

country: United Kingdom

institute: Patrick G Johnston Centre for Cancer Research

description: Gene expression data from untreated macrophage THP-1 cells

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The amplified product was hybridized to the Almac Diagnostics cDNA microarray-based XCEL array (Almac) and analysed using the Affymetrix Genechip 3000 7G scanner (Affymetrix). Microarray raw CEL files which were processed, and RMA normalized using the affy (1.68.0) (RRID:SCR_012835) and affyio (1.60.0) (RRID:SCR_024223) packages. The probes were collapsed to gene-level data using “MaxMean” within the WGCNA (1.7.1) (RRID:SCR_003302) package.

label: Biotin

source_name: Untreated macrophage THP-1 cells

label_protocol: standard Affymetrix protocol

growth_protocol: HCT116 cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, 50 U/mL penicillin, 0.1 mg/mL streptomycin, 2 mM l-glutamine, and 1 mM sodium pyruvate (all Gibco). THP-1 cells were obtained from American Type Culture Collection (ATCC, Manassas, VA, USA) and cultured in RPMI medium (Invitrogen, Paisley, UK) with 10% heat-inactivated FBS, 50 U/mL penicillin, 0.1 mg/mL streptomycin and 0.05 mM β- mercaptoethanol (Sigma). All cells were maintained at 37 °C in a 5% CO2 humidified atmosphere and regularly screened for the presence of mycoplasma using the MycoAlert Mycoplasma Detection Kit (Lonza). Cell lines were cultured for no more than 20 passages following thawing. THP-1 cells were differentiated to M0 macrophages by 48 h treatment with 200 nM Phorbol 12-myristate 13-acetate (Sigma-Aldrich) in complete RPMI media.

extract_protocol: After removing the media, cold PBS was added to the plates and the cells were scraped from the plate. Cell suspensions were then centrifuged, and the cell pellets were re-suspended in ice-cold PBS. Total RNA was extracted from HCT116 and THP-1 cell lines using the Roche High Pure  Extraction Kit (Roche Life Sciences) and amplified using the NuGen Ovation FFPE Amplification System v3 (NuGen San Carlos). The amplified product was hybridized to the Almac Diagnostics cDNA microarray-based XCEL array (Almac) and analysed using the Affymetrix Genechip 3000 7G scanner (Affymetrix).

treatment_protocol: After removing the media, THP-1-derived macrophages were incubated with poly(I:C) in serum-free RPMI media. Poly(I:C) treatments of HCT116 cells were also performed in DMEM serum-free media. Poly(I:C) treatment was 5ug/ml.

value: none; untreated


title: untreated macrophage THP1, replicate 3


title: LoVo METTL3 K513R_3

description:
Library name: Sample11
K513R_3
all_peaks.txt

value: colorectal cancer cells

value: METTL3 K513R


title: CD11b+ cells, rep3

description:
Library name: sample30
Mouse BM CD11b+ total RNA

value: CD11b+ cells


title: LoVo METTL3 K513R_2_IP

description:
Library name: Sample10
K513R_2_IP
all_peaks.txt


title: untreated macrophage THP1, replicate 1


title: LoVo METTL3 K513R_2

description:
Library name: Sample9
K513R_2
all_peaks.txt


title: Vulva_S1

description: 1K plex


title: CD11b+ cells, rep2

description:
Library name: sample29
Mouse BM CD11b+ total RNA


title: LoVo METTL3 K513R_1_IP

description:
Library name: Sample8
K513R_1_IP
all_peaks.txt


title: untreated macrophage THP1, replicate 2


title: Vulva_S4

description: 1K plex


title: Vulva_S3

description: 1K plex


title: CD11b+ cells, rep1

description:
Library name: sample28
Mouse BM CD11b+ total RNA


title: B220+ cells, rep3

description:
Library name: sample27
Mouse BM B220+ total RNA

value: B220+ cells


title: Vulva_S5

description: 1K plex


title: treated macrophage THP1, replicate 4

description: Gene expression data from Poly(I:C) treated macrophage THP-1 cells, 24 hours after treatment

value: Poly(I:C) treated

tag: time point

value: 24 hours after treatment


title: treated macrophage THP1, replicate 2

source_name: Poly(I:C) treated macrophage THP-1 cells, 24 hours after treatment


title: treated macrophage THP1, replicate 3


title: LoVo METTL3 WT_3_IP

description:
Library name: Sample6
WT_3_IP
all_peaks.txt


title: LoVo METTL3 WT_3

description:
Library name: Sample5
WT_3
all_peaks.txt


title: Vulva_S2

description: 1K plex


title: treated macrophage THP1, replicate 1


title: untreated epithelial HCT116, replicate 3

description: Gene expression data from untreated epithelial HCT116 cells

source_name: Untreated epithelial HCT116 cells


title: B220+ cells, rep1

description:
Library name: sample25
Mouse BM B220+ total RNA

value: Bone marrow


title: untreated epithelial HCT116, replicate 4


title: HF/FS diet for 10 weeks, and then switched to an HF/FS diet supplemented with AncestryR for an additional 8 weeks, rep3

type: genomic

city: Zapopan

first: Rebeca

last: Rosas Campos

state: Jalisco

address: Av. Gral Ramón Corona No 2514

department: EMCS

country: Mexico

institute: Tecnologico de Monterrey

hyb_protocol: Infinium Mouse Methylation BeadChip (Illumina, Inc. San Diego, CA, USA) following the manufacturer’s recommended procedures

scan_protocol: Standart Illumina Protocol

data_processing:
Sensible Stepwise Analysis of DNA Methylation BeadChips (SeSAMe) in R (v4.2.2)
processed value definition: β-value

label: Cy3 and Cy5

molecule: genomic DNA

source_name: liver

label_protocol: Standart Illumina Protocol

extract_protocol: Total DNA was extracted from the liver tissue using the QIAamp DNA Micro Kit (Qiagen, Hilden, Germany).

value: liver

value: Ancestry


title: LoVo METTL3 WT_2_IP

description:
Library name: Sample4
WT_2_IP
all_peaks.txt


title: LoVo METTL3 K513R_1

description:
Library name: Sample7
K513R_1
all_peaks.txt


title: CD3e T cells, rep3

description:
Library name: sample24
Mouse BM CD3e T cells total RNA

value: CD3e T cells


title: HF/FS diet for 10 weeks, and then switched to an HF/FS diet supplemented with AncestryR for an additional 8 weeks, rep2


title: CD3e T cells, rep2

description:
Library name: sample23
Mouse BM CD3e T cells total RNA


title: LoVo METTL3 WT_2

description:
Library name: Sample3
WT_2
all_peaks.txt


title: HF/FS diet for 10 weeks, and then switched to an HF/FS diet supplemented with AncestryR for an additional 8 weeks, rep1


title: untreated epithelial HCT116, replicate 1


title: B220+ cells, rep2

description:
Library name: sample26
Mouse BM B220+ total RNA


title: HF/FS group consuming a Western diet (high in fat and fructose/sucrose), rep3

value: HF/FS


title: CD3e T cells, rep1

description:
Library name: sample22
Mouse BM CD3e T cells total RNA


title: LoVo METTL3 WT_1

description:
Library name: Sample1
WT_1
all_peaks.txt

value: METTL3 WT


title: CLP, rep3

description:
Library name: sample21
Mouse BM CLP total RNA

value: CLP


title: HF/FS group consuming a Western diet (high in fat and fructose/sucrose), rep2


title: treated epithelial HCT116, replicate 4

description: Gene expression data from Poly(I:C) treated epithelial HCT116 cells, 24 hours after treatment


title: CLP, rep2

description:
Library name: sample20
Mouse BM CLP total RNA


title: Astrocytes Donor A32 DDX OE mScarlet R5

city: San Diego

first: Christopher

middle: L

last: Hartl

address: Pacific Heights Blvd

department: Cell Biology

country: USA

institute: Epigenome Technologies

description: Library name: 31139-010

data_processing:
(RNA) All primary analysis was carried out using CLC Genomics Server 22.0.2. Raw reads were first trimmed to remove potential read-through adapter sequences at the 3’end. Further, reads were trimmed based on quality scores and ambiguous nucleotides, e.g. due to stretches of Ns. A maximum of 2 ambiguous nucleotides were allowed in a read. The trimmed reads were mapped to Human ribosomal RNA (rRNA) repetitive unit to get an overview or rRNA content in the samples. However, all reads were mapped to the Human genome GRCh38 with ENSEMBL GRCh38 version 98 annotation.  The ‘Empirical analysis of DGE’ algorithm of the CLC Genomics Workbench 22.0.2 was used for differential expression analysis with default settings. It is an implementation of the ‘Exact Test’ for two-group comparisons developed by Robinson and Smyth, 2008 and incorporated in the EdgeR Bioconductor package Robinson et al., 2010.  For all unsupervised analysis, only genes were considered with at least 10 counts summed over all samples. A variance stabilizing transformation was performed on the raw count matrix using the function vst of the R package DESeq2 version 1.28.1. All genes were used for the principal component analysis. The variance values used was calculated agnostically to the pre-defined groups (blind=TRUE). The 35 genes with the highest variance across samples were selected for hierarchical clustering.
Assembly: GRCh38
Supplementary files format and content: Raw and normalized counts, csv

source_name: brain

growth_protocol: Primary human astrocytes were grown on poly-D-lysine coated flasks and maintained in DMEM/F-12 supplemented with 10% FBS, 1% penicillin-streptomycin at 37 degrees in a humidified 5% CO2 incubator. Media was changed every 2-3 days. Cells were passaged with accutase  at ~80% confluence and used between passages 2-4. For RNA-seq experiments, astrocytes were plated at 2 million cells per T25 flask and transduced at ~60-70% confluence.

extract_protocol:
(RNA) Total RNA was extracted from human astrocytes using the Qiagen RNeasy kit, following the manufacturer's protocol. Cells were lysed, and RNA was isolated via column-based purification, including on-column DNase treatment to remove genomic DNA contaminants.
(RNA) The library preparation was done using the QIAseq Stranded mRNA Kit (QIAGEN). From 1000 ng starting material, the mRNA was enriched. The RNA was heat fragmented. After first and second strand synthesis, the cDNA was end-repaired and 3’ adenylated. Sequencing adapters were ligated to the overhangs. Adapted molecules were enriched using by 11 cycles or PCR and purified by a bead based cleanup. ). Library preparation was quality controlled using capillary electrophoresis (Tape D1000).High quality libraries are pooled based in equimolar concentrations.

treatment_protocol: Astrocytes were transduced with lentiviral vectors expressing DDX5-mScarlet or control mScarlet lentiviruses. Viruses was added in complete medium at an MOI of 10. After 16-24 h, the medium was replaced with fresh growth medium. Cells were harvested for RNA extraction 48 hr post-transduction. Independent biological replicates (5 per condition) were processed separately.

value: brain

value: astrocyte

value: DDX5 Overexpression

tag: batch

value: QG-TRNA


title: HF/FS group consuming a Western diet (high in fat and fructose/sucrose), rep1


title: treated epithelial HCT116, replicate 3

source_name: Poly(I:C) treated epithelial HCT116 cells, 24 hours after treatment


title: Control group on a normal diet, rep3

value: ND


title: CLP, rep1

description:
Library name: sample19
Mouse BM CLP total RNA


title: LoVo METTL3 WT_1_IP

description:
Library name: Sample2
WT_1_IP
all_peaks.txt

value: LoVo

value: colorectal cancer cells


title: SW620 RepSox Rep2

city: Zwijnaarde

first: Jordy

last: De Coninck

address: Technologiepark 71

department: Department of Biomedical Molecular Biology

country: Belgium

institute: University Gent

description: Library name: SW620_RX_2

data_processing:
Quality control was performed on raw FASTQ files using FastQC (v0.11.9)
High-quality reads were then mapped to the GRCh38 reference genome using Hisat2 (v2.2.0)
FeatureCounts (v2.0.0) was employed to count the mapped reads, using the corresponding GTF annotation file (NCBI:GCA_000001405.28).
DESeq2 (v1.34.0) was utilized to normalize the read counts and to identify differentially expressed genes (DEGs).
Assembly: GRCh38.p13
Supplementary files format and content: Tab separated count matrix

extract_protocol:
RNA was extracted using RNeasy Kit (Qiagen, #74004), treated with DNase (Qiagen, #79254) and stored at -80ºC.
Samples were sequenced at BGI (Shenzhen, Guangdong, China). mRNA fragments were purified, used for cDNA library preparation, and analyzed through the BGISEQ-500 platform (RRID:SCR_017979).

treatment_protocol: HT-29iZEB1 and SW620 cells were seeded at 600,000 cells per well in a 6-well plate. HT-29iZEB1 were co-incubated with Repsox 10µM and Doxycyclin (1µg/ml) for 24hr. SW620 cells were incubated with Repsox 10µM for 24hr.

value: epithelial

tag: condition

value: RepSox


title: SW620 RepSox Rep1

description: Library name: SW620_RX_1


title: MEP, rep3

description:
Library name: sample18
Mouse BM MEP total RNA

value: MEP


title: Control group on a normal diet, rep2


title: Astrocytes Donor A32 DDX OE mScarlet R3

description: Library name: 31139-008


title: untreated epithelial HCT116, replicate 2

value: none; untreated


title: Astrocytes Donor A32 DDX OE mScarlet R4

description: Library name: 31139-009


title: treated epithelial HCT116, replicate 1

value: Poly(I:C) treated

value: 24 hours after treatment


title: treated epithelial HCT116, replicate 2


title: MEP, rep2

description:
Library name: sample17
Mouse BM MEP total RNA

value: Bone marrow


title: SW620 RepSox Rep3

description: Library name: SW620_RX_3


title: SW620 DMSO Rep3

description: Library name: SW620_DM_3

value: DMSO


title: Astrocytes Donor A32 DDX OE mScarlet R2

description: Library name: 31139-007


title: Control group on a normal diet, rep1

value: liver


title: MEP, rep1

description:
Library name: sample16
Mouse BM MEP total RNA


title: SW620 DMSO Rep1

description: Library name: SW620_DM_1


title: adult brain, ZT18, tim>RpL3-3xFLAG input, replicate 4

city: Ann Arbor

first: Swathi

last: Yadlapalli

address: 109 Zina Pitcher Pl

institute: University of Michigan

description: Library name: ZT18_INPUT_REP4

data_processing:
We used the Illumina DRAGEN RNA pipeline for automated data analysis.
To obtain RPM-normalized coverage track, we performed the following: 1) number of uniquely mapped reads for each sample was counted by "samtools view -c -F 0x904", 2) genome coverage bedGraph was constructed by "bedtools genomecov -split -bg -scale <scaling_factor>" where scaling_factor is 1E6/(#uniquely mapped reads), 3) bedGraph was converted into bigWig by "bedGraphToBigWig".
Assembly: dm6
Supplementary files format and content: table of gene expression quantification (Salmon, Illumina RNA Pipeline)
Supplementary files format and content: bigWig of RPM-normalized genome coverage

organism: Drosophila melanogaster

source_name: adult brain

growth_protocol: Flies were raised on standard cornmeal/yeast media and maintained at room temperature (20 to 22 °C) under a 12h:12h LD schedule. The following flies used in the study: tim-GAL4, UAS-RpL3-3XFLAG. UAS-RpL3-3XFLAG was developed in Vaziri et al. Sci Adv 2020.

extract_protocol:
Each sample utilized 75 adult female and 75 adult male flies. Fly heads were isolated from bodies using flash freezing followed by vortexing. Immediately after collection, the head tissue was frozen on dry ice and stored at -80C until all samples are ready for processing in one batch. The frozen tissue was homogenized in 300 µl of lysis solution (10 mM HEPES pH 7.4, 150 mM KCl, 5 mM MgCl2, 100 µg/ml Cycloheximide), supplemented with 0.5% Triton-X100, 1U/µl ANTI-RNase (ThermoFisher Scientific, AM2690), and EDTA-free protease inhibitor (Sigma, COEDTAF-RO). A 20 µl aliquot of the resulting lysate was saved as the INPUT sample. The remaining lysate was used for co-immunoprecipitation with anti-FLAG magnetic beads following protocol described in Vaziri et al. Sci Adv 2020, yielding the FLAG sample. Each sample was subjected to total RNA extraction employing TRIzol LS Reagent (ThermoFisher Scientific, 10296010) followed by column-based purification (Zymo, R2050) with on-column DNase treatment. Purified RNA was quantified by Nanodrop and Qubit RNA and saved at -80C until library construction.
For each sample, 10ng (INPUT) or 100ng (FLAG) of purified total RNA was used for library construction using the NEBNext Low-Input cDNA Synthesis Module (New England Biolabs). cDNA library was subject to quality control by Tapestation (HSD5000) and Qubit (High Sensitivity DNA) for mean size of ~1500bp. Next, cDNA library was tagmented to prepare Illumina sequencing library (Illumina Nextera XT, UDI indexing). Quality control was performed with Qubit (High Sensitivity DNA) and Tapestation (HSD1000) for mean size of ~300bp. Samples were loaded in equal molar with 3% spike-in PhiX DNA and sequenced on an Illumina NextSeq 1000 platform with paired-end 100bp cycle.

treatment_protocol: Flies were entrained to Light-Dark (LD) cycles where they were exposed to 12-hour Light-Dark (LD) cycles for 5 days before sample collection. The initiation of the light phase is labeled as Zeitgeber Time (ZT) 0, while ZT12 signifies the beginning of the dark period. Flies of genotype tim-GAL4>UAS-RpL3-3XFLAG was expanded and entrained before sample collection.

value: adult brain

value: clock cells timGAL4

value: timGAL4 x UAS-RpL3-3XFLAG

value: constant condition second day (CT)


title: GMP, rep3

description:
Library name: sample15
Mouse BM GMP total RNA

value: GMP


title: adult brain, ZT18, tim>RpL3-3xFLAG co-IP, replicate 4

description: Library name: ZT18_FLAG_REP4


title: Astrocytes Donor A32 mScarlet R5

description: Library name: 31139-005

value: brain

value: astrocyte

value: QG-TRNA


title: BAP40-26

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

description:
Library name: Sample 1
BAP40-26_Read_Count

data_processing:
Reads were annotated and mapped to the human genome assembly GRCh38.p12 using Bowtie2
Differential expression (q<0.05) was determined in DESeq2  compared to vehicle control.
Assembly: GRCh38.p12
Supplementary files format and content: Processed data files are normalized read counts with corresponding Entrez Gene ID after DESeq2 analysis

source_name: primary bronchial epithelial cells differentiated at air-liquid interface

growth_protocol: Primary HBEC (Lonza) were expanded and transferred to transwell inserts for differentiation at the air-liquid interface in 24-well plates each containing 500 uL of assay medium utilizing the PnuemaCult™ ALI medium kit (STEMCELL Technologies, Vancouver, CA).   Cells were cultured at 37C, 5% CO2 with media changes every 48 to 72 hours.  On day 10, 10 ug/mL interleukin-13 was added to media for cells to induce an asthmatic phenotype.  IL-13 was included in every media change after day 10 for cells to induce an asthmatic phenotype.

extract_protocol:
Total RNA was isolated from HBEC (n=4) using Trizol (Thermo Fisher Scientific) and was quantified on a Synergy HTX plate reader equipped with a Take3 module (BioTek).  RNA quality was evaluated based on 260/280 ratio (acceptable range 2.0-2.1) and by examining 18S and 28S peaks (Bioanalyzer 2100, Agilent, Santa Clara, CA). Acceptable RNA quality was based on RIN ≥ 8.0.
mRNA was poly-A selected, and libraries were prepared as previously described (Dasgupta et al., 2022.

treatment_protocol: On day 25, inserts were washed with DPBS (pH 7.0 -- 7.3) and then exposed on the apical surface for 48 hours to either 25 uL 1% dimethyl sulfoxide (DMSO) with a DPBS vehicle or BAP (1 – 40 ug/mL) in DMSO with a DPBS vehicle.


title: Astrocytes Donor A32 DDX OE mScarlet R1

description: Library name: 31139-006

value: DDX5 Overexpression


title: HT-29 iZEB1 pDOX RepSox Rep3

description: Library name: HT_pl_dox_R_3

value: epithelial

value: pDOX

value: RepSox


title: GMP, rep2

description:
Library name: sample14
Mouse BM GMP total RNA


title: adult brain, ZT18, tim>RpL3-3xFLAG input, replicate 3

description: Library name: ZT18_INPUT_REP3


title: SW620 DMSO Rep2

description: Library name: SW620_DM_2


title: HT-29 iZEB1 pDOX RepSox Rep2

description: Library name: HT_pl_dox_R_2


title: adult brain, ZT18, tim>RpL3-3xFLAG co-IP, replicate 3

description: Library name: ZT18_FLAG_REP3


title: Astrocytes Donor A32 mScarlet R3

description: Library name: 31139-003


title: HT-29 iZEB1 pDOX RepSox Rep1

description: Library name: HT_pl_dox_R_1


title: HT-29 iZEB1 pDOX DMSO Rep3

description: Library name: HT_pl_dox_D_3


title: CMP, rep3

description:
Library name: sample12
Mouse BM CMP total RNA

value: CMP


title: Astrocytes Donor A32 mScarlet R2

description: Library name: 31139-002


title: GMP, rep1

description:
Library name: sample13
Mouse BM GMP total RNA


title: CMP, rep2

description:
Library name: sample11
Mouse BM CMP total RNA


title: adult brain, ZT18, tim>RpL3-3xFLAG co-IP, replicate 2

description: Library name: ZT18_FLAG_REP2


title: HT-29 iZEB1 pDOX DMSO Rep1

description: Library name: HT_pl_dox_D_1


title: CMP, rep1

description:
Library name: sample10
Mouse BM CMP total RNA


title: Astrocytes Donor A32 mScarlet R1

description: Library name: 31139-001


title: adult brain, ZT18, tim>RpL3-3xFLAG co-IP, replicate 1

description: Library name: ZT18_FLAG_REP1


title: HT-29 iZEB1 pDOX DMSO Rep2

description: Library name: HT_pl_dox_D_2


title: adult brain, ZT18, tim>RpL3-3xFLAG input, replicate 1

description: Library name: ZT18_INPUT_REP1


title: control-sEVs 05

city: guangzhou

first: bifang

last: mai

address: yanjiang Road107

institute: sun yat sen memorial hospital

description:
Library name: SRL
colunm name in Expression_miRNA.txt:SRL

data_processing:
FastQC 0.11.7 was used for quality control to filter the raw reads into clean reads.  Cutadapt 1.14 was then used to remove adapters, retain tags with a length of ≥17 nt (trimmed reads). The miRDeep2 0.0.8 software was used to quantify known miRNAs and predict novel miRNAs based on all trimmed reads.
Assembly: For miRNA data standardized by CPM, the R package edgeR 3.18.1 was used for identifying differentially expressed miRNAs and generating clustering heatmap. The target genes of the top 20 differentially expressed miRNAs were analyzed using data from miRNA target gene databases (TargetScan), followed by GO and Pathway analysis of the target genes.
Supplementary files format and content: Expression_miRNA.txt FOR each sample
Supplementary files format and content: Expression_miRNA.txt FOR each sample

source_name: plasma

extract_protocol:
miRNA from ICM-sEVs were extracted using QIAzol from miRNeasy Micro kit (Qiagen, 217084) according to manufacturers’ instruction. miRCURY LNA RT kits (Qiagen,339340) were used for reverse transcription of miR-223-3p (miR-223-3p primer,GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACTGGGGT; UniSp6 primer: AACGCTTCACGAATTTGCGT). miRNA-223 was detected using miRCURY Probe PCR kit and miRCURY LNA miRNA Probe PCR Assays (Qiagen, 339371,339350) via qRT-PCR (Roche, LightCycler 96).
The extracted total RNA samples from ICM-EVs were quality-checked and quantified using agarose gel electrophoresis and Nanodrop. After constructing the library, its quality was assessed using the Agilent 2100 Bioanalyzer. Sequencing was then performed on the Illumina NextSeq 500 sequencer for 50 cycles following the supplier's instructions.

value: plasma


title: adult brain, ZT12, tim>RpL3-3xFLAG input, replicate 4

description: Library name: ZT12_INPUT_REP4


title: control-sEVs 04

description:
Library name: LRJ
colunm name in Expression_miRNA.txt:LRJ


title: MPP, rep2

description:
Library name: sample8
Mouse BM MPP total RNA

value: Bone marrow

value: MPP


title: HT-29 iZEB1 mDOX RepSox Rep2

description: Library name: HT_no_dox_R_2

value: mDOX


title: MPP, rep3

description:
Library name: sample9
Mouse BM MPP total RNA


title: HT-29 iZEB1 mDOX RepSox Rep3

description: Library name: HT_no_dox_R_3


title: MPP, rep1

description:
Library name: sample7
Mouse BM MPP total RNA


title: Astrocytes Donor A32 mScarlet R4

description: Library name: 31139-004


title: adult brain, ZT12, tim>RpL3-3xFLAG co-IP, replicate 4

description: Library name: ZT12_FLAG_REP4

value: adult brain


title: control-sEVs 03

description:
Library name: LX
colunm name in Expression_miRNA.txt:LX


title: HT-29 iZEB1 mDOX RepSox Rep1

description: Library name: HT_no_dox_R_1


title: adult brain, ZT18, tim>RpL3-3xFLAG input, replicate 2

description: Library name: ZT18_INPUT_REP2

value: clock cells timGAL4


title: ST-HSC, rep3

description:
Library name: sample6
Mouse BM ST-HSC total RNA

value: ST-HSC


title: adult brain, ZT12, tim>RpL3-3xFLAG input, replicate 3

description: Library name: ZT12_INPUT_REP3

value: timGAL4 x UAS-RpL3-3XFLAG

value: constant condition second day (CT)


title: control-sEVs 02

description:
Library name: LWH
colunm name in Expression_miRNA.txt:LWH


title: control-sEVs 01

description:
Library name: CZY
colunm name in Expression_miRNA.txt:CZY


title: ST-HSC, rep2

description:
Library name: sample5
Mouse BM ST-HSC total RNA


title: control-sEVs 06

description:
Library name: YJ
colunm name in Expression_miRNA.txt:YJ


title: adult brain, ZT12, tim>RpL3-3xFLAG co-IP, replicate 3

description: Library name: ZT12_FLAG_REP3


title: HT-29 iZEB1 mDOX DMSO Rep2

description: Library name: HT_no_dox_D_2

value: DMSO


title: ST-HSC, rep1

description:
Library name: sample4
Mouse BM ST-HSC total RNA


title: adult brain, ZT12, tim>RpL3-3xFLAG input, replicate 2

description: Library name: ZT12_INPUT_REP2


title: HT-29 iZEB1 mDOX DMSO Rep1

description: Library name: HT_no_dox_D_1


title: LT-HSC, rep3

description:
Library name: sample3
Mouse BM LT-HSC total RNA

value: LT-HSC


title: ICM-sEVs 04

description:
Library name: SXH
colunm name in Expression_miRNA.txt:SXH


title: LT-HSC, rep1

description:
Library name: sample1
Mouse BM LT-HSC total RNA


title: adult brain, ZT12, tim>RpL3-3xFLAG input, replicate 1

description: Library name: ZT12_INPUT_REP1


title: F-53B_High_3

city: Nanjing

first: Liehai

last: Hu

address: 22 Hankou Road, Nanjing 210093, P. R. China

department: Medical school

institute: Nanjing University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean data were mapped using STRA software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a pvalue cutoff of 0.05 to judge statistically significant enrichment. Alternative splicing events were detected by using rMATS (version 3.2.5) with a FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for all samples
Supplementary files format and content: tab-delimited text file includes RPKM value for all samples

source_name: Hippocampus

extract_protocol:
Total RNA was extracted using FreeZol Reagent (Vazyme) 1.5μg total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by using KC-digital mRNA Library Prep Kit fowllowing manufacturer's protocol.

value: Hippocampus

tag: age

value: 21 day

tag: Sex

value: male

value: WT

value: 1.5 mg/kg/day F-53B


title: ICM-sEVs 05

description:
Library name: LJL
colunm name in Expression_miRNA.txt:LJL


title: adult brain, ZT12, tim>RpL3-3xFLAG co-IP, replicate 1

description: Library name: ZT12_FLAG_REP1


title: F-53B_High_2


title: cKO lin- Input, rep2

description:
Library name: sample32
ULAC-seq cKO lin- Input, rep2

data_processing:
*library strategy: Ultra-low input acRIP seq (ULAC-seq)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by cutadapt with parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q 20,20 --max-n 0.25 --trim-n.
The clean reads were then mapped to the mouse genome (mm39) with HISAT2 with “--rna-strandness RF” parameters, and supplying the GENCODE Release VM30 gene annotation. A post-alignment filter was preformed to remove alignments to ribosomal RNA (rRNA), secondary alignment and non-concordant mate pairs.
Ac4C peaks on each transcripts of gene were called using homemade Perl scripts according to the strand, separated by “-f 83 (and 163)” or “-f 99 (and 147) with SAMtools.
Peaks were identified as regions concentrated with significantly more normalized reads (fold change > 1.5 and adjusted P-value < 0.05) in IP than their corresponding input samples.
Assembly: mm39
Supplementary files format and content: bigwig files were generated by deepTools. BedWig files can be uploaded to UCSC Genome Browser for visualization.

treatment_protocol: For stem/progenitor cell isolation, bone marrow cells were incubated with biotin-labeled lineage antibody cocktail and enriched using the Lineage Cell Depletion Kit (Miltenyi, Cat# 130-090-858) according to manufacturer’s instruction. After washing, cells were stained with the antibodies and sorted in BD FACSAria Fusion.

value: cKO lin-

value: Input


title: ICM-sEVs 03

description:
Library name: ZTY
colunm name in Expression_miRNA.txt:ZTY

value: plasma


title: F-53B_High_1


title: ICM-sEVs 02

description:
Library name: GSB
colunm name in Expression_miRNA.txt:GSB


title: adult brain RNA-seq, mor-RNAi CT18 repeat-2

description: Library name: RNAseq_morRNAi_CT18_Rep2

data_processing:
We used the Illumina DRAGEN RNA pipeline for automated data analysis.
Assembly: dm6
Supplementary files format and content: table of gene expression quantification (Salmon, Illumina RNA Pipeline)

growth_protocol: Flies were raised on standard cornmeal/yeast media and maintained at room temperature (20 to 22 °C) under a 12h:12h LD schedule. The following flies used in the study were previously described, obtained from the Bloomington Stock Center, or developed for this study: Clk-GAL4 (BDSC#93198), UAS-mor-RNAi (BDSC#34919).

extract_protocol:
Flies of genotype ClkGAL4>UAS-tetR-GFP-NLS was used for a bright GFP marker specific to clock neurons and DAPI was used as a viability marker. A small population of cells were heated at 60C for 5min and used as a dead cell (DAPI+) control. Live clock neurons are defined by GFP+ and DAPI- gating. For each sample, ~2,000 live clock were sorted with FACS sorter (Sony MA900) directly into cell lysis buffer (NEBNext Low-Input cDNA Synthesis Module) in 1.5mL DNA low-bind tube (Eppendorf). Final volume of the lysis buffer (with sorted cells) is ~16uL.
Cells were lysed and half of the lysate was subsequently used for cDNA library preparation following manufacturer protocol. cDNA library was subject to quality control by Tapestation (HSD5000) and Qubit (High Sensitivity DNA) for mean size of ~1500bp. Next, cDNA library was tagmented to prepare Illumina sequencing library (Illumina Nextera XT, UDI indexing). Quality control was performed with Qubit (High Sensitivity DNA) and Tapestation (HSD1000) for mean size of ~300bp. Control/mor-RNAi samples were loaded in equal molar with 3% spike-in PhiX DNA and sequenced on an Illumina NextSeq 1000 platform with paired-end 100bp cycle using P2 flow cell.

treatment_protocol: Flies were entrained to Light-Dark (LD) cycles where they were exposed to 12-hour Light-Dark (LD) cycles for 5 days before sample collection. The initiation of the light phase is labeled as Zeitgeber Time (ZT) 0, while ZT12 signifies the beginning of the dark period. For the control/mor-RNAi samples, we collected samples on the second day after releasing into Dark-Dark free-running condition (DD2).

value: clock neurons ClkGAL4

value: mor-RNAi (;ClkGAL4, UAS-GFP-NLS/UAS-mor-RNAi BDSC#34919;)


title: LT-HSC, rep2

description:
Library name: sample2
Mouse BM LT-HSC total RNA

value: Bone marrow


title: Control_3

value: 0 mg/kg/day


title: HT-29 iZEB1 mDOX DMSO Rep3

description: Library name: HT_no_dox_D_3

value: epithelial

value: mDOX


title: cKO lin- Input, rep1

description:
Library name: sample31
ULAC-seq cKO lin- Input, rep1


title: adult brain RNA-seq, mor-RNAi CT12 repeat-2

description: Library name: RNAseq_morRNAi_CT12_Rep2

value: adult brain

value: constant condition second day (CT)


title: ICM-sEVs 01

description:
Library name: SDS
colunm name in Expression_miRNA.txt:SDS


title: ICM-sEVs 06

description:
Library name: QGH
colunm name in Expression_miRNA.txt:QGH


title: Control_1


title: HT-29 iZEB1 (Clone3) pDOX

data_processing:
Samples were aligned to GRCh38 using STAR2.4.2a with default parameters.
Reads were count using STAR2.4.2a with default parameters and Ensembl v84 as reference.
Counts were normalized and tested for differential expression using the DESeq2 algorithm.
Assembly: GRCh38
Supplementary files format and content: Tab separated count matrices

extract_protocol:
RNA was extracted with the Nucleospin RNA Plus-kit (Machery-Nagel) according to the manufacturer’s instructions.
The mRNA libraries were prepared with the QuantSeq 3’ mRNA-Seq Library Prep FWD kit (Lexogen).

value: pDOX


title: adult brain RNA-seq, mor-RNAi CT0 repeat-2

description: Library name: RNAseq_morRNAi_CT0_Rep2


title: adult brain, ZT12, tim>RpL3-3xFLAG co-IP, replicate 2

description: Library name: ZT12_FLAG_REP2

value: clock cells timGAL4

value: timGAL4 x UAS-RpL3-3XFLAG


title: trxRNAi DSS 3

city: Heraklion

first: Zoe

last: Veneti

address: Nikolaou Plastira 100

country: Greece

institute: Institute of Molecular Biology & Biotechnology Foundation for Research & Technology - Hellas

description:
Library name: Sample 12
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter

data_processing:
Base calling was performed using bcl2fastq software.
FASTQ files were aligned against the drosophila reference genome build dm6 using a two-step approach,. Briefly, reads were mapped to the reference transcriptome with HISAT2 (Daehwan Kim et. al., 2019),  and the remaining unmapped reads were aligned with bowtie2 (Ben Langmead & Steven L Salzberg, 2012).
Read counting on the 3’ UTRs was conducted using the metaseqR2 bioconductor package (Fanidis et.al., Briefings in Bioinformatics, 2021). Read counting and filtering were conducted with default parameters, and normalization was carried out with DESEQ (Anders & Huber, Genome Biology, 2010) as implemented in metaseqR2.  For differential expression analysis, the PANDORA algorithm (Moulos & Hatzis, Nucleic Acid Research 2015) was used to estimate a meta p-value integrating the results from the DESEQ (Anders & Huber, Genome Biology,  2010), DESEQ2 (Love et al., Genome Biology, 2014), edgeR (Robinson et al., Bioinformatics, 2010), limma (Ritchie et al., Nucleic Acids Research, 2015), NBPSeq (Di et. al. Statistical Applications in Genetics and Molecular Biology, 2011), and NOISeq (Tarazona et al., Nucleic Acids Research, 2015) algorithms. All additional parameters were set to default. Genes with meta p.value < 0.05 and absolute log2(FC) > 0.5 were considered as differentially expressed.
Assembly: dm6
Supplementary files format and content: Tab-delimited files containing DESeq normalized counts for each Ensembl gene for Quant-Seq data.

source_name: Intestine

growth_protocol: 3-4 days old mated females from F1 progeny were shifted to 29 °C for 7 days

extract_protocol:
QIAzol lysis buffer, following total RNA isolation using the miRNeasy Micro Kit (Qiagen).
Libraries were prepared using the QuantSeq 3‘mRNA-Seq Library Prep Kit (Lexogen). Briefly, up to 150 ng of RNA were used for first strand synthesis, followed by RNA template removal and second strand synthesis initiated by random primers containing compatible linker sequences at their 5’ end. In-line barcodes were introduced during second strand synthesis, followed by magnetic bead-based purification. The resulting libraries were amplified for up to 19 cycles and purified. Library quantities were assessed using a Qubit 4 Fluorometer and the Qubit dsDNA HS Assay Kit (Invitrogen) and quality was assessed using the Agilent Tapestation 4150 and the High Sensitivity D1000 assay kit, according to manufacturers’ instructions. The quantified libraries were pooled equimolarly, and processed for Adapter Conversion PCR Amplification using the Universal Library Conversion Kit (App-A) (MGI Tech Co., Ltd.) according to manufacturer’s instructions. The quantity of the purified adapter conversion PCR (AC-PCR) product was assessed using a Qubit 4 Fluorometer and the Qubit dsDNA HS Assay Kit (Invitrogen) and the quality was evaluated using the Agilent Tapestation 4150 and the High Sensitivity D1000 assay kit, according to manufacturers’ instructions. This was followed by DNA denaturation, single-strand circularization, enzymatic digestion, enzymatic digestion product cleanup and quality control steps on the AC-PCR product, according manufacturer’s instructions. The resulting ssCirDNA was used for DNB preparation and sequencing on a DNBSEQ-G400 platform at the Genomics Facility of BSRC Alexander Fleming, using a G400 App-A FCS SE100 High-throughput Sequencing Set (MGI Tech Co., Ltd.).

treatment_protocol: flies were fed with 5% sucr or 3%  DSS the last 48h of total incubation time at 29°C

value: Intestine

value: Adult  progenitors

value: esgtsGFP (x) UAS-trxRNAi (BDSC#33703)

value: 7d 29°C, the last 48h in 3% DSS


title: HT-29 iZEB1 (Clone3) mDOX


title: cKO lin- IP, rep2

description:
Library name: sample28
ULAC-seq cKO lin- IP, rep2

value: cKO lin-

value: IP


title: trxRNAi DSS 2

description:
Library name: Sample 11
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter


title: HT-29 iZEB1 (Clone2) mDOX


title: cKO lin- IP, rep1

description:
Library name: sample27
ULAC-seq cKO lin- IP, rep1


title: adult brain RNA-seq, mor-RNAi CT12 repeat-1

description: Library name: RNAseq_morRNAi_CT12_Rep1

value: clock neurons ClkGAL4


title: trxRNAi DSS 1

description:
Library name: Sample 10
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter


title: adult brain RNA-seq, mor-RNAi CT6 repeat-1

description: Library name: RNAseq_morRNAi_CT6_Rep1

value: mor-RNAi (;ClkGAL4, UAS-GFP-NLS/UAS-mor-RNAi BDSC#34919;)


title: WT lin- IP, rep2

description:
Library name: sample26
ULAC-seq WT lin- IP, rep2

value: Bone marrow

value: WT lin-


title: trxRNAi Sucrose 3

description:
Library name: Sample 9
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter

value: 7d 29°C, the last 48h in sucr


title: WT lin- IP, rep1

description:
Library name: sample25
ULAC-seq WT lin- IP, rep1


title: adult brain RNA-seq, mor-RNAi CT0 repeat-1

description: Library name: RNAseq_morRNAi_CT0_Rep1


title: Control_2

value: Hippocampus

value: 21 day

value: male

value: WT

value: 0 mg/kg/day


title: HT-29 iZEB1 (Clone1) pDOX

value: epithelial

value: pDOX


title: trxRNAi Sucrose 2

description:
Library name: Sample 8
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter

value: Intestine

value: Adult  progenitors


title: adult brain RNA-seq, mor-RNAi CT6 repeat-2

description: Library name: RNAseq_morRNAi_CT6_Rep2

value: adult brain

value: constant condition second day (CT)


title: HT-29 iZEB1 (Clone1) mDOX

value: mDOX


title: CLP Input, rep2

description:
Library name: sample24
ULAC-seq CLP Input, rep2

value: CLP

value: Input


title: WT lin- Input, rep2

description:
Library name: sample30
ULAC-seq WT lin- Input, rep2

value: Bone marrow


title: WT lin- Input, rep1

description:
Library name: sample29
ULAC-seq WT lin- Input, rep1

value: WT lin-


title: trxRNAi Sucrose 1

description:
Library name: Sample 7
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter

value: esgtsGFP (x) UAS-trxRNAi (BDSC#33703)

value: 7d 29°C, the last 48h in sucr


title: adult brain, wildtype for rABE comparison ZT0 repeat-2

description: Library name: control-rABE_Rep2

data_processing:
Adapter sequences were trimmed using trimgalore (v0.6.7). Alignment was performed using STAR aligner (v2.7.0a) with Drosophila melanogaster dm6 genome and transcript annotation from the UCSC Genome Browser. Parameter ‘--quantMode GeneCounts --outSAMtype BAM SortedByCoordinate’ was used.
For the adenine base editor experiment, the following processing steps were adopted: 1) mapped reads were marked for PCR and optical duplicates and split by spliced intron junctions with Picard (v3.3.0) and GATK (v4.5.0) “MarkDuplicates” and “SplitNCigarReads” commands, 2) split reads were then called for mutational variants with bcftools (v1.20) “mpileup” command, generating the variant calling file (BCF) with variant and reference counts, 3) variant calls were filtered with bcftools “filter” command to retain calls whose read depths (DP) are at least 20 and ALT allele depths (AD) are at least 2. “Markduplicates” and “SplitNCigarReads” were run with default settings. “mpileup” was run with parameters “-d 100000 -I -a ‘DP,AD,ADF,ADR,INFO/AD,INFO/ADF,INFO/ADR’”. “filter” was run with parameters “-i ‘INFO/AD[0:1-]>=2 & FORMAT/DP[*]>=20’”.
Assembly: dm6
Supplementary files format and content: tab-delimited count tables, STAR alignment output with the ‘--quantMode GeneCounts’ settings
Supplementary files format and content: VCF variant calling files of the control/me31B-rABE variants.

growth_protocol: Flies were raised on standard cornmeal/yeast media and maintained at room temperature (20 to 22 °C) under a 12h:12h LD schedule. The following flies used in the study were previously described, obtained from the Bloomington Stock Center, or developed for this study: Clk-GAL4 (BDSC#93198), UAS-pcm-RNAi (BDSC#34690), UAS-me31B-rABE-FLAG.

extract_protocol:
Flies of genotype ClkGAL4>UAS-tetR-GFP-NLS was used for a bright GFP marker specific to clock neurons and DAPI was used as a viability marker. A small population of cells were heated at 60C for 5min and used as a dead cell (DAPI+) control. Live clock neurons are defined by GFP+ and DAPI- gating. For each sample, ~2,000 live clock were sorted with FACS sorter (Sony MA900) directly into cell lysis buffer (NEBNext Low-Input cDNA Synthesis Module) in 1.5mL DNA low-bind tube (Eppendorf). Final volume of the lysis buffer (with sorted cells) is ~16uL.
Cells were lysed and half of the lysate was subsequently used for cDNA library preparation following manufacturer protocol. cDNA library was subject to quality control by Tapestation (HSD5000) and Qubit (High Sensitivity DNA) for mean size of ~1500bp. Next, cDNA library was tagmented to prepare Illumina sequencing library (Illumina Nextera XT, UDI indexing). Quality control was performed with Qubit (High Sensitivity DNA) and Tapestation (HSD1000) for mean size of ~300bp. Control/pcm-RNAi samples were loaded in equal molar with 3% spike-in PhiX DNA and sequenced on an Illumina NextSeq 1000 platform with paired-end 100bp cycle using P2 flow cell. Control/me31B-rABE samples were sequenced similarly on an Illumina NextSeq 1000 platform with paired-end 300bp cycle using P2 flow cell.

treatment_protocol: Flies were entrained to Light-Dark (LD) cycles where they were exposed to 12-hour Light-Dark (LD) cycles for 5 days before sample collection. The initiation of the light phase is labeled as Zeitgeber Time (ZT) 0, while ZT12 signifies the beginning of the dark period. For the control/pcm-RNAi group, we collected samples on the second day after releasing into Dark-Dark free-running condition (DD2). For the control/me31B-rABE group, we collected samples in the LD cycle.

value: clock neurons ClkGAL4

value: wildtype (;ClkGAL4, UAS-GFP-NLS/+;)

value: cycling condition (ZT)


title: 786-O, Control, rep 3

city: Paris

first: Pontoglio

last: Marco

address: 160 rue de Vaugirard

country: France

institute: Institut Necker Enfants Malades

data_processing:
RNA-seq reads were aligned to the hg38 genome assembly using  STAR version=2.7.0.d
Reads counts per genes were computed with RSEM and the Homo_sapiens.GRCh38.83.gtf annotation
A raw matrix contain the RSEM counts with the human gene names
Assembly: hg38
Supplementary files format and content: Reads counts by sample done by RSEM
Supplementary files format and content: A tab-delimited matrix that  include raw counts values for each sample

source_name: kidney

growth_protocol: 786-O cells were cultured in Roswell Park Memorial Institute (RPMI) medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37C with 5% CO2.

extract_protocol:
Cells were collected in TRIzol and RNA was extracted following the manufacturer’s instructions.
Libraries were prepared from 250 ng of total RNA per sample using the Stranded mRNA Prep kit (Illumina).

treatment_protocol: HNF1B-siRNA or non-targeting-siRNA pools (Dharmacon) were transfected in 786-O cells using Lipofectamine RNAiMAX  at a final concentration of 37.5 nM. Cells were collected in Trizol for RNA extraction 48 hours after transfection.

value: kidney

value: Control


title: CLP Input, rep1

description:
Library name: sample23
ULAC-seq CLP Input, rep1


title: adult brain, wildtype for rABE comparison ZT0 repeat-1

description: Library name: control-rABE_Rep1


title: 786-O, Control, rep 2


title: MEP Input, rep2

description:
Library name: sample22
ULAC-seq MEP Input, rep2

value: MEP


title: Ctrl DSS 3

description:
Library name: Sample 6
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter

value: Intestine

value: esgtsGFP (x) w1118

value: 7d 29°C, the last 48h in 3% DSS


title: HT-29 iZEB1 (Clone2) pDOX

value: epithelial

value: pDOX


title: adult brain RNA-seq, mor-RNAi CT18 repeat-1

description: Library name: RNAseq_morRNAi_CT18_Rep1

value: adult brain

value: mor-RNAi (;ClkGAL4, UAS-GFP-NLS/UAS-mor-RNAi BDSC#34919;)

value: constant condition second day (CT)


title: adult brain, me31B-rABE ZT0 repeat-4

description: Library name: me31B-rABE_Rep4


title: MEP Input, rep1

description:
Library name: sample21
ULAC-seq MEP Input, rep1

value: Bone marrow

value: Input


title: Ctrl DSS 2

description:
Library name: Sample 5
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter

value: Adult  progenitors


title: adult brain, me31B-rABE ZT0 repeat-3

description: Library name: me31B-rABE_Rep3

value: clock neurons ClkGAL4


title: 786-O, BTBD2 KO, rep 3

value: BTBD2 KO


title: adult brain, me31B-rABE ZT0 repeat-2

description: Library name: me31B-rABE_Rep2

value: cycling condition (ZT)


title: Ctrl DSS 1

description:
Library name: Sample 4
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter


title: GMP Input, rep2

description:
Library name: sample20
ULAC-seq GMP Input, rep2

value: GMP


title: 786-O, BTBD2 KO, rep 2

value: kidney


title: Ctrl Sucrose 3

description:
Library name: Sample 3
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter

value: 7d 29°C, the last 48h in sucr


title: adult brain, me31B-rABE ZT0 repeat-1

description: Library name: me31B-rABE_Rep1


title: 786-O, BTBD2 KO, rep 1


title: CMP Input, rep2

description:
Library name: sample18
ULAC-seq CMP Input, rep2

value: CMP


title: GMP Input, rep1

description:
Library name: sample19
ULAC-seq GMP Input, rep1


title: Ctrl Sucrose 2

description:
Library name: Sample 2
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter

value: Intestine

value: esgtsGFP (x) w1118


title: adult brain, wildtype CT18 repeat-2, paired with pcmRNAi_Rep2

description: Library name: control_CT18_Rep2

value: wildtype (;ClkGAL4, UAS-GFP-NLS/+;)


title: CMP Input, rep1

description:
Library name: sample17
ULAC-seq CMP Input, rep1


title: DU145_TS_shCtrl_rep2

city: Bellinzona

first: Giada

last: Sandrini

address: Via Chiesa 5

country: Switzerland

institute: IOR

data_processing:
Sequencing reads were aligned to the GRch38.p12 release of the human genome
Reads were quantified using STAR aligner (STAR-2.6.1c)
Rawcounts were processed according to DESeq pipeline
Assembly: hg38
Supplementary files format and content: tab-delimited file

extract_protocol:
RNA was isolated from adherent and tumor-sphere DU145 cells in three independent replicates, marked with Illumina total prep 96 RNA amplification kit (Ambion).
RNA sequencing was performed using Next Ultra II Directional RNA Library Prep Kit for Illumina starting from 800ng of total RNA each sample and sequenced on the Illumina NextSeq500 with single-end, 75 base pair long reads

value: shCtrl

tag: culture condition

value: tumor sphere

tag: replicate


title: DU145_TS_shCtrl_rep3


title: 0.1% BIT 24H 8_30_17_F

city: Charlottesville

first: Jason

last: Papin

state: Virginia

address: 415 Lane Road Room 2041

department: Biomedical Engineering

institute: University of Virginia

data_processing:
Reads were aligned to the reference P. aeruginosa PA14 genome (NC_008463.1) using the BWA aligner with the MEM algorithm with default parameters
Aligned reads were tallied for each gene using FeatureCounts
Differential expression was then determined with DESeq2
Genome_build: PA14 (NC_008463.1)
Supplementary_files_format_and_content: The counts files contain a table with the raw gene counts for every gene in each condition and replicate
Supplementary_files_format_and_content: Differential expression files are csvs with the results from DeSeq: Logfold change results for each gene between different groups and different timepoints

organism: Pseudomonas aeruginosa

source_name: Persister 24H rep 8

growth_protocol: A frozen stock of PA14 wild-type was streaked on an LB agar plate and grown overnight. Individual colonies were inoculated into a 50 mL flask containing 10 mL of LB and grown overnight with aeration. The overnight cultures were diluted in fresh LB in 500 mL flasks to an OD600 of 0.01 for a total volume of 50 mL and grown for 12 hours to reach stationary phase.

extract_protocol:
One millilitre samples for RNA-sequencing were collected immediately before exposure, 5 and 24 hours after exposure from the untreated and 10X MIC conditions. Samples were mixed with 2 mL of RNAprotect (Qiagen) to stabilize RNA and frozen at -80 C.
RNA libraries were prepared for sequencing using standard Illumina protocols. Ribosomal RNA was depleted using the Ribo-Zero rRNA removal kit (Illumina). Libraries were sequenced on an Illumina HiSeq4000, 2x150bp configuration

treatment_protocol: The cultures were then subsequently exposed to BIT by removing 5 mL of the culture and adding 5mL of antimicrobial at various concentrations (PBS for the untreated condition, 0.2% BIT for the 10X MIC condition, 2% BIT for the 100X MIC condition, and 20% BIT for the 1000X MIC condition).  The flasks were returned to the incubator for 24 hours.

value: Persister


title: 786-O, Control, rep 1

value: Control


title: adult brain, wildtype CT18 repeat-1, paired with pcmRNAi_Rep1

description: Library name: control_CT18_Rep1

value: adult brain

value: constant condition second day (CT)


title: adult brain, wildtype CT12 repeat-2, paired with pcmRNAi_Rep2

description: Library name: control_CT12_Rep2


title: DU145_TS_shCtrl_rep1


title: 0.1% BIT 24H 8_30_17_D

source_name: Persister 24H rep 7


title: DU145_TS_shSigma_rep3

value: shSigma


title: adult brain, wildtype CT12 repeat-1, paired with pcmRNAi_Rep1

description: Library name: control_CT12_Rep1

value: clock neurons ClkGAL4


title: HSC Input, rep2

description:
Library name: sample14
ULAC-seq HSC Input, rep2

extract_protocol:
Total RNA was isolated using the TRIzol reagent.
After acRIP, input samples and IP products were used to construct NGS libraries using Smarter® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian following manufacturer’s protocol.

value: Bone marrow

value: HSC

value: Input


title: DU145_TS_shSigma_rep2


title: MPP Input, rep1

description:
Library name: sample15
ULAC-seq MPP Input, rep1

value: MPP


title: 0.1% BIT 24H 8_10_17_F

source_name: Persister 24H rep 4


title: adult brain, wildtype CT6 repeat-2, paired with pcmRNAi_Rep2

description: Library name: control_CT6_Rep2


title: adult brain, wildtype CT6 repeat-1, paired with pcmRNAi_Rep1

description: Library name: control_CT6_Rep1


title: Ctrl Sucrose 1

description:
Library name: Sample 1
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter

value: Adult  progenitors

value: 7d 29°C, the last 48h in sucr


title: 0.1% BIT 24H 8_30_17_B

source_name: Persister 24H rep 6


title: DU145_adh_shCtrl_rep3

value: adhesion


title: adult brain, wildtype CT0 repeat-2, paired with pcmRNAi_Rep2

description: Library name: control_CT0_Rep2


title: 0.1% BIT 24H 8_10_17_A

source_name: Persister 24H rep 2


title: MPP Input, rep2

description:
Library name: sample16
ULAC-seq MPP Input, rep2

source_name: Bone marrow


title: HSC Input, rep1

description:
Library name: sample13
ULAC-seq HSC Input, rep1


title: adult brain, wildtype CT0 repeat-1, paired with pcmRNAi_Rep1

description: Library name: control_CT0_Rep1


title: CLP IP, rep1

description:
Library name: sample11
ULAC-seq CLP IP, rep1

value: CLP

value: IP


title: DU145_adh_shCtrl_rep2

value: shCtrl


title: 0.1% BIT 24H 8_10_17_B

source_name: Persister 24H rep 1


title: CLP IP, rep2

description:
Library name: sample12
ULAC-seq CLP IP, rep2


title: adult brain, pcm-RNAi CT18 repeat-2

description: Library name: pcmRNAi_CT18_Rep2

value: pcm-RNAi (;ClkGAL4, UAS-GFP-NLS/UAS-pcm-RNAi BDSC#34690;)


title: MEP IP, rep2

description:
Library name: sample10
ULAC-seq MEP IP, rep2

value: MEP


title: DU145_adh_shCtrl_rep1


title: 0% BIT 24H 8_30_17_D

source_name: Untreated 24H rep 8

value: Untreated

value: 0% BIT 24H


title: DU145_adh_shSigma_rep3


title: adult brain, pcm-RNAi CT18 repeat-1

description: Library name: pcmRNAi_CT18_Rep1

value: adult brain

value: constant condition second day (CT)


title: 0% BIT 24H 8_30_17_C

source_name: Untreated 24H rep 7


title: MEP IP, rep1

description:
Library name: sample9
ULAC-seq MEP IP, rep1


title: GMP IP, rep2

description:
Library name: sample8
ULAC-seq GMP IP, rep2

value: GMP


title: adult brain, pcm-RNAi CT12 repeat-2

description: Library name: pcmRNAi_CT12_Rep2

value: clock neurons ClkGAL4


title: DU145_adh_shSigma_rep2

value: shSigma


title: 0% BIT 24H 8_30_17_B

source_name: Untreated 24H rep 6


title: 0.1% BIT 24H 8_10_17_C

source_name: Persister 24H rep 3

value: Persister


title: adult brain, pcm-RNAi CT12 repeat-1

description: Library name: pcmRNAi_CT12_Rep1

source_name: adult brain


title: DU145_TS_shSigma_rep1

value: tumor sphere


title: GMP IP, rep1

description:
Library name: sample7
ULAC-seq GMP IP, rep1

value: Bone marrow


title: DU145_adh_shSigma_rep1


title: 0% BIT 24H 8_30_17_A

source_name: Untreated 24H rep 5


title: FXS6

city: Worcester

first: Sneha

last: Shah

state: Massachusetts

address: 373 Biotech II, Suite 204, Plantation Street

department: Molecular Medicine

institute: UMASS CHAN MEDICAL SCHOOL

description: Library name: FXS6

data_processing:
The FASTQ files were analyzed using the RNA-seq analysis pipeline on Foundry 1. Briefly, the reads were filtered and trimmed using trimmomatic and cutadapt used for adapter removal.
Genome alignment to hg38 Gencode v43 was performed using STAR (v2.6.1). Salmon (v1.5.2) was used to align RNA-Seq reads to reference transcripts and estimate gene and isoform expression levels. Differential expression analysis was done using DESeq2 with a threshold for significance set at p.adj <0.05.
Assembly: hg38 Gencode v43
Supplementary files format and content: CSV file containing genes in rows and samples in columns will be created. Gene counts table contains the estimated read count vaules and abundance table contains transcripts per million (TPM) values.
Supplementary files format and content: CSV file containing genes in rows and samples in columns will be created. Gene counts table contains the estimated read count vaules and abundance table contains transcripts per million (TPM) values.

source_name: Brain

growth_protocol: Post-mortem tissue from individuals was frozen in liquid nitrogen and stored at -80 deg C

extract_protocol:
RNA was extracted using TRIzol™ Reagent (ThermoFisher Scientific # 15596026). The RNA obtained was treated with TURBO™ DNase (Invitrogen # AM2238) and was further purified using the RNA clean and concentrator kit (ZymoResearch # 11-325). RNA quality and abundance were assessed using fragment analysis (Agilent/Advanced Analytical). The quality scores ranged from 3.3 to 6.1 across the samples.
Strand-specific RNA-seq libraries were constructed with 500ng of total RNA using ribosomal RNA depletion and the NEBNext Ultra II Directional RNA library prep kit for Illumina. Samples were PCR amplified for 9 cycles and sequenced using the Illumina NextSeq 2000 P4 XLEAP-SBS kit with 2 x 100 nucleotide paired-end reads.

treatment_protocol: Frozen brain tissues were powdered in liquid nitrogen using a chilled mortar and pestle

tag: tissue region

value: frontal cortex

value: Brain

value: FXS


title: 0% BIT 24H 8_10_17_D

source_name: Untreated 24H rep 4

tag: cell type


title: CMP IP, rep2

description:
Library name: sample6
ULAC-seq CMP IP, rep2

value: CMP

value: IP


title: adult brain, pcm-RNAi CT6 repeat-1

description: Library name: pcmRNAi_CT6_Rep1

value: pcm-RNAi (;ClkGAL4, UAS-GFP-NLS/UAS-pcm-RNAi BDSC#34690;)


title: FXS5

description: Library name: FXS5


title: CMP IP, rep1

description:
Library name: sample5
ULAC-seq CMP IP, rep1


title: adult brain, pcm-RNAi CT0 repeat-2

description: Library name: pcmRNAi_CT0_Rep2


title: adult brain, pcm-RNAi CT6 repeat-2

description: Library name: pcmRNAi_CT6_Rep2


title: FXS3

description: Library name: FXS3


title: 0% BIT 24H 8_10_17_C

source_name: Untreated 24H rep 3


title: adult brain, pcm-RNAi CT0 repeat-1

description: Library name: pcmRNAi_CT0_Rep1


title: FXS2

description: Library name: FXS2


title: MPP IP, rep2

description:
Library name: sample4
ULAC-seq MPP IP, rep2

value: MPP


title: 0% BIT 24H 8_10_17_B

source_name: Untreated 24H rep 2

value: Untreated


title: MPP IP, rep1

description:
Library name: sample3
ULAC-seq MPP IP, rep1


title: 0% BIT 24H 8_10_17_A

source_name: Untreated 24H rep 1

value: 0% BIT 24H


title: HSC IP, rep2

description:
Library name: sample2
ULAC-seq HSC IP, rep2

value: HSC


title: adult brain, Prp3-RNAi ZT14 repeat-3

description: Library name: Prp3RNAi_REP3

data_processing:
Adapter sequences were trimmed using trimgalore (v0.6.7). Alignment was performed using STAR aligner (v2.7.0a) with Drosophila melanogaster dm6 genome and transcript annotation from the UCSC Genome Browser. Parameter ‘--quantMode GeneCounts --outSAMtype BAM SortedByCoordinate’ was used.
Assembly: dm6
Supplementary files format and content: tab-delimited count tables, STAR alignment output with the ‘--quantMode GeneCounts’ settings

growth_protocol: Flies were raised on standard cornmeal/yeast media and maintained at room temperature (20 to 22 °C) under a 12h:12h LD schedule. The following flies used in the study were previously described or obtained from the Bloomington Stock Center: Clk-GAL4 (BDSC#93198), UAS-Prp3-RNAi (BDSC#55256).

extract_protocol:
Flies of genotype ClkGAL4>UAS-tetR-GFP-NLS was used for a bright GFP marker specific to clock neurons and DAPI was used as a viability marker. A small population of cells were heated at 60C for 5min and used as a dead cell (DAPI+) control. Live clock neurons are defined by GFP+ and DAPI- gating. For each sample, ~2,000 live clock were sorted with FACS sorter (Sony MA900) directly into cell lysis buffer (NEBNext Low-Input cDNA Synthesis Module) in 1.5mL DNA low-bind tube (Eppendorf). Final volume of the lysis buffer (with sorted cells) is ~16uL.
Cells were lysed and half of the lysate was subsequently used for cDNA library preparation following manufacturer protocol. cDNA library was subject to quality control by Tapestation (HSD5000) and Qubit (High Sensitivity DNA) for mean size of ~1500bp. Next, cDNA library was tagmented to prepare Illumina sequencing library (Illumina Nextera XT, UDI indexing). Quality control was performed with Qubit (High Sensitivity DNA) and Tapestation (HSD1000) for mean size of ~300bp. Samples were loaded in equal molar with 3% spike-in PhiX DNA and sequenced on an Illumina NextSeq 1000 platform with paired-end 300bp cycle using P2 flow cell.

treatment_protocol: Flies were entrained to Light-Dark (LD) cycles where they were exposed to 12-hour Light-Dark (LD) cycles for 5 days before sample collection. The initiation of the light phase is labeled as Zeitgeber Time (ZT) 0, while ZT12 signifies the beginning of the dark period.

value: adult brain

value: Prp3-RNAi (;ClkGAL4, UAS-GFP-NLS/UAS-Prp3-RNAi BDSC#55256;)

value: cycling condition (ZT)


title: 0.1% BIT 5H 8_30_17_F

source_name: Persister 5H rep 8


title: adult brain, Prp3-RNAi ZT14 repeat-2

description: Library name: Prp3RNAi_REP2

value: clock neurons ClkGAL4


title: FXS1

description: Library name: FXS1


title: HSC IP, rep1

description:
Library name: sample1
ULAC-seq HSC IP, rep1


title: TD6

description: Library name: C6

value: WT


title: 0.1% BIT 5H 8_30_17_D

source_name: Persister 5H rep 7

value: Persister


title: Nat10 cKO lin- cells scRNA-seq

description:
Library name: sample2
10×Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Isolated Lin- BM cells from WT/cKO mice were washed twice and counted on a Cellometer Auto 2000 using the ViaStain™ AOPI Staining Solution.
The library synthesis was conducted according to the instructions of Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10× GENOMICS).

treatment_protocol: For stem/progenitor cell isolation, bone marrow cells were incubated with biotin-labeled lineage antibody cocktail and enriched using the Lineage Cell Depletion Kit (Miltenyi, Cat# 130-090-858) according to manufacturer’s instruction.

value: Bone marrow

value: Nat10 cKO Lin- cells

value: Nat10 cKO


title: 0.1% BIT 5H 8_30_17_A

source_name: Persister 5H rep 6


title: TD5

description: Library name: C5

value: frontal cortex

value: Brain


title: 0.1% BIT 5H 8_30_17_B

source_name: Persister 5H rep 5


title: adult brain, wildtype ZT14 repeat-2, paired with Prp3RNAi_REP2

description: Library name: control_REP2

value: wildtype (;ClkGAL4, UAS-GFP-NLS/+;)


title: Mouse 1 (2 sections)

city: South San Francisco

first: Kimberle

last: Shen

state: CA

address: 1 Dna way

institute: Genentech

data_processing:
SAW pipeline version V7.0.0
Assembly: mm10
Supplementary files format and content: C02943C3.adjusted.cellbin.gef
Library strategy: Spatial Transcriptomics

source_name: brain coronal hemisphere

extract_protocol:
Fresh frozen and mounted in OCT
STOMICS Gene Expression kit

value: brain coronal hemisphere

value: Injected


title: TD2

description: Library name: C2


title: 0.1% BIT 5H 8_10_17_F

source_name: Persister 5H rep 4


title: adult brain, wildtype ZT14 repeat-1, paired with Prp3RNAi_REP1

description: Library name: control_REP1


title: 0.1% BIT 5H 8_10_17_C

source_name: Persister 5H rep 3


title: p28d-Mut-5

city: Shanghai

first: Weitao

last: Zhou

state: Minhang district

address: Block 8, Children's Hospital of Fudan University, Wanyuan Road, Minhang District, Shanghai, China

institute: Children's Hospital of Shanghai Jiaotong University

data_processing:
Raw data were normalized by using the Quantile algorithm of the R package limma.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file include RPKM values for each Sample

source_name: lung

extract_protocol:
Total RNA was isolated and purified by using the miRNeasy Mini Kit (QIAGEN, Germany) in accordance with the manufacturer’s instructions
Total mRNA was enriched using magnetic beads with Oligo(dT), followed by random fragmentation of the mRNA using a fragmentation buffer. With mRNA used as template, the first cDNA strand was synthesized with six-base random hexamers. The second cDNA strand was synthesized by adding buffer, dNTPs and DNA polymerase I. PCR products of the double-stranded cDNA, purified using AMPure XP beads, underwent end-repair, followed by the addition of an A-tail and connection of sequencing adapters. Subsequently, AMPure XP beads were employed for fragment size selection, and a final cDNA library was obtained through PCR enrichment.

value: lung

value: primary cells

value: lung primary cells

value: IARS1 knockdown

value: Day 28


title: p28d-Mut-4


title: p28d-Mut-7


title: SJD08

city: Houston

first: Cintia

middle: Sade

last: de Paiva

state: Texas

address: One Baylor Plaza

department: Ophthalmology

institute: Baylor College of Medicine

description: SjD KCS = Sjӧgren disease keratoconjunctivitis sicca

hyb_protocol: Hybridization of the sample mixed with reporter codeset and capture probeset was done at 65°C for 20 h (according to manufacture's protocol)

scan_protocol: Samples were purified, immobilized on cartridges and scanned on the nCounter® SPRINT Profiler (nanoString Technologies)

data_processing: The raw RCC files were uploaded onto the nSolver software, raw counts were measured, stable houskeeping genes for normalization was identified using NormFinder, an excel plug-in software, and data were subsequently normalized to obtain normalized counts. The normalized counts were used for the final evaluations. The data was analyzed using ROSALIND (https://rosalind.bio/), which features a HyperScale architecture developed by ROSALIND, Inc. (San Diego, California, USA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes, and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library{Perkins, 2012 #1650}. Abundance of various cell populations is calculated on ROSALIND using the Nanostring Cell Type Profiling Module. ROSALIND performs a filtering of Cell Type Profiling results to include results that have scores with a p-Value greater than or equal to 0.05. Fold changes and pValues are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment is performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR). Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library{Hennig, 2024 #1651} that takes into consideration the direction and type of all signals on a pathway, the position, role and type of every gene, etc. The hypergeometric distribution was used to analyze the enrichment of pathways, Gene Ontology, domain structure, and other ontologies. The topGO R library{A. Alexa, 2024 #1523}, was used to determine local similarities and dependencies between GO terms to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including Interpro{Mitchell, 2019 #1530}, NCBI{Geer, 2010 #1525}, MSigDB{Subramanian, 2005 #1532;Liberzon, 2011 #1536}, REACTOME{Fabregat, 2018 #1529}, and WikiPathways{Slenter, 2018 #1528}. Enrichment was calculated relative to a set of background genes relevant for the experiment.

source_name: Conunctival cells

label_protocol: Samples were then submitted to the Baylor College of Medicine Genomic and RNA Profiling core with the NanoString Human Immunology V2 panel (www.nanostring.com) for analysis. Five hundred ninety-four transcripts were quantified with the NanoString nCounter multiplexed target platform using the Human Immunology V2 panel. nCounts of mRNA transcripts were normalized using the geometric means of 15 housekeeping genes (ABCF1, ALAS1, EEF1G, G6PD, GAPDH, GUSB, HPRT1, OAZ1, POLR1B, POLR2A, PPIA, RPL19, SDHA, TBP, TUBB).

extract_protocol: A topical anesthetic was applied onto the eye immediately before collection. Samples of the temporal bulbar conjunctiva were collected using the EyePrim device (Opia Tech, Paris, France). Samples were ejected into tubes containing RNA lysis buffer and 1% 2-mercaptoethanol and immediately stored at -80°C. Total RNA was isolated using an RNeasy Mini Kit (Qiagen, Valencia, California, USA) following the manufacturer's protocol. Samples were eluted into RNase-free water.

value: F

tag: diagnosis

value: SJD KCS

tag: severity level


title: HC21

description: Age and sex matched control

value: Control


title: 0.1% BIT 5H 8_10_17_B

source_name: Persister 5H rep 1

tag: strain

value: Persister


title: p28d-Mut-3

tag: tissue

tag: genotype


title: H3K9me3_JIB04_150nM_Rep2

city: Boston

first: Mohamad Ali

last: Najia

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

description: Library name: H3K9me3_JIB04_150nM_Rep2

library_source: genomic

data_processing:
ChIP-seq libraries were processed using the nf-core/chipseq pipeline v2.0.0 (https://doi.org/10.5281/zenodo.3240506) implemented in the NextFlow software package (v23.10.1). In brief, single-end reads were trimmed of adaptor sequences with trim-galore (v0.6.7) and aligned with BWA (v0.7.17-r1188) to the GRCh38 assembly of the human genome. Reads aligning to ENCODE blacklist sites (ENCFF356LFX) were omitted. Duplicate reads were removed with Picard (v2.27.4) with the MarkDuplicates tool. Peaks for H3K4me3 and H3K27ac ChIP-seq experiments were identified with MACS2 (v2.2.7.1) using the BAM files of the input ChIP-seq control and histone ChIP-seq samples with the following command line parameters: --keep-dup all --broad --broad-cutoff 0.1 --gsize 2701262066. We created bigwig files for visualization using bamCoverage from the deepTools package (v3.5.1) with the following command line options: --binSize 20 --normalizeUsing RPKM --smoothLength 60 --extendReads 150 --centerReads.  To identify genomic regions with differential H3K9me2 or H3K9me3 enrichment in JIB-04 treated cells, we performed window-based analyses using the csaw package (v1.34.0) in R due to the broad distribution of these histone marks on chromatin. Aligned reads were extended to 200 bp and counted into 2kb windows for each ChIP-seq library. Reads were also counted into 10kb bins, and the median average abundance of all bins was used as a global estimate of the background abundance. Windows were filtered to retain only those with a two-fold or greater increase in the average abundance above the scaled background estimate. Counts from the remaining windows were tested for significant ChIP signal enrichment using edgeR (v3.42.4). Briefly, an abundance-dependent trend in the NB dispersions was fitted to all windows, using the estimateDisp function. A GLM was fitted to the counts for each window using the trended NB dispersion. The quasi-likelihood (QL) dispersion was estimated from the GLM deviance. An abundance-dependent trend was robustly fitted to the QL dispersions across all windows, and the QL dispersion estimate for each window was shrunk to this trend. Finally, a P value for differential ChIP signal in each window was computed using the QL F-test.
Assembly: GRCh38
Supplementary files format and content: Counts matrix of NGS reads in a consensus set of H3K27ac peaks across all samples (tab-delimited text file)
Supplementary files format and content: Counts matrix of NGS reads in a consensus set of H3K4me3 peaks across all samples (tab-delimited text file)
Supplementary files format and content: bw files

growth_protocol: OCI-Ly1 cells were cultured in IMDM + 10% FBS + Penicillin-Streptomycin.

extract_protocol:
For ChIP-Seq experiments, 10 million OCI-Ly1 cells were fixed with 1% formaldehyde for 10 minutes at room temperature before termination with 0.125 M glycine. Cells were then lysed in ChIP buffer (0.6% SDS, 10 mM EDTA, and 50 mM Tris-HCl, pH 8.1) and cross-linked chromatin was sonicated to obtain DNA fragments of 300-800 bp. Chromatin was then centrifuged (10 min, 4°C, 13,000 rpm) and the supernatant was diluted 6-fold in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8, and 167 mM NaCl) with protease inhibitors (Roche Diagnostics). Diluted chromatin was incubated with 5 μg of primary antibody overnight at 4°C with agitation. Antibodies were pelleted using 50 μL of Dynabeads (ThermoFisher Scientific). The beads were sequentially washed once with the ChIP wash buffer 1 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, and 150 mM NaCl), the ChIP wash buffer 2 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, and 500 mM NaCl), the ChIP wash buffer 3 (0.25 M LiCl, 1% IGEPAL-CA630, 1% deoxycholic acid, 1 mM EDTA, 10 mM Tris pH 8), and finally the ChIP wash buffer 4 (10 mM Tris-HCl, 1 mM EDTA). Chromatin was eluted using ChIP Elution Buffer (1% SDS, 100mM NaHCO3). The cross-link between protein and DNA was reversed by heat incubation (65°C, overnight), and proteins were then digested with proteinase K. DNA was recovered by phenol-chloroform extraction and ethanol precipitation in presence of 20 µg of glycogen (Sigma Aldrich).
ChIP-seq libraries were prepared using NEBNext DNA Library Prep Master Mix Set for Illumina (NEB cat. no. E6040). Libraries were single-end indexed and sequenced on an Illumina HiSeq 2000 to generate 50 bp single end reads.

treatment_protocol: Cells were treated with various doses of JIB-04 (Stem Cell Technologies cat. no. 73212) or 0.01% DMSO as a vehicle control.

tag: cell line

tag: treatment


title: TD1

description: Library name: C1

value: WT


title: p28d-Mut-2


title: adult brain, Prp3-RNAi ZT14 repeat-1

description: Library name: Prp3RNAi_REP1

source_name: adult brain

value: adult brain

value: clock neurons ClkGAL4

value: Prp3-RNAi (;ClkGAL4, UAS-GFP-NLS/UAS-Prp3-RNAi BDSC#55256;)

value: cycling condition (ZT)


title: WT lin- cells scRNA-seq

city: GuangZhou,GuangDong Province

first: Feng

last: Huang

institute: Guangzhou Laboratory

description:
Library name: sample1
10×Genomics

source_name: Bone marrow

value: Bone marrow

value: WT Lin- cells


title: TD4

description: Library name: C4

source_name: Brain

value: frontal cortex

value: Brain


title: H3K9me3_JIB04_150nM_Rep1

description: Library name: H3K9me3_JIB04_150nM_Rep1


title: p28d-Mut-1

value: lung

value: primary cells


title: p28d-WT-7

value: lung primary cells


title: 0% BIT 5H 8_30_17_C

source_name: Untreated 5H rep 7

value: Untreated

value: 0% BIT 5H


title: 0% BIT 5H 8_30_17_D

source_name: Untreated 5H rep 8


title: 0% BIT 5H 8_30_17_B

source_name: Untreated 5H rep 6


title: H3K9me3_DMSO_Rep2

description: Library name: H3K9me3_DMSO_Rep2

value: DMSO


title: 0% BIT 5H 8_30_17_A

source_name: Untreated 5H rep 5


title: adult brain, wildtype ZT14 repeat-3, paired with Prp3RNAi_REP3

description: Library name: control_REP3

value: wildtype (;ClkGAL4, UAS-GFP-NLS/+;)


title: H3K9me3_JIB04_500nM_Rep1

description: Library name: H3K9me3_JIB04_500nM_Rep1


title: H3K9me3_DMSO_Rep1

description: Library name: H3K9me3_DMSO_Rep1


title: H3K9me3_JIB04_500nM_Rep2

description: Library name: H3K9me3_JIB04_500nM_Rep2


title: ATD08

description: ATD = Aqueous tear deficient dry eye

value: F

value: ATD


title: HC20

description: Age and sex matched control

value: Control


title: p28d-WT-6

value: WT

value: Day 28


title: 0% BIT 5H 8_10_17_D

source_name: Untreated 5H rep 4


title: p28d-WT-5


title: ATD07

description: ATD = Aqueous tear deficient dry eye


title: ATD06

description: ATD = Aqueous tear deficient dry eye


title: H3K9me2_JIB04_500nM_Rep1

description: Library name: H3K9me2_JIB04_500nM_Rep1


title: HC19

description: Age and sex matched control


title: 0% BIT 5H 8_10_17_C

source_name: Untreated 5H rep 3


title: H3K9me2_JIB04_500nM_Rep2

description: Library name: H3K9me2_JIB04_500nM_Rep2


title: ATD05

description: ATD = Aqueous tear deficient dry eye


title: p28d-WT-4


title: 0% BIT 5H 8_10_17_B

source_name: Untreated 5H rep 2


title: H3K9me2_JIB04_150nM_Rep2

description: Library name: H3K9me2_JIB04_150nM_Rep2


title: H3K9me2_JIB04_150nM_Rep1

description: Library name: H3K9me2_JIB04_150nM_Rep1


title: SJD07

value: SJD KCS


title: p28d-WT-3


title: 0% BIT 5H 8_10_17_A

source_name: Untreated 0H rep 1


title: SJD06


title: H3K9me2_DMSO_Rep2

description: Library name: H3K9me2_DMSO_Rep2


title: METTL3 knockout, 60min, RNA-seq rep2

city: Riverside

first: Yinsheng

last: Wang

state: California

address: 501 Big Springs Road

institute: UC-Riverside

data_processing:
Raw reads were aligned to human hg38 reference genome and supplemented with the sequences of the ERCC spike-in control using HISAT2 (v2.2.1) with parameters ‘-rna-strandness RF’
Reads on each gene were counted using featureCounts and then normalized to reads per kilo base per million mapped reads (RPKM)
Assembly: hg38
Supplementary files format and content: tab-delimited text files from featureCounts

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
total RNA was extracted using Trizol reagent. Nascent RNA was captured by using Click-iT Nascent RNA Capture Kit (Invitrogen).
Library preparation was conducted on-beads with SMARTer Stranded Total RNA-seq Kit v2 (Takara)

treatment_protocol: 5-ethynyluridine (EU) was added until its concentration reached 0.5 mM. The cells were harvested at 10, 20, 30, and 60 min later

value: Human embryonic kidney

value: METTL3 knockout

tag: time

tag: molecule subtype

value: Nascent RNA


title: p28d-WT-1


title: H3K9me2_DMSO_Rep1

description: Library name: H3K9me2_DMSO_Rep1


title: 0.1% BIT 0H 8_30_17_F

source_name: Persister 0H rep 8

value: Persister


title: METTL3 knockout, 60min, RNA-seq rep1


title: SJD05


title: ATD04

description: ATD = Aqueous tear deficient dry eye


title: METTL3 knockout, 30min, RNA-seq rep2


title: 0.1% BIT 0H 8_30_17_B

source_name: Persister 0H rep 6


title: HC18

description: Age and sex matched control


title: H3K4me3_JIB04_500nM_Rep1

description:
Library name: H3K4me3_JIB04_500nM_Rep1
H3K4me3.consensus_peaks.featureCounts.txt


title: H3K4me3_JIB04_150nM_Rep2

description:
Library name: H3K4me3_JIB04_150nM_Rep2
H3K4me3.consensus_peaks.featureCounts.txt


title: 0.1% BIT 0H 8_10_17_F

source_name: Persister 0H rep 4


title: METTL3 knockout, 30min, RNA-seq rep1


title: 0.1% BIT 0H 8_30_17_D

source_name: Persister 0H rep 7


title: H3K4me3_JIB04_500nM_Rep2

description:
Library name: H3K4me3_JIB04_500nM_Rep2
H3K4me3.consensus_peaks.featureCounts.txt


title: HC17

description: Age and sex matched control

source_name: Conunctival cells


title: HC16

description: Age and sex matched control


title: 0.1% BIT 0H 8_10_17_C

source_name: Persister 0H rep 3


title: METTL3 knockout, 20min, RNA-seq rep1


title: H3K4me3_JIB04_150nM_Rep1

description:
Library name: H3K4me3_JIB04_150nM_Rep1
H3K4me3.consensus_peaks.featureCounts.txt


title: H3K4me3_DMSO_Rep2

description:
Library name: H3K4me3_DMSO_Rep2
H3K4me3.consensus_peaks.featureCounts.txt


title: METTL3 knockout, 10min, RNA-seq rep2


title: METTL3 knockout, 20min, RNA-seq rep2


title: 0.1% BIT 0H 8_10_17_A

source_name: Persister 0H rep 2


title: H3K4me3_DMSO_Rep1

description:
Library name: H3K4me3_DMSO_Rep1
H3K4me3.consensus_peaks.featureCounts.txt


title: 0.1% BIT 0H 8_10_17_B

source_name: Persister 0H rep 1


title: METTL3 knockout, 10min, RNA-seq rep1


title: H3K27ac_JIB04_500nM_Rep2

description:
Library name: H3K27ac_JIB04_500nM_Rep2
H3K27ac.consensus_peaks.featureCounts.txt


title: HC14

description: Age and sex matched control


title: 0% BIT 0H 8_30_17_B

source_name: Untreated 0H rep 6

value: 0% BIT 0H


title: HC13

description: Age and sex matched control


title: HC15

description: Age and sex matched control


title: 293T, 60min, RNA-seq rep2


title: 0% BIT 0H 8_30_17_A

source_name: Untreated 0H rep 5


title: H3K27ac_JIB04_500nM_Rep1

description:
Library name: H3K27ac_JIB04_500nM_Rep1
H3K27ac.consensus_peaks.featureCounts.txt


title: 293T, 60min, RNA-seq rep1


title: 0% BIT 0H 8_10_17_D

source_name: Untreated 0H rep 4


title: H3K27ac_JIB04_150nM_Rep2

description:
Library name: H3K27ac_JIB04_150nM_Rep2
H3K27ac.consensus_peaks.featureCounts.txt


title: 293T, 30min, RNA-seq rep2


title: H3K27ac_JIB04_150nM_Rep1

description:
Library name: H3K27ac_JIB04_150nM_Rep1
H3K27ac.consensus_peaks.featureCounts.txt


title: 0% BIT 0H 8_10_17_C

source_name: Untreated 0H rep 3


title: HC10

description: Age and sex matched control


title: 293T, 30min, RNA-seq rep1


title: 0% BIT 0H 8_10_17_B

source_name: Untreated 0H rep 2


title: 293T, 20min, RNA-seq rep2


title: H3K27ac_DMSO_Rep1

description:
Library name: H3K27ac_DMSO_Rep1
H3K27ac.consensus_peaks.featureCounts.txt


title: 0% BIT 0H 8_10_17_A


title: HC08

description: Age and sex matched control


title: HC09

description: Age and sex matched control


title: 0.1% BIT 0H 8_30_17_A

source_name: Persister 0H rep 5


title: H3K27ac_DMSO_Rep2

description:
Library name: H3K27ac_DMSO_Rep2
H3K27ac.consensus_peaks.featureCounts.txt


title: 293T, 20min, RNA-seq rep1


title: 293T, 10min, RNA-seq rep2


title: D. rerio, RNA004 chemistry

city: Aurora

first: Laura

last: White

state: CO

address: 12801 E 17th Avenue RC1S

department: Biochemistry & Molecular Genetics

institute: University of Colorado

description: tRNA sequencing (RNA004)

library_source: other

data_processing:
All libraries were rebasecalled with Dorado 0.7.0 using multiple basecalling models as described in the accompanying manuscript; fastqs have been provided from the highest accuracy basecalling model for each library along with the original POD5 file.
Alignments to tRNA references were performed using BWA-MEM version 0.7.16 with the parameters bwa mem -C -W 13 -k 6 -T 20 -x ont2d.
Further description of alignment, modification analysis, custom scripts and tRNA reference files can be found at  github.com/rnabioco/tRNA004
Assembly: custom tRNA references available at github.com/rnabioco/tRNA004
Supplementary files format and content: bedgraphs of full length filtered reads aligned to tRNA references

molecule: other

organism: Danio rerio

source_name: 3dpf embryo

extract_protocol:
Total RNA extraction protocols for each sample type are detailed in the accompanying manuscript; library inputs were size selected for RNA 17-200 nt in length.
complete protocol for tRNA sequencing available at github.com/rnabioco/tRNA004

value: 3dpf embryo


title: Input_JIB04_500nM_Rep2

description: Library name: Input_JIB04_500nM_Rep2


title: Input_JIB04_150nM_Rep1

description: Library name: Input_JIB04_150nM_Rep1


title: PAO1 at 37°C stationary replicate B

city: Atlanta

first: Rachel

middle: Evans

last: Robinson

state: GA

address: 1510 Clifton Road NE

department: Pediatrics

institute: Emory University

description: Library name: WT_37_stat_B

data_processing:
Demultiplexing, quality control, and adaptor trimming using bcl-convert (v3.9.3) (this step only performed by SeqCenter)
Read mapping using bowtie2 (v2.4.5) to reference genome NC_002516.2) for P. aeruginosa PAO1
Raw read quantification using htseq-count (v2.0.2)
Differential gene expression analysis using DESeq2 (v1.38.3)
Assembly: NC_002516.2
Supplementary files format and content: Tab-delimited text file containing raw counts produced by htseq-count for all samples. Note, the first column provides the PA locus number (gene/transcript unique identifier corresponding to reference genome).

source_name: Bacterial

growth_protocol: Bacteria were grown at 37°C or 25°C, as indicated, in LB shaking at 200 rpm. Samples were collected first at exponential phase (OD ~ 0.5) and then again from the same cultures at stationary phase (OD ~2.0).

extract_protocol:
Standard TRI reagent protocol (phenol/chloroform based) for RNA extraction
Library construction was performed by SeqCenter (Pittsburgh, PA, USA) using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus depletion kit and 10 bp IDT for Illumina indices.

treatment_protocol: Cells were harvested by centrifugation and immediately used in RNA extraction protocol (below).

value: Bacterial

value: Wild-type

tag: temperature

tag: growth phase

value: stationary - OD ~ 2.0


title: Input_JIB04_150nM_Rep2

description: Library name: Input_JIB04_150nM_Rep2


title: SJD03

tag: age


title: SJD02

tag: Sex


title: PAO1 at 37°C stationary replicate C

description: Library name: WT_37_stat_C


title: Input_JIB04_500nM_Rep1

description: Library name: Input_JIB04_500nM_Rep1


title: HC12

description: Age and sex matched control


title: HC11

description: Age and sex matched control


title: HC07

description: Age and sex matched control


title: Input_DMSO_Rep2

description: Library name: Input_DMSO_Rep2

value: DMSO


title: PAO1 at 37°C stationary replicate A

description: Library name: WT_37_stat_A


title: SJD04