title: HN120PCR, H3K4me3, Rep2, Cell7


title: HN120PCR, H3K4me3, Rep1, Cell188

status: Public on Nov 18 2024

type: SRA

city: Singapore

first: Lih Feng

last: Cheow

address: 15 Kent Ridge Cres

department: iHealthtech

country: Singapore

institute: National University of Singapore

description:
K4me3_barcodes.txt
K4me3_combined_sorted.bed.gz
K4me3_combined_sorted.bed.gz.tbi

library_source: genomic

data_processing:
Raw .fastqs of single-cells were mapped to the human hg38 reference genome with bowtie2 v2.3.5.1 and the following settings: --end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700
The MarkDuplicates tool from GATK v4.1.4.1 was used to mark and remove duplicate reads while samtools v1.10 was used to index the .bam files. Bedtools v2.27.1 was used to convert .bam files to .beds and .bedgraphs
To create Signac fragment files, individual single-cell .bam files were first processed into .bed files with the following columns: chr, start, end, cell barcode, and a fifth column with the number 1, representing that each row combination only occurred once. Individual bed files were concatenated and sorted with bedtools and indexed with tabix.
Assembly: hg38
Supplementary files format and content: Signac fragment input in .bed format, Signac fragment input index file in .tbi format, barcode file used for Signac analysis, H3K4me3 and H3K27ac separately
Library strategy: snCUT&RUN

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Cells were cultured with RPMI medium supplied by 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin. Medium was replaced every 2-3 days. Cells were cultured in 37°C and 5% CO2 and passaged when cultures reached ~90% confluency. Cells were tested for mycoplasma and positive cell lines were quarantined and treated with PlasmocureTM (InvivoGen) according to the manufacturer’s protocols. Cells were confirmed to be mycoplasma negative two weeks after treatment. Treatment was then stopped, and cells were still confirmed to be mycoplasma negative two weeks after treatment cessation. Cells are only used for experiments after being confirmed to be mycoplasma negative two weeks after treatment cessation.

extract_protocol:
Genomic DNA was extracted using the snCUT&RUN protocol
Libraries were construced with the snCUT&RUN protocol
Libraries were pooled and sequenced with Illumina MiSeq

tag: cell line

tag: cell type

value: Primary patient derived oral cancer cell line

tag: disease state

value: Primary Cisplatin Resistant tumor

tag: antibody


title: HN120PCR, H3K4me3, Rep2, Cell1


title: HN120PCR, H3K4me3, Rep1, Cell186


title: HN120PCR, H3K4me3, Rep1, Cell185


title: HN120PCR, H3K4me3, Rep2, Cell18


title: HN120PCR, H3K4me3, Rep1, Cell187


title: HN120PCR, H3K4me3, Rep1, Cell184


title: HN120PCR, H3K4me3, Rep1, Cell183


title: HN120PCR, H3K4me3, Rep1, Cell182


title: HN120PCR, H3K4me3, Rep1, Cell181


title: HN120PCR, H3K4me3, Rep2, Cell8


title: HN120PCR, H3K4me3, Rep1, Cell178


title: HN120PCR, H3K4me3, Rep2, Cell4


title: HN120PCR, H3K4me3, Rep1, Cell176


title: HN120PCR, H3K4me3, Rep1, Cell175


title: HN120PCR, H3K4me3, Rep1, Cell177


title: HN120PCR, H3K4me3, Rep1, Cell171


title: HN120PCR, H3K4me3, Rep1, Cell172


title: HN120PCR, H3K4me3, Rep1, Cell173


title: HN120PCR, H3K4me3, Rep1, Cell170


title: HN120PCR, H3K4me3, Rep1, Cell167


title: HN120PCR, H3K4me3, Rep1, Cell168


title: HN120PCR, H3K4me3, Rep1, Cell169


title: HN120PCR, H3K4me3, Rep1, Cell161


title: HN120PCR, H3K4me3, Rep1, Cell166


title: HN120PCR, H3K4me3, Rep1, Cell163


title: HN120PCR, H3K4me3, Rep1, Cell164


title: HN120PCR, H3K4me3, Rep1, Cell165


title: HN120PCR, H3K4me3, Rep1, Cell158


title: HN120PCR, H3K4me3, Rep1, Cell160


title: HN120PCR, H3K4me3, Rep1, Cell159


title: HN120PCR, H3K4me3, Rep1, Cell180


title: HN120PCR, H3K4me3, Rep1, Cell156


title: HN120PCR, H3K4me3, Rep1, Cell179


title: HN120PCR, H3K4me3, Rep1, Cell154


title: HN120PCR, H3K4me3, Rep1, Cell155


title: HN120PCR, H3K4me3, Rep1, Cell153


title: HN120PCR, H3K4me3, Rep1, Cell174


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title: HN120PCR, H3K4me3, Rep1, Cell147


title: HN120PCR, H3K4me3, Rep1, Cell149


title: HN120PCR, H3K4me3, Rep1, Cell162


title: HN120PCR, H3K4me3, Rep1, Cell143


title: HN120PCR, H3K4me3, Rep1, Cell146


title: HN120PCR, H3K4me3, Rep1, Cell145


title: HN120PCR, H3K4me3, Rep1, Cell144


title: HN120PCR, H3K4me3, Rep1, Cell141


title: HN120PCR, H3K4me3, Rep1, Cell140


title: HN120PCR, H3K4me3, Rep1, Cell157


title: HN120PCR, H3K4me3, Rep1, Cell139


title: HN120PCR, H3K4me3, Rep1, Cell138


title: HN120PCR, H3K4me3, Rep1, Cell136


title: HN120PCR, H3K4me3, Rep1, Cell134


title: HN120PCR, H3K4me3, Rep1, Cell137


title: HN120PCR, H3K4me3, Rep1, Cell135


title: HN120PCR, H3K4me3, Rep1, Cell133


title: HN120PCR, H3K4me3, Rep1, Cell131


title: HN120PCR, H3K4me3, Rep1, Cell132


title: HN120PCR, H3K4me3, Rep1, Cell130


title: HN120PCR, H3K4me3, Rep1, Cell129


title: HN120PCR, H3K4me3, Rep1, Cell127


title: HN120PCR, H3K4me3, Rep1, Cell125


title: HN120PCR, H3K4me3, Rep1, Cell148


title: HN120PCR, H3K4me3, Rep1, Cell124


title: HN120PCR, H3K4me3, Rep1, Cell122


title: HN120PCR, H3K4me3, Rep1, Cell121


title: HN120PCR, H3K4me3, Rep1, Cell120


title: HN120PCR, H3K4me3, Rep1, Cell142


title: HN120PCR, H3K4me3, Rep1, Cell119


title: HN120PCR, H3K4me3, Rep1, Cell117


title: HN120PCR, H3K4me3, Rep1, Cell115


title: HN120PCR, H3K4me3, Rep1, Cell116


title: HN120PCR, H3K4me3, Rep1, Cell114


title: HN120PCR, H3K4me3, Rep1, Cell112


title: HN120PCR, H3K4me3, Rep1, Cell109


title: HN120PCR, H3K4me3, Rep1, Cell108


title: HN120PCR, H3K4me3, Rep1, Cell111


title: HN120PCR, H3K4me3, Rep1, Cell128


title: HN120PCR, H3K4me3, Rep1, Cell106


title: HN120PCR, H3K4me3, Rep1, Cell126


title: HN120PCR, H3K4me3, Rep1, Cell107


title: HN120PCR, H3K4me3, Rep1, Cell110


title: HN120PCR, H3K4me3, Rep1, Cell103


title: HN120PCR, H3K4me3, Rep1, Cell105


title: HN120PCR, H3K4me3, Rep1, Cell102


title: HN120PCR, H3K4me3, Rep1, Cell123


title: HN120PCR, H3K4me3, Rep1, Cell101


title: HN120PCR, H3K4me3, Rep1, Cell104


title: HN120PCR, H3K4me3, Rep1, Cell99


title: HN120PCR, H3K4me3, Rep1, Cell97


title: HN120PCR, H3K4me3, Rep1, Cell98


title: HN120PCR, H3K4me3, Rep1, Cell118


title: HN120PCR, H3K4me3, Rep1, Cell92


title: HN120PCR, H3K4me3, Rep1, Cell90


title: HN120PCR, H3K4me3, Rep1, Cell88


title: HN120PCR, H3K4me3, Rep1, Cell89


title: HN120PCR, H3K4me3, Rep1, Cell113


title: HN120PCR, H3K4me3, Rep1, Cell91


title: HN120PCR, H3K4me3, Rep1, Cell85


title: HN120PCR, H3K4me3, Rep1, Cell87


title: HN120PCR, H3K4me3, Rep1, Cell86


title: HN120PCR, H3K4me3, Rep1, Cell83


title: HN120PCR, H3K4me3, Rep1, Cell84


title: HN120PCR, H3K4me3, Rep1, Cell80


title: HN120PCR, H3K4me3, Rep1, Cell82


title: HN120PCR, H3K4me3, Rep1, Cell77


title: HN120PCR, H3K4me3, Rep1, Cell72


title: HN120PCR, H3K4me3, Rep1, Cell100


title: HN120PCR, H3K4me3, Rep1, Cell76


title: HN120PCR, H3K4me3, Rep1, Cell71


title: HN120PCR, H3K4me3, Rep1, Cell75


title: HN120PCR, H3K4me3, Rep1, Cell70


title: HN120PCR, H3K4me3, Rep1, Cell79


title: HN120PCR, H3K4me3, Rep1, Cell78


title: HN120PCR, H3K4me3, Rep1, Cell74


title: HN120PCR, H3K4me3, Rep1, Cell68


title: HN120PCR, H3K4me3, Rep1, Cell81


title: HN120PCR, H3K4me3, Rep1, Cell66


title: HN120PCR, H3K4me3, Rep1, Cell65


title: HN120PCR, H3K4me3, Rep1, Cell67


title: HN120PCR, H3K4me3, Rep1, Cell64


title: HN120PCR, H3K4me3, Rep1, Cell73


title: HN120PCR, H3K4me3, Rep1, Cell63


title: HN120PCR, H3K4me3, Rep1, Cell62


title: HN120PCR, H3K4me3, Rep1, Cell60


title: HN120PCR, H3K4me3, Rep1, Cell58


title: HN120PCR, H3K4me3, Rep1, Cell56


title: HN120PCR, H3K4me3, Rep1, Cell59


title: HN120PCR, H3K4me3, Rep1, Cell61


title: HN120PCR, H3K4me3, Rep1, Cell69


title: HN120PCR, H3K4me3, Rep1, Cell55


title: HN120PCR, H3K4me3, Rep1, Cell54


title: HN120PCR, H3K4me3, Rep1, Cell51


title: HN120PCR, H3K4me3, Rep1, Cell48


title: HN120PCR, H3K4me3, Rep1, Cell50


title: HN120PCR, H3K4me3, Rep1, Cell49


title: HN120PCR, H3K4me3, Rep1, Cell45


title: HN120PCR, H3K4me3, Rep1, Cell44


title: HN120PCR, H3K4me3, Rep1, Cell47


title: HN120PCR, H3K4me3, Rep1, Cell46


title: HN120PCR, H3K4me3, Rep1, Cell40


title: HN120PCR, H3K4me3, Rep1, Cell43


title: HN120PCR, H3K4me3, Rep1, Cell38


title: HN120PCR, H3K4me3, Rep1, Cell36


title: HN120PCR, H3K4me3, Rep1, Cell41


title: HN120PCR, H3K4me3, Rep1, Cell37


title: HN120PCR, H3K4me3, Rep1, Cell42


title: HN120PCR, H3K4me3, Rep1, Cell39


title: HN120PCR, H3K4me3, Rep1, Cell35


title: HN120PCR, H3K4me3, Rep1, Cell34


title: HN120PCR, H3K4me3, Rep1, Cell57


title: HN120PCR, H3K4me3, Rep1, Cell33


title: HN120PCR, H3K4me3, Rep1, Cell32


title: HN120PCR, H3K4me3, Rep1, Cell31


title: HN120PCR, H3K4me3, Rep1, Cell27


title: HN120PCR, H3K4me3, Rep1, Cell30


title: HN120PCR, H3K4me3, Rep1, Cell29


title: HN120PCR, H3K4me3, Rep1, Cell26


title: HN120PCR, H3K4me3, Rep1, Cell28


title: HN120PCR, H3K4me3, Rep1, Cell53


title: HN120PCR, H3K4me3, Rep1, Cell52


title: HN120PCR, H3K4me3, Rep1, Cell25


title: HN120PCR, H3K4me3, Rep1, Cell24


title: HN120PCR, H3K4me3, Rep1, Cell23


title: HN120PCR, H3K4me3, Rep1, Cell21


title: HN120PCR, H3K4me3, Rep1, Cell20


title: HN120PCR, H3K4me3, Rep1, Cell22


title: HN120PCR, H3K4me3, Rep1, Cell19


title: HN120PCR, H3K4me3, Rep1, Cell18


title: HN120PCR, H3K4me3, Rep1, Cell17


title: HN120PCR, H3K4me3, Rep1, Cell16


title: HN120PCR, H3K4me3, Rep1, Cell11


title: HN120PCR, H3K4me3, Rep1, Cell12


title: HN120PCR, H3K4me3, Rep1, Cell9


title: HN120PCR, H3K4me3, Rep1, Cell8


title: HN120PCR, H3K4me3, Rep1, Cell13


title: HN120PCR, H3K4me3, Rep1, Cell5


title: HN120PCR, H3K4me3, Rep1, Cell10


title: HN120PCR, H3K4me3, Rep1, Cell14


title: HN120PCR, H3K4me3, Rep1, Cell2


title: HN120PCR, H3K4me3, Rep1, Cell3


title: HN120PCR, H3K4me3, Rep1, Cell1


title: HN120PCR, H3K4me3, Rep1, Cell4


title: HN120PCR, H3K4me3, Rep1, Cell6


title: HN120Met, H3K4me3, Rep2, Cell187

value: Metastatic tumor


title: HN120Met, H3K4me3, Rep2, Cell186


title: HN120Met, H3K4me3, Rep2, Cell188


title: HN120Met, H3K4me3, Rep2, Cell184


title: HN120Met, H3K4me3, Rep2, Cell183


title: HN120Met, H3K4me3, Rep2, Cell185


title: HN120Met, H3K4me3, Rep2, Cell182


title: HN120Met, H3K4me3, Rep2, Cell179


title: HN120Met, H3K4me3, Rep2, Cell180


title: HN120Met, H3K4me3, Rep2, Cell177


title: HN120PCR, H3K4me3, Rep1, Cell15


title: HN120PCR, H3K4me3, Rep1, Cell7


title: HN120Met, H3K4me3, Rep2, Cell178


title: HN120Met, H3K4me3, Rep2, Cell175


title: HN120Met, H3K4me3, Rep2, Cell176


title: HN120Met, H3K4me3, Rep2, Cell173


title: HN120Met, H3K4me3, Rep2, Cell169


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title: HN120Met, H3K4me3, Rep2, Cell171


title: HN120Met, H3K4me3, Rep2, Cell168


title: HN120Met, H3K4me3, Rep2, Cell174


title: HN120Met, H3K4me3, Rep2, Cell167


title: HN120Met, H3K4me3, Rep2, Cell161


title: HN120Met, H3K4me3, Rep2, Cell162


title: HN120Met, H3K4me3, Rep2, Cell165


title: HN120Met, H3K4me3, Rep2, Cell163


title: HN120Met, H3K4me3, Rep2, Cell160


title: HN120Met, H3K4me3, Rep2, Cell166


title: HN120Met, H3K4me3, Rep2, Cell164


title: HN120Met, H3K4me3, Rep2, Cell158


title: HN120Met, H3K4me3, Rep2, Cell159


title: HN120Met, H3K4me3, Rep2, Cell157


title: HN120Met, H3K4me3, Rep2, Cell155


title: HN120Met, H3K4me3, Rep2, Cell181


title: HN120Met, H3K4me3, Rep2, Cell156


title: HN120Met, H3K4me3, Rep2, Cell154


title: HN120Met, H3K4me3, Rep2, Cell152


title: HN120Met, H3K4me3, Rep2, Cell153


title: HN120Met, H3K4me3, Rep2, Cell148


title: HN120Met, H3K4me3, Rep2, Cell150


title: HN120Met, H3K4me3, Rep2, Cell149


title: HN120Met, H3K4me3, Rep2, Cell151


title: HN120Met, H3K4me3, Rep2, Cell146


title: HN120Met, H3K4me3, Rep2, Cell144


title: HN120Met, H3K4me3, Rep2, Cell142


title: HN120Met, H3K4me3, Rep2, Cell141


title: HN120Met, H3K4me3, Rep2, Cell143


title: HN120Met, H3K4me3, Rep2, Cell145


title: HN120Met, H3K4me3, Rep2, Cell139


title: HN120Met, H3K4me3, Rep2, Cell137


title: HN120Met, H3K4me3, Rep2, Cell170


title: HN120Met, H3K4me3, Rep2, Cell147


title: HN120Met, H3K4me3, Rep2, Cell138


title: HN120Met, H3K4me3, Rep2, Cell133


title: HN120Met, H3K4me3, Rep2, Cell134


title: HN120Met, H3K4me3, Rep2, Cell136


title: HN120Met, H3K4me3, Rep2, Cell129


title: HN120Met, H3K4me3, Rep2, Cell132


title: HN120Met, H3K4me3, Rep2, Cell127


title: HN120Met, H3K4me3, Rep2, Cell128


title: HN120Met, H3K4me3, Rep2, Cell125


title: HN120Met, H3K4me3, Rep2, Cell126


title: HN120Met, H3K4me3, Rep2, Cell140


title: HN120Met, H3K4me3, Rep2, Cell130


title: HN120Met, H3K4me3, Rep2, Cell124


title: HN120Met, H3K4me3, Rep2, Cell123


title: HN120Met, H3K4me3, Rep2, Cell120


title: HN120Met, H3K4me3, Rep2, Cell122


title: HN120Met, H3K4me3, Rep2, Cell119


title: HN120Met, H3K4me3, Rep2, Cell121


title: HN120Met, H3K4me3, Rep2, Cell118


title: HN120Met, H3K4me3, Rep2, Cell117


title: HN120Met, H3K4me3, Rep2, Cell135


title: HN120Met, H3K4me3, Rep2, Cell113


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title: HN120Met, H3K4me3, Rep2, Cell131


title: HN120Met, H3K4me3, Rep2, Cell116


title: HN120Met, H3K4me3, Rep2, Cell112


title: HN120Met, H3K4me3, Rep2, Cell111


title: HN120Met, H3K4me3, Rep2, Cell114


title: HN120Met, H3K4me3, Rep2, Cell108


title: HN120Met, H3K4me3, Rep2, Cell106


title: HN120Met, H3K4me3, Rep2, Cell110


title: HN120Met, H3K4me3, Rep2, Cell105


title: HN120Met, H3K4me3, Rep2, Cell109


title: HN120Met, H3K4me3, Rep2, Cell107


title: HN120Met, H3K4me3, Rep2, Cell103


title: HN120Met, H3K4me3, Rep2, Cell99


title: HN120Met, H3K4me3, Rep2, Cell102


title: HN120Met, H3K4me3, Rep2, Cell104


title: HN120Met, H3K4me3, Rep2, Cell97


title: HN120Met, H3K4me3, Rep2, Cell101


title: HN120Met, H3K4me3, Rep2, Cell90


title: HN120Met, H3K4me3, Rep2, Cell100


title: HN120Met, H3K4me3, Rep2, Cell98


title: HN120Met, H3K4me3, Rep2, Cell91


title: HN120Met, H3K4me3, Rep2, Cell87


title: HN120Met, H3K4me3, Rep2, Cell86


title: HN120Met, H3K4me3, Rep2, Cell88


title: HN120Met, H3K4me3, Rep2, Cell85


title: HN120Met, H3K4me3, Rep2, Cell92


title: HN120Met, H3K4me3, Rep2, Cell81


title: HN120Met, H3K4me3, Rep2, Cell84


title: HN120Met, H3K4me3, Rep2, Cell83


title: HN120Met, H3K4me3, Rep2, Cell82


title: HN120Met, H3K4me3, Rep2, Cell71


title: HN120Met, H3K4me3, Rep2, Cell80


title: HN120Met, H3K4me3, Rep2, Cell67


title: HN120Met, H3K4me3, Rep2, Cell78


title: HN120Met, H3K4me3, Rep2, Cell77


title: HN120Met, H3K4me3, Rep2, Cell76


title: HN120Met, H3K4me3, Rep2, Cell73


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title: HN120Met, H3K4me3, Rep2, Cell65


title: HN120Met, H3K4me3, Rep2, Cell89


title: HN120Met, H3K4me3, Rep2, Cell66


title: HN120Met, H3K4me3, Rep2, Cell63


title: HN120Met, H3K4me3, Rep2, Cell64


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title: HN120Met, H3K4me3, Rep2, Cell59


title: HN120Met, H3K4me3, Rep2, Cell62


title: HN120Met, H3K4me3, Rep2, Cell60


title: HN120Met, H3K4me3, Rep2, Cell68


title: HN120Met, H3K4me3, Rep2, Cell58


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title: HN120Met, H3K4me3, Rep2, Cell70


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title: HN120Met, H3K4me3, Rep2, Cell55


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title: HN120Met, H3K4me3, Rep2, Cell52


title: HN120Met, H3K4me3, Rep2, Cell69


title: HN120Met, H3K4me3, Rep2, Cell47


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title: HN120Met, H3K4me3, Rep2, Cell48


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title: HN120Met, H3K4me3, Rep2, Cell51


title: HN120Met, H3K4me3, Rep2, Cell45


title: HN120Met, H3K4me3, Rep2, Cell43


title: HN120Met, H3K4me3, Rep2, Cell72


title: HN120Met, H3K4me3, Rep2, Cell53


title: HN120Met, H3K4me3, Rep2, Cell39


title: HN120Met, H3K4me3, Rep2, Cell37


title: HN120Met, H3K4me3, Rep2, Cell42


title: HN120Met, H3K4me3, Rep2, Cell46


title: HN120Met, H3K4me3, Rep2, Cell40


title: HN120Met, H3K4me3, Rep2, Cell57


title: HN120Met, H3K4me3, Rep2, Cell33


title: HN120Met, H3K4me3, Rep2, Cell41


title: HN120Met, H3K4me3, Rep2, Cell35


title: HN120Met, H3K4me3, Rep2, Cell34


title: HN120Met, H3K4me3, Rep2, Cell31


title: HN120Met, H3K4me3, Rep2, Cell32


title: HN120Met, H3K4me3, Rep2, Cell30


title: HN120Met, H3K4me3, Rep2, Cell27


title: HN120Met, H3K4me3, Rep2, Cell28


title: HN120Met, H3K4me3, Rep2, Cell29


title: HN120Met, H3K4me3, Rep2, Cell26


title: HN120Met, H3K4me3, Rep2, Cell24


title: HN120Met, H3K4me3, Rep2, Cell22


title: HN120Met, H3K4me3, Rep2, Cell38


title: HN120Met, H3K4me3, Rep2, Cell21


title: HN120Met, H3K4me3, Rep2, Cell20


title: HN120Met, H3K4me3, Rep2, Cell19


title: HN120Met, H3K4me3, Rep2, Cell36


title: HN120Met, H3K4me3, Rep2, Cell17


title: HN120Met, H3K4me3, Rep2, Cell15


title: HN120Met, H3K4me3, Rep2, Cell11


title: HN120Met, H3K4me3, Rep2, Cell8


title: HN120Met, H3K4me3, Rep2, Cell12


title: HN120Met, H3K4me3, Rep2, Cell10


title: HN120Met, H3K4me3, Rep2, Cell7


title: HN120Met, H3K4me3, Rep2, Cell9


title: HN120Met, H3K4me3, Rep2, Cell4


title: HN120Met, H3K4me3, Rep2, Cell14


title: HN120Met, H3K4me3, Rep2, Cell13


title: HN120Met, H3K4me3, Rep2, Cell6


title: HN120Met, H3K4me3, Rep2, Cell2


title: HN120Met, H3K4me3, Rep2, Cell5


title: HN120Met, H3K4me3, Rep2, Cell3


title: HN120Met, H3K4me3, Rep2, Cell25


title: HN120Met, H3K4me3, Rep2, Cell1


title: HN120Met, H3K4me3, Rep1, Cell91


title: HN120Met, H3K4me3, Rep2, Cell23


title: HN120Met, H3K4me3, Rep2, Cell18


title: HN120Met, H3K4me3, Rep1, Cell88


title: HN120Met, H3K4me3, Rep1, Cell87


title: HN120Met, H3K4me3, Rep1, Cell89


title: HN120Met, H3K4me3, Rep1, Cell86


title: HN120Met, H3K4me3, Rep2, Cell16


title: HN120Met, H3K4me3, Rep1, Cell85


title: HN120Met, H3K4me3, Rep1, Cell83


title: HN120Met, H3K4me3, Rep1, Cell82


title: HN120Met, H3K4me3, Rep1, Cell81


title: HN120Met, H3K4me3, Rep1, Cell80


title: HN120Met, H3K4me3, Rep1, Cell78


title: HN120Met, H3K4me3, Rep1, Cell92


title: HN120Met, H3K4me3, Rep1, Cell75


title: HN120Met, H3K4me3, Rep1, Cell73


title: HN120Met, H3K4me3, Rep1, Cell71


title: HN120Met, H3K4me3, Rep1, Cell69


title: HN120Met, H3K4me3, Rep1, Cell90


title: HN120Met, H3K4me3, Rep1, Cell74


title: HN120Met, H3K4me3, Rep1, Cell70


title: HN120Met, H3K4me3, Rep1, Cell67


title: HN120Met, H3K4me3, Rep1, Cell68


title: HN120Met, H3K4me3, Rep1, Cell64


title: HN120Met, H3K4me3, Rep1, Cell66


title: HN120Met, H3K4me3, Rep1, Cell65


title: HN120Met, H3K4me3, Rep1, Cell62


title: HN120Met, H3K4me3, Rep1, Cell63


title: HN120Met, H3K4me3, Rep1, Cell60


title: HN120Met, H3K4me3, Rep1, Cell58


title: HN120Met, H3K4me3, Rep1, Cell61


title: HN120Met, H3K4me3, Rep1, Cell57


title: HN120Met, H3K4me3, Rep1, Cell56


title: HN120Met, H3K4me3, Rep1, Cell84


title: HN120Met, H3K4me3, Rep1, Cell76


title: HN120Met, H3K4me3, Rep1, Cell77


title: HN120Met, H3K4me3, Rep1, Cell79


title: HN120Met, H3K4me3, Rep1, Cell55


title: HN120Met, H3K4me3, Rep1, Cell54


title: HN120Met, H3K4me3, Rep1, Cell72


title: HN120Met, H3K4me3, Rep1, Cell51


title: HN120Met, H3K4me3, Rep1, Cell44


title: HN120Met, H3K4me3, Rep1, Cell45


title: HN120Met, H3K4me3, Rep1, Cell52


title: HN120Met, H3K4me3, Rep1, Cell43


title: HN120Met, H3K4me3, Rep1, Cell53


title: HN120Met, H3K4me3, Rep1, Cell59


title: HN120Met, H3K4me3, Rep1, Cell41


title: HN120Met, H3K4me3, Rep1, Cell50


title: HN120Met, H3K4me3, Rep1, Cell38


title: HN120Met, H3K4me3, Rep1, Cell49


title: HN120Met, H3K4me3, Rep1, Cell46


title: HN120Met, H3K4me3, Rep1, Cell47


title: HN120Met, H3K4me3, Rep1, Cell48


title: HN120Met, H3K4me3, Rep1, Cell35


title: HN120Met, H3K4me3, Rep1, Cell30


title: HN120Met, H3K4me3, Rep1, Cell42


title: HN120Met, H3K4me3, Rep1, Cell27


title: HN120Met, H3K4me3, Rep1, Cell37


title: HN120Met, H3K4me3, Rep1, Cell29


title: HN120Met, H3K4me3, Rep1, Cell26


title: HN120Met, H3K4me3, Rep1, Cell34


title: HN120Met, H3K4me3, Rep1, Cell36


title: HN120Met, H3K4me3, Rep1, Cell28


title: HN120Met, H3K4me3, Rep1, Cell40


title: HN120Met, H3K4me3, Rep1, Cell33


title: HN120Met, H3K4me3, Rep1, Cell24


title: HN120Met, H3K4me3, Rep1, Cell32


title: HN120Met, H3K4me3, Rep1, Cell25


title: HN120Met, H3K4me3, Rep1, Cell22


title: HN120Met, H3K4me3, Rep1, Cell23


title: HN120Met, H3K4me3, Rep1, Cell20


title: HN120Met, H3K4me3, Rep1, Cell39


title: HN120Met, H3K4me3, Rep1, Cell19


title: HN120Met, H3K4me3, Rep1, Cell16


title: HN120Met, H3K4me3, Rep1, Cell17


title: HN120Met, H3K4me3, Rep1, Cell18


title: HN120Met, H3K4me3, Rep1, Cell31


title: HN120Met, H3K4me3, Rep1, Cell14


title: HN120Met, H3K4me3, Rep1, Cell21


title: HN120Met, H3K4me3, Rep1, Cell11


title: HN120Met, H3K4me3, Rep1, Cell13


title: HN120Met, H3K4me3, Rep1, Cell10


title: HN120Met, H3K4me3, Rep1, Cell9


title: HN120Met, H3K4me3, Rep1, Cell12


title: HN120Met, H3K4me3, Rep1, Cell5


title: HN120Met, H3K4me3, Rep1, Cell8


title: HN120Met, H3K4me3, Rep1, Cell4


title: HN120Met, H3K4me3, Rep1, Cell3


title: HN120Met, H3K4me3, Rep1, Cell6


title: HN120Met, H3K4me3, Rep1, Cell1


title: HN120Pri, H3K4me3, Rep2, Cell186

value: Primary tumor


title: HN120Pri, H3K4me3, Rep2, Cell187


title: HN120Pri, H3K4me3, Rep2, Cell188


title: HN120Pri, H3K4me3, Rep2, Cell185


title: HN120Met, H3K4me3, Rep1, Cell2


title: HN120Pri, H3K4me3, Rep2, Cell184


title: HN120Pri, H3K4me3, Rep2, Cell181


title: HN120Pri, H3K4me3, Rep2, Cell182


title: HN120Pri, H3K4me3, Rep2, Cell183


title: HN120Pri, H3K4me3, Rep2, Cell180


title: HN120Met, H3K4me3, Rep1, Cell15


title: HN120Pri, H3K4me3, Rep2, Cell177


title: HN120Pri, H3K4me3, Rep2, Cell178


title: HN120Pri, H3K4me3, Rep2, Cell176


title: HN120Pri, H3K4me3, Rep2, Cell175


title: HN120Pri, H3K4me3, Rep2, Cell173


title: HN120Pri, H3K4me3, Rep2, Cell172


title: HN120Pri, H3K4me3, Rep2, Cell174


title: HN120Pri, H3K4me3, Rep2, Cell171


title: HN120Pri, H3K4me3, Rep2, Cell170


title: HN120Pri, H3K4me3, Rep2, Cell168


title: HN120Pri, H3K4me3, Rep2, Cell167


title: HN120Pri, H3K4me3, Rep2, Cell166


title: HN120Pri, H3K4me3, Rep2, Cell169


title: HN120Pri, H3K4me3, Rep2, Cell163


title: HN120Pri, H3K4me3, Rep2, Cell165


title: HN120Pri, H3K4me3, Rep2, Cell164


title: HN120Pri, H3K4me3, Rep2, Cell159


title: HN120Pri, H3K4me3, Rep2, Cell156


title: HN120Pri, H3K4me3, Rep2, Cell179


title: HN120Pri, H3K4me3, Rep2, Cell162


title: HN120Pri, H3K4me3, Rep2, Cell161


title: HN120Pri, H3K4me3, Rep2, Cell153


title: HN120Pri, H3K4me3, Rep2, Cell160


title: HN120Pri, H3K4me3, Rep2, Cell157


title: HN120Pri, H3K4me3, Rep2, Cell158


title: HN120Pri, H3K4me3, Rep2, Cell152


title: HN120Pri, H3K4me3, Rep2, Cell155


title: HN120Pri, H3K4me3, Rep2, Cell151


title: HN120Pri, H3K4me3, Rep2, Cell150


title: HN120Pri, H3K4me3, Rep2, Cell154


title: HN120Pri, H3K4me3, Rep2, Cell148


title: HN120Pri, H3K4me3, Rep2, Cell146


title: HN120Pri, H3K4me3, Rep2, Cell147


title: HN120Pri, H3K4me3, Rep2, Cell149


title: HN120Pri, H3K4me3, Rep2, Cell143


title: HN120Pri, H3K4me3, Rep2, Cell141


title: HN120Pri, H3K4me3, Rep2, Cell142


title: HN120Pri, H3K4me3, Rep2, Cell140


title: HN120Met, H3K4me3, Rep1, Cell7


title: HN120Pri, H3K4me3, Rep2, Cell139


title: HN120Pri, H3K4me3, Rep2, Cell138


title: HN120Pri, H3K4me3, Rep2, Cell137


title: HN120Pri, H3K4me3, Rep2, Cell136


title: HN120Pri, H3K4me3, Rep2, Cell135


title: HN120Pri, H3K4me3, Rep2, Cell133


title: HN120Pri, H3K4me3, Rep2, Cell132


title: HN120Pri, H3K4me3, Rep2, Cell131


title: HN120Pri, H3K4me3, Rep2, Cell134


title: HN120Pri, H3K4me3, Rep2, Cell126


title: HN120Pri, H3K4me3, Rep2, Cell127


title: HN120Pri, H3K4me3, Rep2, Cell130


title: HN120Pri, H3K4me3, Rep2, Cell145


title: HN120Pri, H3K4me3, Rep2, Cell144


title: HN120Pri, H3K4me3, Rep2, Cell123


title: HN120Pri, H3K4me3, Rep2, Cell129


title: HN120Pri, H3K4me3, Rep2, Cell124


title: HN120Pri, H3K4me3, Rep2, Cell118


title: HN120Pri, H3K4me3, Rep2, Cell121


title: HN120Pri, H3K4me3, Rep2, Cell116


title: HN120Pri, H3K4me3, Rep2, Cell125


title: HN120Pri, H3K4me3, Rep2, Cell122


title: HN120Pri, H3K4me3, Rep2, Cell119


title: HN120Pri, H3K4me3, Rep2, Cell120


title: HN120Pri, H3K4me3, Rep2, Cell117


title: HN120Pri, H3K4me3, Rep2, Cell113


title: HN120Pri, H3K4me3, Rep2, Cell114


title: HN120Pri, H3K4me3, Rep2, Cell110


title: HN120Pri, H3K4me3, Rep2, Cell112


title: HN120Pri, H3K4me3, Rep2, Cell111


title: HN120Pri, H3K4me3, Rep2, Cell109


title: HN120Pri, H3K4me3, Rep2, Cell108


title: HN120Pri, H3K4me3, Rep2, Cell128


title: HN120Pri, H3K4me3, Rep2, Cell107


title: HN120Pri, H3K4me3, Rep2, Cell106


title: HN120Pri, H3K4me3, Rep2, Cell104


title: HN120Pri, H3K4me3, Rep2, Cell105


title: HN120Pri, H3K4me3, Rep2, Cell103


title: HN120Pri, H3K4me3, Rep2, Cell102


title: HN120Pri, H3K4me3, Rep2, Cell100


title: HN120Pri, H3K4me3, Rep2, Cell99


title: HN120Pri, H3K4me3, Rep2, Cell101


title: HN120Pri, H3K4me3, Rep2, Cell92


title: HN120Pri, H3K4me3, Rep2, Cell97


title: HN120Pri, H3K4me3, Rep2, Cell98


title: HN120Pri, H3K4me3, Rep2, Cell87


title: HN120Pri, H3K4me3, Rep2, Cell115


title: HN120Pri, H3K4me3, Rep2, Cell89


title: HN120Pri, H3K4me3, Rep2, Cell86


title: HN120Pri, H3K4me3, Rep2, Cell91


title: HN120Pri, H3K4me3, Rep2, Cell90


title: HN120Pri, H3K4me3, Rep2, Cell88


title: HN120Pri, H3K4me3, Rep2, Cell84


title: HN120Pri, H3K4me3, Rep2, Cell83


title: HN120Pri, H3K4me3, Rep2, Cell85


title: HN120Pri, H3K4me3, Rep2, Cell81


title: HN120Pri, H3K4me3, Rep2, Cell82


title: HN120Pri, H3K4me3, Rep2, Cell79


title: HN120Pri, H3K4me3, Rep2, Cell80


title: HN120Pri, H3K4me3, Rep2, Cell77


title: HN120Pri, H3K4me3, Rep2, Cell76


title: HN120Pri, H3K4me3, Rep2, Cell73


title: HN120Pri, H3K4me3, Rep2, Cell74


title: HN120Pri, H3K4me3, Rep2, Cell72


title: HN120Pri, H3K4me3, Rep2, Cell69


title: HN120Pri, H3K4me3, Rep2, Cell71


title: HN120Pri, H3K4me3, Rep2, Cell68


title: HN120Pri, H3K4me3, Rep2, Cell67


title: HN120Pri, H3K4me3, Rep2, Cell58


title: HN120Pri, H3K4me3, Rep2, Cell65


title: HN120Pri, H3K4me3, Rep2, Cell66


title: HN120Pri, H3K4me3, Rep2, Cell64


title: HN120Pri, H3K4me3, Rep2, Cell63


title: HN120Pri, H3K4me3, Rep2, Cell59


title: HN120Pri, H3K4me3, Rep2, Cell57


title: HN120Pri, H3K4me3, Rep2, Cell62


title: HN120Pri, H3K4me3, Rep2, Cell55


title: HN120Pri, H3K4me3, Rep2, Cell61


title: HN120Pri, H3K4me3, Rep2, Cell54


title: HN120Pri, H3K4me3, Rep2, Cell53


title: HN120Pri, H3K4me3, Rep2, Cell78


title: HN120Pri, H3K4me3, Rep2, Cell60


title: HN120Pri, H3K4me3, Rep2, Cell56


title: HN120Pri, H3K4me3, Rep2, Cell75


title: HN120Pri, H3K4me3, Rep2, Cell70


title: HN120Pri, H3K4me3, Rep2, Cell52


title: HN120Pri, H3K4me3, Rep2, Cell50


title: HN120Pri, H3K4me3, Rep2, Cell51


title: HN120Pri, H3K4me3, Rep2, Cell49


title: HN120Pri, H3K4me3, Rep2, Cell48


title: HN120Pri, H3K4me3, Rep2, Cell45


title: HN120Pri, H3K4me3, Rep2, Cell47


title: HN120Pri, H3K4me3, Rep2, Cell44


title: HN120Pri, H3K4me3, Rep2, Cell46


title: HN120Pri, H3K4me3, Rep2, Cell43


title: HN120Pri, H3K4me3, Rep2, Cell41


title: HN120Pri, H3K4me3, Rep2, Cell40


title: HN120Pri, H3K4me3, Rep2, Cell42


title: HN120Pri, H3K4me3, Rep2, Cell39


title: HN120Pri, H3K4me3, Rep2, Cell37


title: HN120Pri, H3K4me3, Rep2, Cell36


title: HN120Pri, H3K4me3, Rep2, Cell35


title: HN120Pri, H3K4me3, Rep2, Cell33


title: HN120Pri, H3K4me3, Rep2, Cell34


title: HN120Pri, H3K4me3, Rep2, Cell32


title: HN120Pri, H3K4me3, Rep2, Cell31


title: HN120Pri, H3K4me3, Rep2, Cell27


title: HN120Pri, H3K4me3, Rep2, Cell30


title: HN120Pri, H3K4me3, Rep2, Cell29


title: HN120Pri, H3K4me3, Rep2, Cell25


title: HN120Pri, H3K4me3, Rep2, Cell22


title: HN120Pri, H3K4me3, Rep2, Cell20


title: HN120Pri, H3K4me3, Rep2, Cell23


title: HN120Pri, H3K4me3, Rep2, Cell21


title: HN120Pri, H3K4me3, Rep2, Cell24


title: HN120Pri, H3K4me3, Rep2, Cell18


title: HN120Pri, H3K4me3, Rep2, Cell15


title: HN120Pri, H3K4me3, Rep2, Cell17


title: HN120Pri, H3K4me3, Rep2, Cell14


title: HN120Pri, H3K4me3, Rep2, Cell13


title: HN120Pri, H3K4me3, Rep2, Cell12


title: HN120Pri, H3K4me3, Rep2, Cell38


title: HN120Pri, H3K4me3, Rep2, Cell11


title: HN120Pri, H3K4me3, Rep2, Cell9


title: HN120Pri, H3K4me3, Rep2, Cell10


title: HN120Pri, H3K4me3, Rep2, Cell26


title: HN120Pri, H3K4me3, Rep2, Cell28


title: HN120Pri, H3K4me3, Rep2, Cell7


title: HN120Pri, H3K4me3, Rep2, Cell5


title: HN120Pri, H3K4me3, Rep2, Cell6


title: HN120Pri, H3K4me3, Rep2, Cell4


title: HN120Pri, H3K4me3, Rep2, Cell3


title: HN120Pri, H3K4me3, Rep2, Cell1


title: HN120Pri, H3K4me3, Rep2, Cell2


title: HN120Pri, H3K4me3, Rep2, Cell16


title: HN120Pri, H3K4me3, Rep1, Cell92


title: Wild-type 1

city: Sevilla

first: Marta

last: Pulido-Sánchez

state: Sevilla

address: Ctra. de Utrera Km.1, Sevilla

country: Spain

institute: Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide

library_source: transcriptomic

data_processing:
Adapter-trimming and pre-filtering of the RNA-Seq raw reads was carried out using the FASTQ Toolkit v.1.0.0. Quality of the reads was checked with FastQC and then mapped to the P. putida KT2440 reference genome (GenBank: NC_002947.4) using Bowtie2 v.2.3.5.1. Mapped data were converted to BAM files using Samtools v1.11 and gene counts were calculated with featureCounts (Subread package) using default parameters against the Pseudomonas Genome Database gene annotation file for Pseudonas putida KT2440 (TIGR).
Assembly: GCF_000007565.2
Supplementary files format and content: Comma-delimited text file containing raw counts for each sample

molecule: total RNA

organism: Pseudomonas putida

growth_protocol: Overnight cultures of three biological replicates of wild-type P. putida KT2440tel and the ppGpp0 mutant were 1:100-diluted in fress lysogeny broth (LB), and incubated at 30ºC and 180 rpm shaking until stationary phase (OD600=4.0).

extract_protocol:
Aliquots of 500 µL were harvested by centrifugation, frozen with liquid nitrogen and stored at -80 ºC. Cell pellets were resuspended in 1 mL of TRIsure™ (Bioline) and incubated for 10 min at 60 ºC. Samples were centrifuged and supernatants were transferred to Phase Lock Gel™ tubes (5PRIME). Each tube was added 200 µL of chloroform, mixed by inversion, kept in ice for 15 min and then centrifuged. Next, tubes were added 400 µL of phenol:chloroform:isoamyl alcohol (25:24:1) and then centrifuged. Aqueous phase was transferred to a new tube and 1 volume of isopropanol was added, mixed by inversion and kept in ice for 10 min. Tubes were centrifuged and pellets were washed with 1 mL of cold ethanol 70 % (v/v). Pellets were dried at room temperature and resuspended in RNAse-free water. Remaining DNA was degraded by treatment with TURBO™ DNase kit (Thermo Fischer) and purified using the RNAeasy Mini Kit (QIAGEN) following the manufacturers' instructions. Complete absence of DNA traces was checked by PCR. Samples containing 5 µg of total RNA were sent to the CABIMER Genomics Facility (Seville, Spain).
Depletion of rRNA and preparation of cDNA libraries were carried out using the Illumina Stranded TOTAL RNA preparation RIBO-ZERO PLUS kit. Libraries were normalized to 0.5 nM, equimolar-mixed and sequenced using an Illumina® NextSeq™ 500 system with a Mid-Output flow cell to obtain 2 x 75 bp length paired-end reads. Libraries are fr-firstranded.

tag: strain


title: ppGpp0 3


title: Wild-type 2


title: ΔflgM/Psal-fliA 3

growth_protocol: Overnight cultures of three biological replicates of the P. putida KT2442-derivatives ΔfliA and ΔflgM/Psal-fliA strains were 1:500-diluted in fress lysogeny broth (LB) supplemented with 2 mM sodium salicylate, and incubated at 30ºC and 180 rpm shaking until exponential phase (OD600=0.3).

extract_protocol:
Aliquots of 1 mL were harvested by centrifugation, frozen with liquid nitrogen and stored at -80 ºC. Cell pellets were resuspended in 1 mL of TRIsure™ (Bioline) and incubated for 10 min at 60 ºC. Samples were centrifuged and supernatants were transferred to Phase Lock Gel™ tubes (5PRIME). Each tube was added 200 µL of chloroform, mixed by inversion, kept in ice for 15 min and then centrifuged. Next, tubes were added 400 µL of phenol:chloroform:isoamyl alcohol (25:24:1) and then centrifuged. Aqueous phase was transferred to a new tube and 1 volume of isopropanol was added, mixed by inversion and kept in ice for 10 min. Tubes were centrifuged and pellets were washed with 1 mL of cold ethanol 70 % (v/v). Pellets were dried at room temperature and resuspended in RNAse-free water. Remaining DNA was degraded by treatment with TURBO™ DNase kit (Thermo Fischer) and purified using the RNAeasy Mini Kit (QIAGEN) following the manufacturers' instructions. Complete absence of DNA traces was checked by PCR. Samples containing 5 µg of total RNA were sent to the CABIMER Genomics Facility (Seville, Spain).
Depletion of rRNA and preparation of cDNA libraries were carried out using the Illumina Stranded TOTAL RNA preparation RIBO-ZERO PLUS kit. Libraries were normalized to 0.5 nM, equimolar-mixed and sequenced using an Illumina® NextSeq™ 500 system with a Mid-Output flow cell to obtain 2 x 75 bp length paired-end reads. Libraries are fr-firstranded.


title: ppGpp0 2


title: ppGpp0 1


title: HN120Pri, H3K4me3, Rep2, Cell19


title: ΔflgM/Psal-fliA 1


title: ΔflgM/Psal-fliA 2


title: HN120Pri, H3K4me3, Rep1, Cell91


title: ΔfliA 3


title: HN120Pri, H3K4me3, Rep1, Cell88


title: ΔfliA 1


title: ΔfliA 2


title: HN120Pri, H3K4me3, Rep2, Cell8


title: HN120Pri, H3K4me3, Rep1, Cell85


title: Wild-type 3


title: MuSCs, old NAM/PN pool 4

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

data_processing:
Sequencing raw data (bcl) were demultiplexed on Instrument with Dragen vers 3.10.11
The fastq files were aligned against the reference genome by RNAstar v2.5.3a.
The raw sequencing counts per gene were generated using htseq_count v2.16.2 using Mus_musculus.GRCm38.101.gtf
Assembly: GRCm38
Supplementary files format and content: raw_count_s8g55487_OldCells.csv (comma-separated file containing count data per gene (row) per mouse (column))

organism: Mus musculus

source_name: muscle stem cells

growth_protocol: After FACS isolation, MuSC were seeded in Growth Medium containing the treatment. Culture conditions are maintained for 3 days in a humidified incubator at 37 °C in 5% CO2

extract_protocol:
RNA was extracted using RNAdvance Tissue Kit (Beckman Coulter). Quality control was performed with Fragment Analyzer (Advanced Analytical).
Libraries were synthesized using QuantSeq 3' mRNA-Seq V2 Library Prep Kit FWD with UDI(Lexogen, 193.384) QuantSeqLibraries were quantified with the Quant-iT Picogreen (Invitrogen, 10545213) on a FilterMax F3 (Molecular Devices, F3). Size pattern was assessed with Fragment Analyzer-96 with the DNF-474-0500 High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies, DNF-474-0500).
Libraries (Average size: 350 bp) were pooled at an equimolar ratio and clustered at a concentration of 650 pM on a P3 50 flow cell

treatment_protocol: Cells were seeded in growth medium containing, the combination NAM/PN was added to the cells at a final concentration of 1mM. 1% DMSO was used as the vehicle condition.

value: muscle stem cells

tag: treatment

value: NAM/PN

tag: age

value: Old

tag: pool id


title: HN120Pri, H3K4me3, Rep1, Cell86


title: HN120Pri, H3K4me3, Rep1, Cell84


title: MuSCs, old NAM/PN pool 3


title: HN120Pri, H3K4me3, Rep1, Cell83


title: HN120Pri, H3K4me3, Rep1, Cell90


title: HN120Pri, H3K4me3, Rep1, Cell89


title: HN120Pri, H3K4me3, Rep1, Cell82


title: MuSCs, old control pool 3

value: Control


title: HN120Pri, H3K4me3, Rep1, Cell80


title: MuSCs, old NAM/PN pool 2


title: HN120Pri, H3K4me3, Rep1, Cell87


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, ORM12h, zt15, replicate 5

city: BORDEAUX

first: jean-christophe

last: Helbling

state: --None--

address: Université de Bordeaux - INRAE, Rue Leo Saignat, 146

department: Alimentation humaine

country: France

institute: INRAE

data_processing:
workflow Nextflow (v21.10.6) and nf-core/rnaseq (v3.6) pipeline onto genotoul bioinformatics platform Toulouse
Sequence reads were trimmed for adaptor/low quality sequence using trimgalore (v0.6.7) and cutadapt (v3.4)
Trimmed sequence reads were mapped to GRCm39/mm109 using HISAT2 aligner (v2.2.0) and reads mapped to unique transcripts were counted with FeatureCounts (Subread v2.0.3) annotation module
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Hippocampus

extract_protocol:
RNA was harvested using pS6-TRAP protocol. 50ng of TRAP purified mRNA was used for the construction of sequencing libraries.
TRAP-mRNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep (Illumina, 20040534) and IDT for Illumina RNA UD Indexes Set B and Set C (Illumina, 20040554 and 20040555) following manufactured's protocols

tag: tissue

value: Hippocampus

tag: genotype

value: WT

tag: diet

tag: time

value: ORM training +12h


title: HN120Pri, H3K4me3, Rep1, Cell77


title: HN120Pri, H3K4me3, Rep1, Cell79


title: HN120Pri, H3K4me3, Rep1, Cell81


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, ORM12h, zt15, replicate 6


title: MuSCs, old control pool 2


title: MuSCs, old control pool 4


title: MuSCs, old control pool 1


title: HN120Pri, H3K4me3, Rep1, Cell72


title: HN120Pri, H3K4me3, Rep1, Cell74


title: HN120Pri, H3K4me3, Rep1, Cell78


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, ORM12h, zt15, replicate 2


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, ORM12h, zt15, replicate 3


title: HN120Pri, H3K4me3, Rep1, Cell71


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, ORM12h, zt15, replicate 1


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, Home cage, zt15, replicate 5

value: Home Cage


title: HN120Pri, H3K4me3, Rep1, Cell73


title: HN120Pri, H3K4me3, Rep1, Cell70


title: HN120Pri, H3K4me3, Rep1, Cell75


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, Home cage, zt15, replicate 4


title: MuSCs, old NAM/PN pool 1


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, Home cage, zt15, replicate 3


title: HN120Pri, H3K4me3, Rep1, Cell69


title: HN120Pri, H3K4me3, Rep1, Cell76


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, ORM12h, zt15, replicate 4


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, Home cage, zt15, replicate 1


title: Hippocampus, High Fat High Sugar, ad libitum, ORM12h, zt15, replicate 6

value: High Fat High Sugar ad libitum


title: HN120Pri, H3K4me3, Rep1, Cell67


title: HN120Pri, H3K4me3, Rep1, Cell65


title: Hippocampus, High Fat High Sugar, ad libitum, ORM12h, zt15, replicate 4


title: Hippocampus, High Fat High Sugar, ad libitum, ORM12h, zt15, replicate 3


title: HN120Pri, H3K4me3, Rep1, Cell64


title: HN120Pri, H3K4me3, Rep1, Cell63


title: HN120Pri, H3K4me3, Rep1, Cell62


title: Hippocampus, High Fat High Sugar, ad libitum, ORM12h, zt15, replicate 2


title: Hippocampus, High Fat High Sugar, ad libitum, ORM12h, zt15, replicate 1


title: HN120Pri, H3K4me3, Rep1, Cell61


title: HN120Pri, H3K4me3, Rep1, Cell59


title: Hippocampus, High Fat High Sugar, ad libitum, Home cage, zt15, replicate 6


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, Home cage, zt15, replicate 2


title: HN120Pri, H3K4me3, Rep1, Cell60


title: HN120Pri, H3K4me3, Rep1, Cell68


title: Hippocampus, High Fat High Sugar, ad libitum, Home cage, zt15, replicate 5


title: HN120Pri, H3K4me3, Rep1, Cell58


title: Hippocampus, High Fat High Sugar, ad libitum, Home cage, zt15, replicate 4


title: Hippocampus, High Fat High Sugar, ad libitum, Home cage, zt15, replicate 3


title: HN120Pri, H3K4me3, Rep1, Cell57


title: Hippocampus, High Fat High Sugar, ad libitum, Home cage, zt15, replicate 1


title: HN120Pri, H3K4me3, Rep1, Cell56


title: HN120Pri, H3K4me3, Rep1, Cell55


title: Hippocampus, Normal Chow, ad libitum, ORM12h, zt15, replicate 6

value: Normal Chow ad libitum


title: HN120Pri, H3K4me3, Rep1, Cell54


title: Hippocampus, High Fat High Sugar, ad libitum, ORM12h, zt15, replicate 5


title: HN120Pri, H3K4me3, Rep1, Cell53


title: Hippocampus, Normal Chow, ad libitum, ORM12h, zt15, replicate 4


title: Hippocampus, Normal Chow, ad libitum, ORM12h, zt15, replicate 5


title: HN120Pri, H3K4me3, Rep1, Cell66


title: HN120Pri, H3K4me3, Rep1, Cell51


title: HN120Pri, H3K4me3, Rep1, Cell52


title: Hippocampus, Normal Chow, ad libitum, ORM12h, zt15, replicate 3


title: HN120Pri, H3K4me3, Rep1, Cell50


title: Hippocampus, Normal Chow, ad libitum, ORM12h, zt15, replicate 1


title: HN120Pri, H3K4me3, Rep1, Cell48


title: Hippocampus, Normal Chow, ad libitum, Home cage, zt15, replicate 6


title: HN120Pri, H3K4me3, Rep1, Cell49


title: Hippocampus, Normal Chow, ad libitum, Home cage, zt15, replicate 5


title: HN120Pri, H3K4me3, Rep1, Cell47


title: Hippocampus, High Fat High Sugar, ad libitum, Home cage, zt15, replicate 2


title: Hippocampus, Normal Chow, ad libitum, Home cage, zt15, replicate 4


title: HN120Pri, H3K4me3, Rep1, Cell45


title: Hippocampus, Normal Chow, ad libitum, Home cage, zt15, replicate 2


title: Hippocampus, Normal Chow, ad libitum, Home cage, zt15, replicate 1


title: HN120Pri, H3K4me3, Rep1, Cell43


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, ORM1h, zt3, replicate 6

value: ORM training +1h


title: HN120Pri, H3K4me3, Rep1, Cell46


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, ORM1h, zt3, replicate 5


title: Hippocampus, Normal Chow, ad libitum, Home cage, zt15, replicate 3


title: HN120Pri, H3K4me3, Rep1, Cell41


title: HN120Pri, H3K4me3, Rep1, Cell44


title: HN120Pri, H3K4me3, Rep1, Cell42


title: HN120Pri, H3K4me3, Rep1, Cell40


title: Hippocampus, Normal Chow, ad libitum, ORM12h, zt15, replicate 2


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, ORM1h, zt3, replicate 3


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, ORM1h, zt3, replicate 4


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, ORM1h, zt3, replicate 1


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, Home cage, zt3, replicate 6


title: HN120Pri, H3K4me3, Rep1, Cell38


title: HN120Pri, H3K4me3, Rep1, Cell39


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, Home cage, zt3, replicate 5


title: HN120Pri, H3K4me3, Rep1, Cell35


title: HN120Pri, H3K4me3, Rep1, Cell37


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, Home cage, zt3, replicate 3


title: HN120Pri, H3K4me3, Rep1, Cell33


title: HN120Pri, H3K4me3, Rep1, Cell36


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, Home cage, zt3, replicate 1


title: Hippocampus, High Fat High Sugar, ad libitum, ORM1h, zt3, replicate 6


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, Home cage, zt3, replicate 4


title: Hippocampus, High Fat High Sugar, ad libitum, ORM1h, zt3, replicate 5


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, ORM1h, zt3, replicate 2


title: Hippocampus, High Fat High Sugar Time Restricted Feeding, ad libitum, Home cage, zt3, replicate 2


title: HN120Pri, H3K4me3, Rep1, Cell30


title: Hippocampus, High Fat High Sugar, ad libitum, ORM1h, zt3, replicate 2


title: Hippocampus, High Fat High Sugar, ad libitum, ORM1h, zt3, replicate 3


title: HN120Pri, H3K4me3, Rep1, Cell26


title: Hippocampus, High Fat High Sugar, ad libitum, ORM1h, zt3, replicate 1


title: HN120Pri, H3K4me3, Rep1, Cell32


title: HN120Pri, H3K4me3, Rep1, Cell29


title: Hippocampus, High Fat High Sugar, ad libitum, Home cage, zt3, replicate 6


title: Hippocampus, High Fat High Sugar, ad libitum, ORM1h, zt3, replicate 4


title: HN120Pri, H3K4me3, Rep1, Cell27


title: HN120Pri, H3K4me3, Rep1, Cell28


title: HN120Pri, H3K4me3, Rep1, Cell31


title: HN120Pri, H3K4me3, Rep1, Cell22


title: HN120Pri, H3K4me3, Rep1, Cell25


title: HN120Pri, H3K4me3, Rep1, Cell24


title: Hippocampus, High Fat High Sugar, ad libitum, Home cage, zt3, replicate 1


title: HN120Pri, H3K4me3, Rep1, Cell34


title: HN120Pri, H3K4me3, Rep1, Cell21


title: Hippocampus, High Fat High Sugar, ad libitum, Home cage, zt3, replicate 2


title: Hippocampus, High Fat High Sugar, ad libitum, Home cage, zt3, replicate 5


title: Hippocampus, Normal Chow, ad libitum, ORM1h, zt3, replicate 5


title: HN120Pri, H3K4me3, Rep1, Cell19


title: HN120Pri, H3K4me3, Rep1, Cell18


title: Hippocampus, High Fat High Sugar, ad libitum, Home cage, zt3, replicate 4


title: HN120Pri, H3K4me3, Rep1, Cell17


title: Hippocampus, Normal Chow, ad libitum, ORM1h, zt3, replicate 6


title: HN120Pri, H3K4me3, Rep1, Cell23


title: Hippocampus, Normal Chow, ad libitum, ORM1h, zt3, replicate 4


title: HN120Pri, H3K4me3, Rep1, Cell14


title: Hippocampus, High Fat High Sugar, ad libitum, Home cage, zt3, replicate 3


title: HN120Pri, H3K4me3, Rep1, Cell12


title: HN120Pri, H3K4me3, Rep1, Cell11


title: HN120Pri, H3K4me3, Rep1, Cell20


title: Hippocampus, Normal Chow, ad libitum, Home cage, zt3, replicate 4


title: Hippocampus, Normal Chow, ad libitum, ORM1h, zt3, replicate 3


title: HN120Pri, H3K4me3, Rep1, Cell16


title: Hippocampus, Normal Chow, ad libitum, Home cage, zt3, replicate 3


title: Hippocampus, Normal Chow, ad libitum, ORM1h, zt3, replicate 2


title: HN120Pri, H3K4me3, Rep1, Cell15


title: Hippocampus, Normal Chow, ad libitum, Home cage, zt3, replicate 1


title: HN120Pri, H3K4me3, Rep1, Cell8


title: HN120Pri, H3K4me3, Rep1, Cell7


title: HN120Pri, H3K4me3, Rep1, Cell13


title: Hippocampus, Normal Chow, ad libitum, ORM1h, zt3, replicate 1


title: Donor8913_PN

data_processing:
Sequencing raw data (bcl) were demultiplexed and transformed in fastq files using cassava v1.8.2.
The fastq files were aligned against the reference genome by RNAstar v2.5.3a.
The raw sequencing counts per gene were generated using htseq_count v2.16.2 using Homo_sapiens.GRCh38.101.gtf
Assembly: GRCh38
Supplementary files format and content: raw_count_s20g60671_HSMM.csv
Supplementary files format and content: comma-separated file containing count data per gene (row) per sample (column)

source_name: Human Skeletal Muscle Myoblasts

growth_protocol: hMPs were expanded in Skeletal Muscle Cell Growth Medium (AmsBio, SKM-M) in a humidified incubator at 37 °C in 5% CO2

extract_protocol:
RNA was extracted using RNAdvance Tissue Kit (Beckman Coulter). Quality control was performed with Fragment Analyzer (Advanced Analytical).
Libraries were quantified with the Quant-iT Picogreen (Invitrogen, 10545213) on a FilterMax F3 (Molecular Devices, F3). Size pattern was assessed with Fragment Analyzer-96 with the DNF-474-0500 High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies, DNF-474-0500).
Libraries (Average size: 350 bp) were pooled at an equimolar ratio and clustered at a concentration of 650 pM on a single read sequencing flow cell.

treatment_protocol: 24 hours after cell seeding, NAM, PN or the combination (NAM/PN) were added to the cells at a final concentration of 1mM. 1% DMSO was used as the vehicle condition.

value: Human Skeletal Muscle Myoblasts

tag: donor

tag: Sex

value: female

value: PN


title: HN120Pri, H3K4me3, Rep1, Cell4

value: Primary patient derived oral cancer cell line


title: Hippocampus, Normal Chow, ad libitum, Home cage, zt3, replicate 6


title: Hippocampus, Normal Chow, ad libitum, Home cage, zt3, replicate 5


title: MuSCs_HC_CD56pos_rep3

type: RNA

city: Lyon

first: Benedicte

last: Chazaud

address: 8 Avenue Rockefeller

department: Institut NeuroMyoGène

institute: Université Claude Bernard Lyon 1

description: Gene expression of CD56npos MuSCs from healthy control patient n3

hyb_protocol: Agilent protocol

scan_protocol: Agilent protocol

data_processing: Agilent protocol

source_name: Healthy Control MuSCs CD56pos fraction n3

label_protocol: Agilent protocol

growth_protocol: Primary cells were cultured in growth medium as in Gitiaux et al. (Arthritis Rheumatol. 2018 70:134-145. doi: 10.1002/art.40328), in Ham’s F-12 medium (Gibco) containing 15% fetal bovine serum.

extract_protocol: Total RNAs were extracted using NucleoSpin® RNA Plus XS kit (Macherey-Nagel #740990.50).

treatment_protocol: Immuno-magnetic cell sorting. Cells were trypsinized, centrifuged and resuspended in 170 µl of magnetic-activated cell sorting (MACS) buffer (Phosphate-Buffered Saline solution (PBS) containing 5% Bovine Serum Albumin (BSA, Sigma #A9647), 1 mol/l of Ethylenediaminetetraacetic Acid Disodium (EDTA, Sigma #ED2SS). Thirty µl of superparamagnetic microbeads conjugated to a CD56 primary antibody (Miltenyi #130-050-401) was mixed with the cell suspension and incubated for 30 min at 4 °C. After a wash with MACS buffer, the cell suspension was passed through a 30 µm filter (Miltenyi #130-041-407) and dripped into a LC column (Miltenyi #130-042-202) held in a MiniMACS magnetic separation unit (Miltenyi). Eluted cells were recovered as CD56neg cells. Column was then removed from the magnetic separation unit, and flushed with MACS buffer to recover CD56pos cells.

value: Skeletal Muscle

tag: gender

value: male

tag: diagnostic

value: healthy condition


title: Donor7_ComboNAM-PN

value: NAM and PN


title: HN120Pri, H3K4me3, Rep1, Cell10

value: Primary tumor


title: HN120Pri, H3K4me3, Rep1, Cell9


title: MuSCs_HC_CD56neg_rep3

description: Gene expression of CD56neg MuSCs from healthy control patient n3

source_name: Healthy Control MuSCs CD56neg fraction n3


title: Donor7_PN


title: Donor8913_NAM

value: NAM


title: Donor512_CTRL

value: Vehicle


title: Donor512_NAM


title: Hippocampus, Normal Chow, ad libitum, Home cage, zt3, replicate 2

value: Hippocampus

value: WT


title: Donor8913_CTRL


title: MuSCs_HC_CD56neg_rep1

description: Gene expression of CD56neg MuSCs from healthy control patient n1

source_name: Healthy Control MuSCs CD56neg fraction n1


title: HN120Pri, H3K4me3, Rep1, Cell5


title: MuSCs_HC_CD56neg_rep2

description: Gene expression of CD56neg MuSCs from healthy control patient n2

source_name: Healthy Control MuSCs CD56neg fraction n2


title: MuSCs_HC_CD56pos_rep1

description: Gene expression of CD56npos MuSCs from healthy control patient n1

source_name: Healthy Control MuSCs CD56pos fraction n1


title: HN120Pri, H3K4me3, Rep1, Cell3


title: HN120Pri, H3K4me3, Rep1, Cell6


title: Donor4_NAM


title: Donor7_NAM


title: HN120Pri, H3K4me3, Rep1, Cell2


title: Donor8913_ComboNAM-PN


title: MuSCs_DMD_CD56neg_rep3

description: Gene expression of CD56neg MuSCs from DMD patient n3

source_name: DMD MuSCs CD56neg fraction n3

value: pathological condition (DMD)


title: Donor7_CTRL


title: MuSCs_DMD_CD56pos_rep2

description: Gene expression of CD56npos MuSCs from DMD patient n2

source_name: DMD MuSCs CD56pos fraction n2


title: HN120Pri, H3K4me3, Rep1, Cell1


title: Donor4_ComboNAM-PN


title: MuSCs_HC_CD56pos_rep2

description: Gene expression of CD56npos MuSCs from healthy control patient n2

source_name: Healthy Control MuSCs CD56pos fraction n2


title: Donor512_ComboNAM-PN


title: Donor512_PN


title: MuSCs_DMD_CD56pos_rep3

description: Gene expression of CD56npos MuSCs from DMD patient n3

source_name: DMD MuSCs CD56pos fraction n3


title: Donor29_NAM


title: Fib2 silenced N. benthamiana_replicate 3

city: Kansas City

first: Jared

middle: P.

last: May

state: MO

address: 5009 Rockhill Road Spencer Chemistry Building Room 405B

country: USA

institute: University of Missouri-Kansas City

data_processing:
FASTQ files (paired-end) were mapped against either fully processed rRNAs or the 45S precursor (Genbank: KP824745.1) from N. benthamiana using Bowtie2  with end-to-end (--very-fast) presets.
5’ and 3’ end read coverage was calculated from plus-strand reads using the bedtools Genome Coverage tool. The 5' end read positions were shifted to the -1 position before calculating the total 5' and 3' end read counts for each rRNA site.
RiboMethScores were calculated as described by Galvanin et. al. (2019) (PMID: 30539563)
Assembly: GenBank: KP824745.1
Supplementary files format and content: .xlsx file with total 5' and 3' end read counts for the 18S, 5.8S, and 25S rRNAs. Processed data also includes RiboMethScores for each position of the 18S, 5.8S, and 25S rRNAs.
Library strategy: RiboMethSeq

organism: Nicotiana benthamiana

source_name: Mature leaves

growth_protocol: Nicotiana benthamiana plants were grown at 25°C following a 12-hour light/dark cycle at 65% relative humidity in a growth chamber with an LED light intensity of 250 µmol m-2s-1.

extract_protocol:
Total RNA was extracted from 100 mg of N. benthamiana leaf tissue and treated with on-column DNase I using the RNeasy Plant Mini Kit (Qiagen). RNA fragmentation was achieved by incubating 500-800 ng of total RNA in bicarbonate buffer (pH 9.2) at 95°C for 8 minutes, followed by ethanol precipitation for purification. Following end-repair, RNA fragments were purified using the RNeasy MinElute Cleanup Kit (Qiagen) and fragmentation was confirmed by agarose gel electrophoresis.
The NEBNext Small RNA library prep (New England Biolabs) commercial protocol was used for library construction.

treatment_protocol: Mock-infected plants were agroinfiltrated with the p14 silencing suppressor from Pothos latent virus. PEMV2-infected plants were agroinfiltrated with both p14 and a binary construct (pCB-PEMV2) expressing full-length infectious PEMV2. Infections lasted 3 days prior to harvesting leaf tissue. Fib2-silenced plants were generated using virus-induced gene silencing (VIGS). Binary constructs encoding Tobacco rattle virus (TRV) were used to express a fragment of Fib2 that results in gene silencing. Fib2-silencing was achieved by 11 days post-infiltration of TRV2 constructs.

value: Mature leaves

value: LAB strain

value: Fib2-silenced using virus-induced gene silencing (VIGS)

value: Fib2-silenced (uninfected)


title: MuSCs_DMD_CD56pos_rep1

description: Gene expression of CD56npos MuSCs from DMD patient n1

source_name: DMD MuSCs CD56pos fraction n1


title: Donor29_CTRL

value: Human Skeletal Muscle Myoblasts


title: Fib2 silenced N. benthamiana_replicate 2


title: Donor4_PN

value: female

value: PN


title: Donor29_ComboNAM-PN


title: Donor4_CTRL


title: Donor29_PN


title: GFP_RXRA_OCA_s24-Biol Rep2

city: Innsbruck

first: Jose Miguel

last: Ramos Pittol

address: Innrain 80-82

department: Institute of Biochemistry

country: Austria

institute: University of Innsbruck

description:
s24
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx

data_processing:
Quality control on the sequence reads from the raw FASTQ files was done with FastQC (v0.11.8). TrimGalore (v0.6.5) was used to trim reads based on quality and adapter presence after which FastQC was again used to check the resulting quality.
Trimmed sequences were aligned to the reference genome GRCh38_snp_tran using HISAT2
Read counts were generated with the Rsubread FeatureCounts module (v2.0.0) using the Homo_sapiens.GRCh38.102 annotation
Differential expressed (DE) genes were determined with DESeq2 package (version 1.36.0). Shrinkage of effect size was performed on Deseq2 results using theapeglmmethod through the function lfcShrink
Assembly: GRCh38.102
Supplementary files format and content: tab-delimited text file includes TPM values for each sample
Supplementary files format and content: Excel files include pairwise comparisons generated with DESEQ2

molecule: polyA RNA

source_name: Liver

growth_protocol: HepG2 cells were grown in DMEM 1g/l glucose (Lonza, 12-707F) supplemented with 10% fetal bovine serum (FBS) and 1% L-glutamine (Lonza, 17-605E) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries
Libraries were prepared using TruSeq Stranded mRNA Library Prep (Illumina) following manufacturer's protocols.

treatment_protocol: FXRa2, FXRa2-L434R or GFP were induced with 2 µg/ml Doxycycline hydrochloride (D3447, Sigma-Aldrich) for 48 hours in full culture media. Afterwards, medium was exchanged to DMEM supplemented with 1% FBS and either 10µM OCA or DMSO 0.1% as vehicle treatment for 16 hours.

value: Liver

value: Doxycycline-inducible GFP + constitutive RXRA

value: OCA


title: Set-3:Scramble shRNA treated ME-1 cells-Rep3 (Day 7)

city: Worcester

first: Rui

last: Li

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

data_processing:
The RNA-seq analysis were performed with OneStopRNASeq1
Paired-end reads were aligned to human primary genome hg38, with star_2.5.3a 2, annotated with GENCODE GRCh38.p12 annotation release 293
Aligned exon fragments with mapping quality higher than 20 were counted toward gene expression with featureCounts_1.5.2
Differential expression (DE) analysis was performed with  DESeq2_1.20.05 modeling all samples.
Within DE analysis, 'ashr' was used to create log2 Fold Change (LFC) shrinkage for each comparison6
Assembly: GRCh38.p12
Supplementary files format and content: Excel format, TPM normalized expression value

source_name: ME-1 cells

extract_protocol: none provided by the submitter

tag: aml subtype

value: inv(16) cell line

tag: treatment ime

value: Day 7


title: MuSCs_DMD_CD56neg_rep2

description: Gene expression of CD56neg MuSCs from DMD patient n2

source_name: DMD MuSCs CD56neg fraction n2

value: Skeletal Muscle

value: male


title: MuSCs_DMD_CD56neg_rep1

description: Gene expression of CD56neg MuSCs from DMD patient n1

source_name: DMD MuSCs CD56neg fraction n1


title: GFP_RXRA_OCA_s8-Biol Rep1

description:
s8
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx

tag: cell line


title: GFP_RXRA_OCA_s40-Biol Rep3

description:
s40
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: PEMV2-infected N. benthamiana (3 dpi)_replicate 3

value: wild-type


title: Fib2 silenced N. benthamiana_replicate 1


title: GFP_RXRA_DMSO_s39-Biol Rep3

description:
s39
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx

value: DMSO


title: GFP_RXRA_DMSO_s7-Biol Rep1

description:
s7
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: Set-3:Scramble shRNA treated ME-1 cells-Rep2 (Day 7)


title: Set-3:Scramble shRNA treated ME-1 cells-Rep1 (Day 7)


title: GFP_H2b-Neon_OCA_s32-Biol Rep2

description:
s32
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx

value: Doxycycline-inducible GFP + constitutive H2b-Neon


title: PEMV2-infected N. benthamiana (3 dpi)_replicate 2

value: Mature leaves


title: GFP_RXRA_DMSO_s23-Biol Rep2

description:
s23
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: PEMV2-infected N. benthamiana (3 dpi)_replicate 1

value: LAB strain


title: GFP_H2b-Neon_OCA_s48-Biol Rep3

description:
s48
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: Set-3:NRP1 shRNA treated ME-1 cells-Rep3 (Day 7)


title: Mock-infected N. benthamiana (3 dpi)_replicate 3

value: Mock-infected


title: GFP_H2b-Neon_DMSO_s47-Biol Rep3

description:
s47
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: GFP_H2b-Neon_DMSO_s31-Biol Rep2

description:
s31
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: GFP_H2b-Neon_OCA_s16-Biol Rep1

description:
s16
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: Set-3:NRP1 shRNA treated ME-1 cells-Rep2 (Day 7)


title: Mock-infected N. benthamiana (3 dpi)_replicate 2


title: Set-3:NRP1 shRNA treated ME-1 cells-Rep1 (Day 7)


title: FXRa2-L434R_RXRA_OCA_s6-Biol Rep1

description:
s6
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx

value: Doxycycline-inducible FXRa2-L434R + constitutive RXRA


title: GFP_H2b-Neon_DMSO_s15-Biol Rep1

description:
s15
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: Mock-infected N. benthamiana (3 dpi)_replicate 1


title: Set-1:Scramble shRNA treated ME-1 cells-Rep3 (Day 7)


title: Set-1:Scramble shRNA treated ME-1 cells-Rep2 (Day 7)


title: Set-1:Scramble shRNA treated ME-1 cells-Rep1 (Day 7)


title: FXRa2-L434R_RXRA_OCA_s38-Biol Rep3

description:
s38
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: FXRa2-L434R_RXRA_OCA_s22-Biol Rep2

description:
s22
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: FXRa2-L434R_RXRA_DMSO_s21-Biol Rep2

description:
s21
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: FXRa2-L434R_RXRA_DMSO_s37-Biol Rep3

description:
s37
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: FXRa2_RXRA_OCA_s4-Biol Rep1

description:
s4
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx

value: Doxycycline-inducible FXRa2 + constitutive RXRA


title: FXRa2_RXRA_DMSO_s3-Biol Rep1

description:
s3
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: FXRa2-L434R_RXRA_DMSO_s5-Biol Rep1

description:
s5
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: FXRa2_RXRA_OCA_s36-Biol Rep3

description:
s36
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: Set-1:MYH11 shRNA treated ME-1 cells-Rep3 (Day 7)


title: FXRa2_RXRA_OCA_s20-Biol Rep2

description:
s20
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: WUI_3

city: Guangzhou

first: Yan

last: Guo

address: Jinying road

country: China

institute: Guangdong ProvincPlant Protection Research Institute, Guangdong academy of Agricultural Science

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts.
The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA.
The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA.
Predicting the target gene of miRNA was performed by psRobot_tar in psRobot for plants or miRanda for animals.
Assembly: https://www.ncbi.nlm.nih.gov/genome/?term=Laodelphax+striatellus
Supplementary files format and content: tab-delimited text files include readcount values for each Sample

organism: Laodelphax striatellus

source_name: Ovaries

extract_protocol:
Total RNA was extracted from every sample using Trizol Reagent. A total amount of 3 μg total RNA per sample was used as input material for the small RNA library.
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Ovaries

value: Wolbachia uninfected


title: WUI_2


title: WUI_1


title: FXRa2_H2b-Neon_OCA_s44-Biol Rep3

description:
s44
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx

value: Liver

value: Doxycycline-inducible FXRa2 + constitutive H2b-Neon


title: Set-1:MYH11 shRNA treated ME-1 cells-Rep1 (Day 7)


title: FXRa2_RXRA_DMSO_s35-Biol Rep3

description:
s35
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: WI_2

value: Wolbachia infected


title: ∆PHRF1 HeLa cells 3

city: Chapel Hill

first: Kanishk

last: Jain

state: NC

address: 120 Mason Farm Rd. CB #7260, Genetic Medicine Building, Ste 3010

institute: UNC Chapel Hill

data_processing:
Partek Flow version 10.0
Raw sequencing reads in FASTQ format were aligned to the human reference genome (GRCh38) using STAR aligner (version 2.7.3a). Alignment and transcript quantification were performed using Partek Flow software (version 10.0; Partek Incorporated, St. Louis, MO, USA). Transcript quantification utilized the Partek E/M algorithm within Partek Flow. Differential gene expression analysis was carried out using DESeq2 (version 1.26.0) within the Partek Flow environment.
Assembly: GRCh38
Supplementary files format and content: all processed data files are in .xlsx format and contain counts.

source_name: HeLa

extract_protocol:
Total RNA was extracted from HeLa cells using TRIzol according to the manufacturer's protocol.
An mRNA library was constructed by Novogene using a poly-A capture kit according to manufacturer's protocol.

value: HeLa


title: Set-1:MYH11 shRNA treated ME-1 cells-Rep2 (Day 7)

value: inv(16) cell line

value: Day 7


title: FXRa2_RXRA_DMSO_s19-Biol Rep2

description:
s19
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: FXRa2_H2b-Neon_OCA_s12-Biol Rep1

description:
s12
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx

value: OCA


title: FXRa2_H2b-Neon_DMSO_s27-Biol Rep2

description:
s27
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: 48hr

city: Baltimore

first: Harley

last: Edwards

state: Maryland

address: 1000 Hilltop Circle

department: CBEE

institute: University of Maryland, Baltimore County

data_processing:
Data directly taken from the Illumina GA II and Illumina basecalls was Bustard 1.4.0.
ELAND was used for alignments to the genome and intron calls.
Casava was used for counts and RPKM found in the sheet.
Assembly: FGSC A4
Supplementary files format and content: Rpnuc, count, RPKM

organism: Aspergillus nidulans

source_name: FGSC A4

growth_protocol: an 8-liter carboy containing 4 liters of minimal medium was inoculated with conidia to make a suspension with a final concentration of 106 conidia/ml. Filter sterilized air was vigorously bubbled through the suspension to ensure aeration and agitation for 20 hr at room temperature, resulting in a logarithmic phase suspension of mycelial growth. Subsequently, 200 ml aliquots of the mycelial culture were harvested by vacuum filtration onto 9-cm Whatman no. 1 filter paper discs. Duplicate time point “0” samples was immediately frozen in liquid nitrogen. For the aerial time course, additional harvested mycelium on filter was placed onto 5 mm glass beads that were in 9-cm glass petri dishes containing liquid Aspergillus minimum medium to wick via the beads to maintain the moisture of the filter paper. Media levels were monitored and additional medium was added as needed to ensure filter papers remained wet. The time points were selected to ensure that key developmental stages were observed in a synchronous fashion (aerial hyphae ~6 h, vesicle formation 6-12 h, metulae cell formation ~12 h, phialide cell formation 12-18 h, conidiophore initiation 18-24 h, and mature conidiophore with conidial chains 24-48 h).  Plates were numbered and placed in randomized positions under constant fluorescent light in a biosafety cabinet with a lowered glass sash and no airflow. Duplicate filter papers were collected for each time point.

extract_protocol: At 0, 6, 12, 18, 24, 30 and 48 hours, RNA was purified and cDNA constructed using the Illumina mRNA seq prep kit

value: FGSC A4

value: WT

tag: time point


title: 30hr


title: FXRa2_H2b-Neon_DMSO_s43-Biol Rep3

description:
s43
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx

value: DMSO


title: FXRa2_H2b-Neon_DMSO_s11-Biol Rep1

description:
s11
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx


title: ∆PHRF1 HeLa cells 2


title: ∆PHRF1 HeLa cells 1


title: 24hr


title: CONTROL-replicate2

city: Munich

first: Arthur

last: Liesz

address: Feodor-Lynen-Straße 17

department: Institute for Stroke and Dementia (ISD)

country: Germany

institute: LMU Hospital

description: snRNA-seq

library_source: transcriptomic single cell

data_processing:
Libraries were sequenced on an Illumina NextSeq 2000, aiming for 25,000 reads per nuclei.
Cell Ranger software was used to process raw data, align reads to the human hg38 reference genome and summarize unique molecular identifier (UMI) counts. Filtered gene-barcode matrices containing only barcodes with UMI counts that passed the threshold for cell detection were used for further analysis.
Filtered UMI count matrices were processed using R and the R package Seurat.
Assembly: Human hg38 reference genome
Supplementary files format and content: Cell Ranger outputs; Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

molecule: nuclear RNA

source_name: brain (medulla)

extract_protocol:
Single nuclei suspensions were prepared from flash-frozen human brain tissues using the Chromium Nuclei Isolation Kit with RNase Inhibitor (PN-1000494, 10x Genomics). Single nuclei suspensions were then submitted to a microscopic inspection of integrity and further processed according to manufacturer’s (10x) protocols at a concentration of 4.000-8.000 nuclei/µl.
Single nuclei mRNA libraries were prepared using the 10x Chromium Single Cell 3’ v.3.1. Solution. Quality control of all cDNA samples was performed with a Bioanalyzer 2100 (Agilent Technologies) and libraries were quantified with the Qubit dsDNA HS kit (ThermoFisher).

value: brain (medulla)

tag: disease state

value: Control (no COVID-19)


title: Control HeLa cells 3


title: CONTROL-replicate1

description: snRNA-seq


title: COVID-replicate2

description: snRNA-seq


title: 18hr


title: COVID-replicate1

description: snRNA-seq


title: PBMC cells, PRRSVCS2

city: Chiang Mai

first: patipan

last: hnokaew

state: Mueang Chiang Mai

address: 239 Huay Kaew Rd, Tambon Su Thep, Mueang Chiang Mai District, Chiang Mai 50200, Thailand

department: Office of Research Administration

country: Thailand

institute: Chiang Mai University

data_processing:
FastQC version 0.12.0
Trimmomatic version 0.32
HISAT2
UCSC genome browser
DESeq2 version 1.44.0
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Sus scrofa

source_name: whole blood

extract_protocol:
RNA was extracted from PBMC cells using RNAzol®RT reagent (Sigma–Aldrich, St. Louis, MO, USA) and Direct-zolTM RNA Miniprep kit (Zymo Research, Irvine, CA, USA), with minor modifications
Sequencing libraries were generated using a TruSeq® Stranded mRNA library prep Kit for Illumina (Illumina Inc., San Diego, CA, USA) following the manufacturer’s recommendations

value: whole blood

value: monocytes

tag: cell type

value: porcine peripheral blood mononuclear cells

tag: stimulation

value: PRRSV

value: Caesalpinia sappan extract supplementation


title: WI_1

value: Ovaries

tag: treatment


title: FXRa2_H2b-Neon_OCA_s28-Biol Rep2

description:
s28
DESEQ2_DMSO vs OCA comparisons.xlsx
DESEQ2_FXR vs GFP comparisons.xlsx

value: Liver

value: Doxycycline-inducible FXRa2 + constitutive H2b-Neon


title: 6hr


title: PBMC cells, PRRSV2

value: control


title: 12hr


title: Control HeLa cells 1

value: HeLa


title: PBMC cells, PRRSVCS1


title: 0hr


title: PBMC cells, CTRL1

value: CTRL


title: WI_3

value: Wolbachia infected


title: ∆PHRF1 cells 3


title: PBMC cells, PRRSV1


title: PBMC cells, CTRL2


title: 623_recurrent [NS_Hs_NeuroInflam_v1.0]

city: Basel

first: Sabrina

middle: Annie

last: Hogan

address: Hebelstrasse 20

institute: University of Basel

hyb_protocol: Gene expression code sets were hybridized in a thermocycler for 18 h at 65 °C prior to being processed in the nCounter Prep Station (Nanostring Technologies, USA)

scan_protocol: Gene expression was assessed using the nCounter Neuroinflammation panels comprising 770 genes  (including 10 house-keeping genes, NanoString Technologies, Seattle, WA), using 50 ng of total RNA per tumor sample

data_processing:
each panel was normalised separately using the limma package and  between-samples cyclic loess normalization
The matrix table displays log2 transformed cpm

label: Neuroinflamation panel

source_name: GMB

label_protocol: slides were stained using a mixture of conjugated antibodies for identification of tissue morphology: anti-GFAP-594 (Novus Biologicals, NBP2-33184DL594; 1:1000) and anti-CD64 (purified with Abcam purification kit (ab102784) and conjugated with AlexaFluor647 (ab269235); 1:50) for the labeling of tumor cells and myeloid cells, respectively. In addition, Syto83 was used for DNA labeling (ThermoFisher Scientific, USA, 1:25)

growth_protocol: GBM tissue samples were collected directly in the operating theater during primary (first) and recurrent (second) surgeries and immediately stored in RNAlater stabilization solution (Thermo Fisher Scientific, USA) on ice and stored at -80 °C until further use.

extract_protocol: Tumors were mechanically dissociated in lysis buffer using a syringe equipped with a 23G needle, and total RNA was extracted using the AllPrep DNA/RNA/protein mini Kit (Qiagen, USA, Cat. No. / ID: 80004) according to the manufacturer’s protocol

value: recurrent

tag: relapse time (d)

tag: patientid


title: Control HeLa cells 2


title: ∆PHRF1 cells 1


title: chip, urf_f_2

city: Rehovot

first: Ido

last: Goldstein

address: POB 12

department: Institute of Biochemistry, Food Science and Nutrition

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Fastq files were mapped to the mm10 mouse genome assembly using Bowtie2
Assembly: mm10

source_name: liver

extract_protocol:
Liver pieces (150 mg) were cross-linked with phosphate-buffered saline (PBS) containing 2mM disuccinimidyl glutarate (DSG, Santa Cruz Biotechnology, cat# sc-285455). Livers were homogenized with a Dounce homogenizer and rotated for 30 min at room temperature. Crosslinked samples were washed in phosphate buffered saline (PBS), resuspended in ChIP lysis (0.5% SDS, 10mM EDTA, 50mM Tris-HCl pH8) buffer and sonicated to release 100-1000 bp fragments. Antibody against PPARa was conjugated to magnetic beads for 2 h at 4°C. Chromatin was immunoprecipitated with antibody-bead conjugates for 16 h at 4°C. Immunocomplexes were washed sequentially with the following buffers:low salt buffer (0.01% SDS, 1% Triton x-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl), high salt buffer (0.01% SDS, 1% Triton x-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, 500 mM NaCl), LiCl buffer (0.25M LiCl, 1% IGEPAL CA630, 1% deoxycholic acid, 1mM EDTA, 10 mM Tris pH 8.1) and twice with TE buffer (10 mM Tris-HCl, 1 mM EDTA pH 8). Chromatin was eluted, de-crosslinked for 4 h at 65°C and deproteinized with proteinase K (Hy Labs, cat# EPR9016) for 1 h at 50°C..DNA was subsequently isolated using MinElute DNA purification kit.
ChIP DNA libraries were prepared using the KAPA HyperPrep Kit (KAPA biosystems, cat# KR0961).

tag: tissue

value: liver

tag: genotype

value: wt

value: 24h fasting


title: 623_primary [NS_Hs_NeuroInflam_v1.0]

value: primary


title: chip, adf_f_2

value: alternate day fasting


title: Control cells 3


title: 608_primary [NS_Hs_NeuroInflam_v1.0]


title: chip, urf_f_1


title: Control cells 2


title: 608_recurrent [NS_Hs_NeuroInflam_v1.0]


title: RNA_URF_2

data_processing:
Fastq files were mapped to the mm10 mouse genome assembly using Bowtie2
Assembly: mm10
Supplementary files format and content: BAM files contain aligned reads

growth_protocol: Mice were subjected to either a 4-week alternate day fasting (ADF) regimen or unrestricted feeding (URF). At the end of the experiment mice were divided to 3 groups: the first group was euthanized after a 24 h fasting period (ADF_f or URF_f). The second group fasted for 24 h followed by ad libitum refeeding for 24 h at the end of which they were euthanized (ADF_re or URF_re). The third group did not experience any type of fasting (unrestricted feeding). Each group has 3 replicates.

extract_protocol:
Total RNA was isolated from liver pieces (30 mg) using NucleoSpin kit (Macherey-Nagel cat# 740955.25) according to the manufacturer’s protocol.
For quality control of RNA yield and library synthesis products, the RNA ScreenTape and D1000 ScreenTape kits (both from Agilent Technologies), Qubit® RNA HS Assay kit, and Qubit® DNA HS Assay kit (both from Invitrogen) were used for each specific step. mRNA libraries were prepared from 1 µg RNA using the KAPA Stranded mRNA-Seq Kit, with mRNA Capture Beads (KAPA biosystems, cat# KK8421).

value: unrestricted feeding


title: RNA_URF_3


title: RNA_URF_1


title: Control cells 1


title: ∆PHRF1 cells 2


title: 599_recurrent [NS_Hs_NeuroInflam_v1.0]


title: T4wPC (A180)

city: Bar Harbor

first: Chih-Hao

last: Chang

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
Bulk RNA of the 9 excised tissues (heart, hippocampus, hypothalamus, kidney, liver, prefrontal cortex, skeletal muscle, small intestine, and spleen) (4 samples per treatment and time combination) was isolated with the QIAGEN miRNeasy mini extraction kit (QIAGEN) and cDNA was synthesized with the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems). RNA quality was assessed with a Bioanalyzer 2100 (Agilent Technologies). Poly(A)-selected RNA-seq libraries were generated using the Illumina TruSeq RNA Sample preparation kit v2. RNA-seq was performed in a 150-bp paired-end format with a minimum of 40 million reads per sample on the Illumina HiSeq platform according to the manufacturer’s instructions. RNA-seq reads were filtered and trimmed for quality scores >30 using a custom python script. The filtered reads were aligned to Mus musculus GRCm38 using RSEM (v1.2.12) (58) with Bowtie2 (v2.2.0)(21) (command: rsem-calculate-expression -p 12--phred33-quals --seed-length 25 --forward-prob 0 --time --output-genome-bam -- bowtie2).RSEM calculates expected counts and transcript per million (TPM). The expected counts from RSEM were used in the Bioconductor edgeR 3.20.9 package(22-24) to determine differentially expressed genes.
Assembly: Mus musculus GRCm38
Supplementary files format and content: .Rdata contains FPKM counts
Supplementary files format and content: tab-delimited text file contains expected count, TPM, and FPKM

source_name: Prefrontal cortex

extract_protocol:
Bulk RNA of the 9 excised tissues (heart, hippocampus, hypothalamus, kidney, liver, prefrontal cortex, skeletal muscle, small intestine, and spleen) (4 samples per treatment and time combination) was isolated with the QIAGEN miRNeasy mini extraction kit (QIAGEN) and cDNA was synthesized with the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems).
Poly(A)-selected RNA-seq libraries were generated using the Illumina TruSeq RNA Sample preparation kit v2.

treatment_protocol: mice were treated with 2DG (6g/L) through water or just water for 96 hours or 4 weeks

value: Prefrontal cortex

tag: strain

value: WT

tag: timepoint

value: 4 weeks

value: male


title: N4wK (A002)

source_name: Kidney

value: Kidney

value: Control

tag: Sex


title: T4wHC (A179)

source_name: Hippocampus

value: Hippocampus


title: T4wHT (A178)

source_name: Hypothalamus

value: Hypothalamus


title: 599_primary [NS_Hs_NeuroInflam_v1.0]


title: chip, adf_f_1


title: T4wSI (A177)

source_name: Ilium

value: Ilium


title: MCF7, Ctrl, c-Fos-IP, rep2

city: Fuzhou

first: Sunwang

last: Xu

address: Chazhong Road 20th

institute: The First Affiliated Hospital of Fujian Medical University

data_processing:
Raw FASTQ sequencing reads were mapped to hg38 human genome using Bowtie2 and uniquely mapped reads were processed further for peak identification. Peak calling over input control was performed using MACS 2.0 with an FDR value cut-off of 0.05 and normalization by signal per million reads. Differential ChIP peak analysis between different groups was performed with DESeq2.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Breast

extract_protocol:
Cells were crosslinked with 1% formaldehyde in culture medium at room temperature for 10 min and quenched with 125 mM glycine. Then the cross-linked cells were collected, lysed and sonicated. The cleared extract was subjected to immunoprecipitation with 3 μg of anti-c-Fos antibody (CST, Cat# 2250), or non-specific IgG control antibody (CST, Cat# 3900) overnight at 4 ℃ with constant rotation. The isolated complexes were precipitated with protein A/G agarose beads. After washing, elution and reverse-cross-linking, the ChIP DNA was purified
The purified ChIP DNA was used to prepare ChIP sequencing libraries by using NEBNext End Repair/dA-Tailing Module (NEB, #E7442) followed by adaptor ligation with NEBNext Ultra Ligation Module (NEB, #4775). The ChIP and input DNA libraries were amplified for 15 cycles and sequenced using the Illumina NovaSeq 6000 platform with paired-end as the sequencing mode.

value: Breast

value: Breast cancer cell


title: 551_recurrent [NS_Hs_NeuroInflam_v1.0]

value: recurrent


title: N4wHT (A007)


title: T4wH (A175)

source_name: Heart

value: Heart


title: T4wK (A173)


title: 551_primary [NS_Hs_NeuroInflam_v1.0]


title: MCF7, Ctrl, input, rep2


title: MCF7, Ctrl, input, rep1


title: T4wL (A174)

source_name: Liver

value: Liver


title: 545_recurrent [NS_Hs_NeuroInflam_v1.0]


title: T96PC (A171)

value: 96 hours


title: MCF7, NR4A1-KO, c-Fos-IP, rep2


title: T96HC (A170)


title: MCF7, NR4A1-KO, input, rep2


title: T96SI (A168)


title: 545_primary [NS_Hs_NeuroInflam_v1.0]

value: primary


title: MCF7, Ctrl, c-Fos-IP, rep1


title: T4wSM (A176)

source_name: Skeletal muscle

value: Skeletal muscle


title: 496_recurrent [NS_Hs_NeuroInflam_v1.0]


title: T96K (A164)


title: T96H (A166)


title: 532_recurrent [NS_Hs_NeuroInflam_v1.0]


title: T96HT (A169)


title: T96SM (A167)


title: T96S (A163)

source_name: Spleen

value: Spleen


title: T96HC (A152)

value: WT


title: MCF7, NR4A1-KO, c-Fos-IP, rep1


title: T4wS (A172)

value: 4 weeks


title: T96PC (A153)

value: Prefrontal cortex

value: male


title: T96HT (A151)


title: 417_recurrent [NS_Hs_NeuroInflam_v1.0]


title: Spinal Cord A

city: Seattle

first: Anja

last: Kordowski

state: Washington

address: 1920 Terry Ave

institute: Seattle Children's Hospital

description: FFPE 10x Visium spatial transcriptomic sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequencing files were mapped to the human genome hg38 using the Space Ranger's default settings
The gene expression was quantified based on unique molecular identifier counts
LR_scores.csv files:
Cell-cell interaction (CCI) and corresponding ligand-receptor (LR) expression analysis was performed with the Python-based software stLearn as described previously (Pham, D., Tan, X., Balderson, B. et al. Robust mapping of spatiotemporal trajectories and cell-cell interactions in healthy and diseased tissues. Nat Commun 14, 7739 (2023)). In brief, the overall steps in the stLearn pipeline are:
1. Load known ligand-receptor gene pairs (LR database from NATMI/connectomeDB2020).
2. Identify spots where significant interactions between these pairs occur (within 200um range).
3. For each LR pair and each celltype-celltype combination, count the instances where neighbours of a signficant spot for that LR pair link two given cell types.
4. Identify signficant interactions with p<.05 from cell type information permutation.
Assembly: hg38
Supplementary files format and content: filtered_feature_bc_matrix.h5: list of detected cell-associated spatial barcodes
Supplementary files format and content: scalefactors_json.json: scalefactors
Supplementary files format and content: tissue_hires_image.png: hi-resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-resolution image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and corresponding coordinates specifying spots
Supplementary files format and content: LR_scores.csv
Library strategy: Spatial Transcriptomics

source_name: DIPG tumor-infiltrated brainstem

extract_protocol:
Fresh tumor samples were Formalin-Fixed and Paraffin-Embedded. Tissue samples were sectioned on a cryostat at a thickness of 5µm and transferred onto a microscope glass slide
Spatial transcriptomic sequencing libraries were prepared with the 10x Visium CytAssist Spatial Gene Expression for FFPE kit according to the manufacturer's protocol

value: DIPG tumor-infiltrated brainstem

tag: tissue region

value: Spinal cord


title: Spinal Cord B


title: Medulla C

value: Medulla


title: T96SI (A150)

value: Ilium


title: T96SM (A149)


title: 532_primary [NS_Hs_NeuroInflam_v1.0]


title: Medulla B


title: T96H (A148)


title: T96L (A165)


title: 380_recurrent [NS_Hs_NeuroInflam_v1.0]


title: T96L (A147)


title: 496_primary [NS_Hs_NeuroInflam_v1.0]


title: 380_primary [NS_Hs_NeuroInflam_v1.0]


title: Medulla A


title: T96K (A146)

value: Kidney


title: 417_primary [NS_Hs_NeuroInflam_v1.0]


title: 356_recurrent [NS_Hs_NeuroInflam_v1.0]


title: T96PC (A144)


title: Pons B

value: Pons


title: T96HT (A142)

value: Hypothalamus


title: T96SM (A140)


title: T96SI (A141)


title: Pons D


title: Pons C


title: 291_recurrent [NS_Hs_NeuroInflam_v1.0]

value: recurrent


title: T96S (A145)


title: T96H (A139)

value: Heart


title: T96HC (A143)

value: Hippocampus

value: 96 hours


title: 291_primary [NS_Hs_NeuroInflam_v1.0]

value: primary


title: N96PC (A117)

value: Control


title: Butt, Old,  Patient 3

city: Boston

first: George

last: Church

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

description: 10X Genomics

data_processing:
10x Genomics (v2.2.0) mkfastq and count
Assembly: hg38
Supplementary files format and content: tab separated raw count and matrix files

source_name: Skin

extract_protocol:
To generate a single cell suspension from adult skin, the process involved cutting healthy skin into thin strips in PBS. The top 200 μm layer was isolated using a dermatome with a Pilling Wecprep blade and a .008 gauge Goulian guard. Grid slits were introduced into the skin sheets for enzymatic access, followed by a 1-hour treatment with 2U/ml dispase II in RPMI at 37°C. Subsequently, the epidermis was peeled from the dermis, and both fragments were separately digested in a petri dish at 37°C 5% CO2 in RF-10 media with 1.6 mg/ml type IV collagenase (Worthington, CLS-4) overnight (12 hours). The work was conducted within class II biological safety cabinets using autoclave-sterilized equipment. The media was collected using a serological pipette and filtered through a sterile 100 μm cell strainer (BD Falcon, 352360). After washing the petri dish and strainer with RF-10 to gather any remaining cells, centrifugation was employed to pellet the cells at 500 x g for 5 minutes. The supernatant was discarded, and the pellet was gently resuspended in 1 ml RF-10 through pipetting up and down. Cell counting was performed using a hemocytometer after staining 10 μl of the sample with a 1:1 mixture of 0.4% trypan blue (Sigma, T8154) to identify dead cells.
scRNA-seq libraries were generated following the manufacturer's instructions using the Chromium 10x Single-Cell Instrument (10x Genomics) and 10x Genomics Chromium Single Cell 3’ GEM Library and Gel Bead Kit v2. Each channel was loaded with cells, aiming for 5,000 cells per sample, with cell concentration measured by Moxi GO II (Orflo Technologies). The cDNA amplification and sample identification were performed in the Bio-Rad C1000 Touch Thermal cycler with 96 Deep-Well Reaction Module, utilizing 12 cycles. Amplified cDNAs and final libraries were assessed using a Fragment Analyzer (AATI) with a High Sensitivity NGS Analysis Kit (Advanced Analytical) to determine the average fragment length of the 10x cDNA libraries. Quantification of the libraries was done via qPCR using the Kapa Library Quantification kit. Subsequently, the libraries were diluted to a final concentration of 2 nM and pooled together for each run of NovaSeq sequencing. The NovaSeq 6000 Sequencing System (Illumina) was used for sequencing all the libraries.

value: Skin

tag: age

value: Old

tag: patient id


title: N96HT (A115)

value: WT


title: Pons A


title: T96K (A137)

value: male


title: Butt, Middle,  Patient 2

description: 10X Genomics

value: Middle


title: N96H (A112)


title: 282_recurrent [NS_Hs_NeuroInflam_v1.0]


title: T96S (A136)

value: Spleen


title: 356_primary [NS_Hs_NeuroInflam_v1.0]


title: Midbrain

value: DIPG tumor-infiltrated brainstem

value: Midbrain


title: Arm, Middle,  Patient 2

description: 10X Genomics


title: N96HC (A116)


title: 195_recurrent [NS_Hs_NeuroInflam_v1.0]


title: 185_primary [NS_Hs_NeuroInflam_v1.0]


title: T4wPC (A099)

value: Prefrontal cortex

value: 4 weeks


title: T96L (A138)

value: Liver


title: Butt, Young,  Patient 1

description: 10X Genomics

value: Young


title: 282_primary [NS_Hs_NeuroInflam_v1.0]


title: N96SI (A114)

value: Ilium


title: Arm, Young, Patient 1

description: 10X Genomics


title: N96SM (A113)

value: Skeletal muscle


title: T4wSM (A095)


title: 195_primary [NS_Hs_NeuroInflam_v1.0]


title: 185_recurrent [NS_Hs_NeuroInflam_v1.0]

value: recurrent


title: Arm, Old,  Patient 3

description: 10X Genomics


title: N96L (A111)

value: 96 hours


title: N96S (A109)

value: Control


title: 182_recurrent [NS_Hs_NeuroInflam_v1.0]


title: T4wHC (A098)

value: Hippocampus


title: T4wH (A094)

value: Heart


title: N96K (A110)

value: Kidney

value: WT


title: T4wSI (A096)

value: male


title: 182_primary [NS_Hs_NeuroInflam_v1.0]

value: primary


title: snRNA-Seq of Homo sapiens: Donor 6 Bladder UO

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Raw sequencing data were demultiplrxrd and aligned using cellranger v7.1.0 with genome GRCh38-2020A (pre-built GRCh38 genome reference provided by 10X Genomics).
Transcriptome filtering, sample integration, batch correction, and clustering were performed using Seurat v4.3.0.1.
Assembly: GRCh38-2020A  (pre-built GRCh38 genome reference provided by 10X Genomics).
Supplementary files format and content: We provide normalized RNA expression, barcodes.tsv, and features.tsv for each sample subset for a given bladder comaprtment (urothelial, stromal, or immune). Cell types with matched barcodes.tsv are provided as a part of the supplemental data.

source_name: Bladder

extract_protocol:
10x Chromium Next GEM Single Cell 3ʹ Kit v3.1. Barcoded single cell RNA seq libraries were prepared for each sample and subjected to 150 base paired-end sequencing on Illumina NovaSeq.
Each sample library was loaded on 4 lanes of flowcell generating 4 sets of fastq files.

value: Bladder

tag: collection location

value: UO


title: scRNA-Seq of Homo sapiens: Donor 6 Bladder UO


title: T4wL (A093)


title: snRNA-Seq of Homo sapiens: Donor 6 Bladder Neck

value: Neck


title: 94_recurrent [NS_Hs_NeuroInflam_v1.0]


title: N4wPC (A090)

value: Prefrontal cortex

value: 4 weeks


title: N4wHT (A088)

value: Hypothalamus


title: T4wS (A091)

value: Spleen


title: 38_recurrent [NS_Hs_NeuroInflam_v1.0]


title: 94_primary [NS_Hs_NeuroInflam_v1.0]


title: 38_primary [NS_Hs_NeuroInflam_v1.0]


title: T4wHT (A097)


title: MCF7, NR4A1-KO, input, rep1

value: Breast

tag: cell line

value: Breast cancer cell


title: scRNA-Seq of Homo sapiens: Donor 6 Bladder Neck


title: T4wK (A092)


title: N4wL (A084)

value: Liver


title: endometrium, RIF_10, rep10

city: Shenzhen

first: zhu

last: kongfu

address: NanShan

institute: The Hong Kong University - Shenzhen Hospital

data_processing:
The raw sequencing data was separately processed using CellRanger pipeline (v.7.0.0) with default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: endometrium

extract_protocol:
A one-step dissociation protocol was used to disperse fresh endometrium tissue. Before dissociation, the tissue was rinsed with cold Phosphate Buffered Saline (PBS, Gibco) on a Petri dish to remove blood and mucus. Excess PBS was removed after rinsing. The tissue was then minced into small pieces using surgical blade with a small amount of benchtop medium (1% FBS + 1% Penicillin-Streptomycin + 1% Glutamine) or PBS to prevent tissue from drying out. Tissue digestion was then immediately performed using DMEM-F12 (Gibco) reconstituted DNase I (4mg/ml, Worthington) and Collagenase III (2.5mg/ml, Worthington) in a 50-ml Falcon tube, which was horizontally incubated at 37 °C water bath with constant shaking for 1 hour. After digestion, the cell suspension were filtered through 40μm sieves (BD Bioscience) and then loaded onto Ficoll-Paque (GE Healthcare) density gradient for red blood cell removal. Further removal of red blood cells was conducted using red blood lysis solution (Meitianni) for 5 minutes at room temperature. Dead cells were removed using the MACS dead cell removal kit (130-090-101, Miltenyi) following the manufacturer’s protocol. The cell viability and concentration of final resulted single-cell suspension was assessed for subsequent scRNA-seq experiments.
The qualified endometrial single-cell suspensions of were placed in a cold box (4 °C), and appropriate number of cells were loaded onto the Chromium Controller platform within 2 hours. Single-cell encapsulation, barcoding, reverse transcription, cDNA generation and library construction were performed following the manufacturer’s protocol (Single Cell 3' reagent kit v3.1, 10X Genomics). Single-cell libraries of each donor were sequenced with a pair-end mode (150bp) on a DNBSEQ-T7 instrument (GenePlus Technology) with a minimum sequencing depth of 50,000 reads/ per cell.

value: endometrium

value: female

tag: group

value: RIF


title: N4wH (A085)

value: Heart

value: Control


title: scRNA-Seq of Homo sapiens: Donor 6 Bladder UVJ

value: UVJ


title: snRNA-Seq of Homo sapiens: Donor 6 Bladder Dome

value: Dome


title: N4wK (A083)

value: Kidney

value: WT

value: male


title: endometrium, RIF_9, rep9


title: N96PC (A081)

value: Prefrontal cortex

value: 96 hours


title: N4wS (A082)

value: 4 weeks


title: N4wSI (A087)

value: Ilium


title: scRNA-Seq of Homo sapiens: Donor 6 Bladder Dome

value: Bladder


title: N96HC (A080)

value: Hippocampus


title: endometrium, RIF_8, rep8


title: N4wSM (A086)

value: Skeletal muscle


title: Melanocytes with mutant BRAFV600E in shDsg1 CM #3

city: Chicago

first: Ziyou

last: Ren

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

data_processing:
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library
library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data ( clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end cleanreads were aligned to the reference genome using Hisat2 v2.0.5.
Assembly: hg38
Supplementary files format and content: gene count value

source_name: skin

growth_protocol: Keratinocytes and melanocytes were isolated from neonatal foreskin provided by the Northwestern University Skin Biology and Diseases Research-Based Center as previously described (Roth-Carter et al., 2022). Keratinocytes were grown in M154 medium (Thermo Fisher Scientific) supplemented with human keratinocyte growth supplement (Thermo Fisher Scientific), 1,000 x gentamycin/amphotericin B solution (ThermoFisher Scientific), and 0.07mM CaCl2. Melanocytes were cultured in OptiMEM (Thermo Fisher Scientific) containing 5% fetal bovine serum (MilliporeSigma), 10 ng/ml bFGF (ConnStem), 1 ng/ml heparin (MilliporeSigma), 0.1 mM N6, 2’-O-dibutyryladenosine 3:5-cyclic monophosphate (MilliporeSigma), 0.1 mM 3-isobutyl-1-methyl xanthine (MilliporeSigma), and 1% penicillin/streptomycin (Corning). All cells were maintained at 37 °C with 5% CO2.

extract_protocol:
RNA was harvested using Quick-RNA miniprep kit (Zymo).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP

treatment_protocol: Conditioned media (CM) from keratinocytes were prepared by following previously published procedure (Arnette et al., 2020). Melanocytes were transduced with wild type BRAF or mutant BRAFV600E, then treated with CM from keratinocytes expressing shCTL or shDsg1 for 3 days.

value: skin

value: human melanocytes

value: melanocytes

value: Melanocytes were transduced with mutant BRAFV600E and treated with CM from keratinocytes expressing shDsg1


title: endometrium, LH11_3, rep3

value: endometrium

value: female


title: Melanocytes with mutant BRAFV600E in shDsg1 CM #2


title: endometrium, RIF_5, rep5

value: RIF


title: Melanocytes with mutant BRAFV600E in shDsg1 CM #1


title: N96H (A076)

value: Heart

value: Control


title: N96SI (A078)

value: WT

value: male


title: endometrium, RIF_4, rep4


title: Melanocytes with mutant BRAFV600E in shCTL CM #3

value: Melanocytes were transduced with mutant BRAFV600E and treated with CM from keratinocytes expressing shCTL


title: N96S (A073)

value: Spleen

value: 96 hours


title: N96L (A075)

value: Liver


title: N96SM (A077)


title: Melanocytes with mutant BRAFV600E in shCTL CM #2


title: N96K (A074)

value: Kidney


title: N96HT (A079)

value: Hypothalamus


title: N96PC (A072)

value: Prefrontal cortex


title: endometrium, LH3_3, rep3


title: Melanocytes with mutant BRAFV600E in shCTL CM #1

value: skin

value: human melanocytes


title: N96HC (A071)

value: Hippocampus


title: N96HT (A070)


title: snRNA-Seq of Homo sapiens: Donor 6 Bladder UVJ

value: Bladder

value: UVJ


title: N96SI (A069)

value: Ilium


title: N96SM (A068)

value: Skeletal muscle