title: Definitive Endoderm cells, saracatinib 3

city: Xi’an

first: Xiaoming

last: Ding

address: 277 Yanta west Rd.

institute: The First Affiliated Hospital of c Jiaotong University

data_processing:
The raw data, in fastq format, underwent initial processing using custom Perl scripts. In this phase, adapter sequences were removed, and reads with low quality were filtered out. Low quality was defined as instances where more than 60% of the entire dataset comprised lines with a quality value less than or equal to 25. Additionally, reads with a high ratio of undetermined bases (N) exceeding 5% were excluded. This preprocessing step resulted in the generation of clean reads suitable for subsequent analysis. The clean reads were individually aligned to the reference genome in an orientation-specific manner using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to yield mapped reads. The count of reads mapped to each gene was determined using FeatureCounts (http://subread.sourceforge.net/). Furthermore, Fragments Per Kilobase Million (FPKM) values for each gene were calculated based on both the gene's length and the count of reads mapped to that gene. Differential expression analysis was performed using DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html), where genes with an absolute log2 fold change (| log2FC |) greater than 1 and an adjusted p-value less than 0.05 were considered significantly differentially expressed genes.
Assembly: GRCh38.p13 (GCA_000001405.28)
Supplementary files format and content: Fragments Per Kilobase Million (FPKM) values for each gene were calculated based on both the gene's length and the count of reads mapped to that gene (.txt file).

growth_protocol: To investigate the role of saracatinib in definitive endoderm (DE) differentiation, we treated differentiating embryonic stem cells. Initially, the cells were cultured for three days to induce DE differentiation. Embryonic stem cells were seeded at a density of 1×10^6 cells per well on Matrigel-coated 6-well plates. The differentiation medium used was DMEM supplemented with B27, Glutamax, 50 ng/mL Activin A, and 2.5 μM CHIR99021 for 24 hours. Subsequently, CHIR99021 was removed from the medium for the following two days.

extract_protocol:
Initially, messenger RNA (mRNA) was isolated from 1 μg of total RNA using oligo (dT) magnetic beads, followed by a fragmentation process using divalent cations at elevated temperatures in the ABclonal First Strand Synthesis Reaction Buffer.
First-strand cDNAs were synthesized using random hexamer primers and Reverse Transcriptase (RNase H), with the mRNA fragments serving as templates. This was followed by the generation of second-strand cDNAs using DNA polymerase I, RNaseH, buffer, and deoxyribonucleotide triphosphates (dNTPs). The resulting double-stranded cDNA fragments were then ligated with adapters to prepare the paired-end library.

treatment_protocol: The experimental group comprised the treatment group, where 0.5 μM saracatinib was added to the cells throughout the differentiation period (3 days). As a control group, an equal volume of DMSO was added to the cells to serve as a volume control.

tag: cell line

tag: cell type

value: ESCs

value: saracatinib


title: seedling roots of WT bio rep 1, 4 DAG

status: Public on Dec 24 2023

type: SRA

city: Jinan

first: Pengcheng

last: Li

address: 202 Gongye North Road

country: China

institute: Shandong Academy of Agricultural Sciences

library_source: transcriptomic

data_processing:
To get clean sequencing reads, the sequencing data was filtered with SOAPnuke by removing reads containing sequencing adapter, with a low-quality base ratio higher than 20%, and with an unknown base ('N' base) ratio higher than 5%.
The expression level of genes was calculated by RSEM (v1.3.1)
Assembly: TAIR10
Supplementary files format and content: TPM values and read counts for each gene in all samples

molecule: total RNA

organism: Arabidopsis thaliana

source_name: root

growth_protocol: For seed germination, seeds were sterilized with a mixture containing 75% (v/v) ethanol and 0.05% (v/v) Triton X-100 for 10 minutes and then plated onto solid 1/2 Murashige and Skoog (MS) medium containing 1% (w/v) sucrose. The plates were kept in the dark in a refrigerator (4~5°C) for about 3 days and then transferred into a growth chamber (16-h light/8-h dark, 22~23°C).

extract_protocol:
Total RNA was extracted from the root tips of 4-day-old seedlings using a PureLink RNA Micro Kit (Invitrogen)
Library construction was performed with a BGI Optimal Dual-mode mRNA Library Prep Kit (LR00R96, BGI) and an MGIEasy circularization kit

tag: tissue

value: root

tag: genotype

tag: treatment


title: Definitive Endoderm cells, saracatinib 1

organism: Homo sapiens


title: Definitive Endoderm cells, saracatinib 2


title: seedling roots of nac103-11 rab8d-2 bio rep 3, 4 DAG


title: Definitive Endoderm cells, control 1

value: DMSO


title: Definitive Endoderm cells, control 2


title: seedling roots of gun1-101 rab8d-2 bio rep 2, 4 DAG


title: seedling roots of rab8d-2 bio rep 3, 4 DAG


title: iPS_control_2

city: Columbus

first: Rolf

last: Stottmann

state: OHIO

address: 575 Children's Crossroads

department: Pediatrics

country: USA

institute: Nationwide Children's Hospital

data_processing:
Low-quality reads (q<10), and adaptor sequences were eliminated from raw reads usingbbdukversion 37.64
Each sample was aligned to the GRCh38.p9 assembly of the Homo sapiensreference from NCBI
using version 2.6.0c of the RNA-Seqaligner STAR
Features were identified from the GFF file that came with the assembly fromGencode(V28)
Feature coverage counts were calculated usingfeatureCounts
Significant differentially expressed features between the two groups are those that have an absolute value of foldchange >= 1.5 and an adjusted p-value of <= 0.10 (10% FDR)
Assembly: GRCh38.p9
Supplementary files format and content: AllData_230314_Stottmann_GSL-KI-3283_RNASeq_Results.xlsx contains raw and normalized counts for each Sample
Supplementary files format and content: 230314_Stottmann_GSL-KI-3283_RNASeq_Results.xlsx contains differential expression analysis for each group of replicate Samples

source_name: iPSC

growth_protocol: The STEMdiff™ SMADi Neural Induction Kit (STEMCELL) was used to generate neural rosettes from high-quality iPSC colonies. Briefly, iPSCs were dissociated into single cells and plated into an Aggrewell 800 well (STEMCELL) at 10,000 cells per well, forming embryoid bodies. These were fed daily and replated on day five by filtering through a 37µM reversible strainer (STEMCELL) into a 24-well plate containing coverslips coated in Matrigel. On day 8, percent neural rosette formation was visually confirmed to be 75% or above before harvesting

extract_protocol:
Total RNA was extracted from iPSCs or neural rosettes using the Trizol (Tri Reagent, Sigma Aldrich) protocol with post-extraction cleanup. Samples were kept on ice until storage at -80°C. RNA concentration was quantified via Nanodrop.
Ribosomal RNA depletion using NEBNext rRNA Depletion kit (Human/Mouse/Rat)
Libary generation using NEBNext UltraII Directional RNA Library Prep kit with IDT dual unique with UMI illumina adapters

value: iPSC

value: control


title: iPS_control_3


title: NR_control_3

source_name: neural rosette

value: neural rosette


title: iPS_patient_1

value: patient


title: NR_patient_2


title: iPS_patient_2


title: NR_patient_1


title: iPS_patient_3


title: NR_patient_3


title: iPS_control_1


title: iPS_KO_3

value: KO


title: iPS_KO_2


title: NR_control_2


title: Definitive Endoderm cells, control 3


title: NR_KO_3


title: NR_control_1


title: NR_KO_2


title: NR_KO_1


title: K562 4C-Seq bait I, repeat #1

city: London

first: Niklas

last: Feldhahn

address: The Commonwealth Building, Hammersmith Hospital, Du Cane Road

department: Department of Medicine

country: United Kingdom

institute: Imperial College London

library_source: genomic

data_processing:
Bait and adapter sequencer were trimmed from raw reads using cutadapt v3.0 with -e 0.2 flag
Reads were aligned to the GRCh38 genome with Bowtie v2.3 or BWA MEM v0.7.17
Downstream analysis was done following the Pipe4C pipeline described by Krijger et al. 2019 Methods (doi:10.1016/j.ymeth.2019.07.014).
Assembly: hg38
Supplementary files format and content: RPKM normalised bigwig files for track visualisation by genome browsers.

molecule: genomic DNA

growth_protocol: Leukaemia cells from patients were isolated from peripheral blood/bone marrow or leukopheresis using density gradient separation and erythrocyte lysis, and then subjected to 4C-Seq. AML/CML cell lines were grown at a density 0.5-3mio/ml in RPMI1640 media with 20% FBS, 1% Pen/Strep and 1X Glutamax.

extract_protocol:
Cells were washed with PBS, counted and subjected to the 4C-Seq protocol described by Stadhouders, R. et al. (doi:10.1038/nprot.2013.018). In brief, formaldehyde crosslinked DNA was digested by EcoR1 and ligated consecutively. Reverse crosslinked DNA was then digested by Dpn2 followed by circularization in a 14ml volume to decrease the likelihood of inter-ligations.
Circularised DNA was amplified using bait specific PCR primers including a 5’ overhang comprising the P5 or P7 Illumina adapter sequence, an Illumina sequencing primer sequence, a barcode and/or an index sequence, and a bait specific primer at the 3’ end as described by Stadhouders, R. et al. (doi:10.1038/nprot.2013.018). The number of cycles was minimised to ensure the reaction was stopped when still linear. All steps were quality checked as described by Stadhouders, R. et al. 4C-seq libraries were then sequenced.


title: HEL CTCFsh1 4C-Seq bait I, repeat #1

source_name: HEL

value: HEL

value: RNAi


title: KCL22 4C-Seq bait I, repeat #1


title: KCL22 4C-Seq bait D repeat #1


title: HEL CTRLsh 4C-Seq bait I, repeat #1


title: K562 4C-Seq bait D, repeat #1


title: HL60 4C-Seq bait I, repeat #1


title: K562 4C-Seq bait A, repeat #2


title: HEL CTCFsh2 4C-Seq bait I, repeat #1


title: KCL22 4C-Seq bait A, repeat #2


title: HEL 4C-Seq bait I, repeat #1


title: HL60 4C-Seq bait A, repeat #1


title: AML-OCI3 4C-Seq bait A, repeat #1


title: M139 4C-Seq bait B, repeat #1

source_name: primary CML cells

value: primary CML cells


title: HEL 4C-Seq bait A, repeat #1


title: AML-OCI3 4C-Seq bait I, repeat #1


title: K562, H3K4me3, rep1 (DNBSEQ)

city: Moscow

first: Arkadiy

last: Golov

address: Vavilova, 34/5

country: Russia

institute: Institute of Gene Biology, RAS

data_processing:
Raw MChIP-C reads were mapped to the hg19 genome build with BWA-MEM (with -SP5M flags).
Mapped reads were parsed, uniquely mapped distal read pairs (>5,000 bp apart; cis) were selected and deduplicated with the pairtools package (v.0.3.0).
Binary BAM files were produced from pairtools output and reads mapping to the H3K4me3 ChIP-seq peaks were selected with the samtools (v.1.15.1).
BigWig proximity ligation profiles (merged or separated by individual viewpoints) were generated with the deeptools (v.3.5.1).
Assembly: hg19
Supplementary files format and content: bigWig: viewpoint specific and merged MChIP-C proximity ligation coverage in 100bp and 250bp genomic bins, ChIP-seq occupancy coverage in 50bp genomic bins
Supplementary files format and content: bed: genomic intervals corresponding to the positions of MChIP-C viewpoints
Supplementary files format and content: bedpe: pairs of genomic interval representing MChIP-C identified physical genomic interactions

growth_protocol: K562 cells were cultivated in DMEM medium supplemented with 10% fetal bovine serum and 1× penicillin/streptomycin in a humidified 37 °C incubator with 5% CO2

extract_protocol:
MChIP-C: Cells were crosslinked for 10 min at room temperature in fresh full growth medium supplemented with 2% formaldehyde. Crosslinked cells were permeabilized in PBS supplemented with 0.01% digitonin on ice, chromatin was subjected to 1h digestion with 35-40 U of micrococcal nuclease (Thermo Scientific, EN0181). Next, DNA ends were repaired with 100 U of T4 Polynucleotide Kinase (NEB, M0201L) and 50U of Klenow fragment (NEB, M0210L). Blunted DNA ends were proximity ligated with 75U of T4 DNA ligase (ThermoScientific, EL0012). Chromatin was sheared on ice with a VirSonic 100 cell disrupter with 3 15-sec pulses on “15” power setting, separated with 3 min periods of recovery, transferred to RIPA buffer and immunoprecipitated with anti-H3K4me3 antibodies (Active motif, 39016) and protein A/G magnetic beads (Thermo Scientific, 26162). DNA was reverse-crosslinked and isolated with phenol-chloroform extraction and ethanol precipitation. ChIP-seq:  Cells were crosslinked for 10 min at room temperature in fresh full growth medium supplemented with 2% formaldehyde. Crosslinked cells were permeabilized in PBS supplemented with 0.01% digitonin on ice. Permeabilized cells were resuspended in ice cold ChIP lysis buffer (50 mM Tris-HCl pH 8.0, 1% SDS, 10 mM EDTA), chromatin was sheared with 4 30-sec ultrasound pulses on “15” power setting of VirSonic 100 sonicator. Incubation with antibodies, immunoprecipitation, DNA isolation were performed as described in MChIP-C protocol.
MChIP-C and ChIP-seq NGS libraries were prepared from immunoprecipitated DNA with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645) according to the manufacturer’s recommendations, with the following modifications: 1) we decreased the reaction volumes two-fold; 2) instead of the adaptor included in the kit, we used 1 μL of barcoded Y-shaped Illumina TruSeq adapters (Illumina, 20015960 and 20015961) per reaction and extended ligation time to 1h.  We used either 17 μL (~0.37×) (for MChIP-C) or 35 μL (0.76×) (for ChIP-seq) of AMPure XP beads (Beckman Coulter, A63881) in the pre-PCR clean-up. Adapter-ligated material was amplified with 12-14 cycles of PCR using KAPA HiFi HotStart PCR Kit (Roche, 07958897001) and universal P5/P7 Illumina primers.
OTHER:MChIP-C, ChIP-seq

value: Human erythroleukemia


title: KCL22 4C-Seq bait A, repeat #1


title: M139 4C-Seq bait A, repeat #1


title: M135 4C-Seq bait A, repeat #1


title: M141 4C-Seq bait A, repeat #1


title: iPS_KO_1


title: M135 4C-Seq bait B, repeat #1


title: M128 4C-Seq bait A, repeat #2


title: M125 4C-Seq bait B, repeat #2


title: M128 4C-Seq bait B, repeat #2


title: M141 4C-Seq bait B, repeat #1


title: M125 4C-Seq bait A, repeat #2


title: M126 4C-Seq bait B, repeat #1


title: M128 4C-Seq bait A, repeat #1


title: M125 4C-Seq bait B, repeat #1


title: M124 4C-Seq bait B, repeat #1


title: M101 4C-Seq bait B, repeat #1


title: K562 4C-Seq bait B, repeat #1


title: M126 4C-Seq bait A, repeat #1


title: M125 4C-Seq bait A, repeat #1


title: M102 4C-Seq bait B, repeat #1


title: M102 4C-Seq bait A, repeat #1


title: M128 4C-Seq bait B, repeat #1


title: H1299 KAT5 Y47A OE H4ac rep2

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to hg38 by HISAT2 (v2.1.0).
Bigwig is generated with Deeptools (v3.5.2).
Assembly: hg38
Supplementary files format and content: bigwig file, ChIP density profiles for genome browser.

growth_protocol: H1299 is cultured in RPMI1640 with 10% FBS.

extract_protocol:
Eluted DNA were decrosslinked and extracted by QIAquick PCR Purification Kit (QIAGEN, Cat. 28106).
Libraries were constructed using Illumina standard protocols.

value: Human lung cancer

value: KAT5 Y47A OE


title: H1299 KAT5 dN OE H4ac rep2

value: KAT5 dN OE


title: H1299 KAT5 FL OE H4ac rep3

value: KAT5 FL OE


title: H1299 KAT5 dN OE H4ac rep3


title: H1299 KAT5 Y47A OE H4ac rep3


title: H1299 KAT5 dN OE H4ac rep1


title: H1299 KAT5 Y47A OE H4ac rep1


title: H1299 KAT5 FL OE H4ac rep2


title: myeloid-specific FoxO1-knockout 2, I/R

city: Beijing

first: Yao

last: He

address: 38 Xueyuan Road, Haidian District

department: Pharmacology

institute: Peking University

data_processing:
Raw data quality control were performed using FastQC (version v0.12.0)
Raw sequencing data quality was first filtered by Trim_galore (version 0.6.2), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed
Clean reads were mapped to the reference genome of mm39 reference genome using Hisat2 (version 2.2.1) with default parameters
Perform gene quantification of clean data using Salmon (version 1.10.2)
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Mus musculus

source_name: Kidney

extract_protocol:
Kidney tissue was digested with collagenase. RNA was harvested using TRIzol™ Reagent (Thermo Fisher). 1.3 ug of tota RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (USA) following manufacturer's protocols.

treatment_protocol:
To achieve conditional knockout of FoxO1, 8–10-week-old Lyz2-CreERT2 FoxO1flox/flox mice were injected intraperitoneally with tamoxifen (75  mg per kg body weight, dissolved in corn oil) (Solarbio, #IT0030) for 5 successive days.
After mice were anesthetized with an intraperitoneal injection of pentobarbital (60 mg/kg), the right renal was removed, and the left renal artery and vein were identified and clamped for 35 minutes with a non-traumatic clamp. Then the clamp was released and reperfusion was observed for 5 minutes to ensure reflow process. The incision was then closed and the animal was allowed to recover.

value: Kidney

tag: disease state

value: ischemia-reperfusion injury-induced acute kidney injury

value: myeloid-specific FoxO1-knockout


title: Control 1, I/R

value: WT


title: Control 3, I/R


title: myeloid-specific FoxO1-knockout 3, I/R


title: Control 4, I/R


title: myeloid-specific FoxO1-knockout 4, I/R


title: myeloid-specific FoxO1-knockout 1, I/R


title: Control 2, I/R


title: M124 4C-Seq bait A, repeat #1


title: H1299 KAT5 FL OE H4ac rep1


title: H1299 INPUT


title: M101 4C-Seq bait A, repeat #1


title: H1299 KAT5 dN OE KAT5 rep1


title: H1299 KAT5 dN OE KAT5 rep2


title: Gentamicin-induced mutation 32

city: Shanghai

first: Tianmin

last: Wang

address: Huaxia Middle Road, 393

department: School of Life Science and Technology

institute: ShanghaiTech University

description:
mutant32
mutation_info.xlsx

data_processing:
For 3’ -end-seq, firstly, sequencing raw data was subjected to FastQC (v0.11.9) for quality control and cutadapt (2.10) for adaptor trimming. In detail, fastqc was used with default parameters, cutadapt command was used with parameters -q 10,10 --minimum-length 100:100 --max-n 3 --pair-filter=any -o. The data was then demultiplexed by cutadapt based on the unique RNA adaptors. Paired-end reads were aligned to E. coli reference genome (NC_000913.3) by bowtie2 (2.4.1) with parameters -X 1000 -I 18 --no-mixed --no-discordant. The mapped reads were converted to bam files by samtools (1.10). To minimize the effect of sequencing depth on further analysis, we subsampled every bam file to the equal number of 4.5 million paired-end reads. Reads were counted for bam files using R (4.0.2) method summarizeOverlaps from GenomicAlignments package (v1.26.0) in a strand specific manner, with the following options “mode = "Union", ignore.strand = FALSE, singleEnd = FALSE, preprocess.reads = invertStrand”.
For RNA-seq data, data processing was similar to our previous report (Wang et al., Environmental Microbiology 2022). Adaptor trimming, alignment to genome and gene read count table were all the same with 3’-end-seq as shown above.
For genome re-sequencing, after demultiplexing, we trimmed adaptor sequences by cutadapt (v0.11.9) and adopted breseq (0.35.3) to identify mutations from the first read of the NGS data in a default clonal mode against the reference genome (NC000913.3).
Assembly: NC000913.3
Supplementary files format and content: comma-delimited text file for expression matrix
Supplementary files format and content: xlsx file for 3' -end-seq CPM of PRSEs and mutation information

organism: Escherichia coli

growth_protocol: In all experiments, E. coli K12 BW25113 was used (originally from CICC, 23872) as the wildtype strain. Single colony was picked up from a stock LB agar plate and was grown aerobically with shaking at 220 rpm in Luria-Bertani (LB) broth (10 g/L tryptone (Oxoid, LP0042), 10 g/L NaCl (Macklin, S805275), 5 g/L yeast extract (Oxoid, LP0021)) medium overnight (typically 12 h) as the seed culture. All cultures were carried out at 37 °C with shaking at 200 rpm.

extract_protocol:
For RNA exactraction, bacteria lysate was prepared using lysozyme and proteinase K. Total RNA was then purified by RNAClean XP beads (Beckman, A63987). For genomic DNA, TIANamp Bacteria DNA kit (TIANGEN, DP302) were used. See decrisption in our paper for details.
3' -end-seq library preparation method was adopted from a previous multiplexed RNA-seq library preparation method reported by Avraham et al. Systematic modifications were introduced to repurpose it to keep 3’ end information of bacterial transcripts. To prepare RNA-seq library, here we did not follow routine RNA-seq library construction method, in order to minimize the batch effect introduced when applying different library preparation protocols. Genome re-sequencing were prepared by a Tn5-based library construction method. See protocol details in our paper.

treatment_protocol: Overnight seed cultures were diluted by 1:350 into 700 μL of fresh medium and grown in a 48-well plate in a microplate reader (Tecan, Spark). When the cultures grew to OD600 ~ 0.2, we carried out another dilution of 1:50 into fresh medium and cultivated with the same condition. When subcultures reached an OD600 of ~ 0.25, 10 μL gentamicin (Selleck, S4030) was supplemented to make a final concentration of 6 mg/L.

tag: strain

value: mutant


title: Gentamicin-induced mutation 31

description:
mutant31
mutation_info.xlsx


title: Gentamicin-induced mutation 30

description:
mutant30
mutation_info.xlsx


title: Gentamicin-induced mutation 33

description:
mutant33
mutation_info.xlsx


title: H1299 KAT5 Y47A OE KAT5 rep3


title: Gentamicin-induced mutation 28

description:
mutant28
mutation_info.xlsx


title: Gentamicin-induced mutation 29

description:
mutant29
mutation_info.xlsx


title: H1299 KAT5 Y47A OE KAT5 rep1


title: Gentamicin-induced mutation 25

description:
mutant25
mutation_info.xlsx


title: Gentamicin-induced mutation 26

description:
mutant26
mutation_info.xlsx


title: H1299 KAT5 FL OE KAT5 rep2


title: Gentamicin-induced mutation 24

description:
mutant24
mutation_info.xlsx


title: H1299_NTT_RNA-seq_rep3

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to hg38 by HISAT2 (v2.1.0).
Read counts were generated by HTSeq (v0.11.3).
Assembly: hg38
Supplementary files format and content: txt file, read counts from HTseq.

molecule: polyA RNA

extract_protocol:
Total RNA were extracted by RNeasy Plus Mini Kit (QIAGEN, Cat. 74136).
Libraries were constructed using Illumina standard protocols.

value: TIP60 KO1/TIP60 OE dN


title: H1299_NTT_RNA-seq_rep1


title: H1299 KAT5 FL OE KAT5 rep1


title: Gentamicin-induced mutation 22

description:
mutant22
mutation_info.xlsx


title: H1299 KAT5 dN OE KAT5 rep3


title: Gentamicin-induced mutation 21

description:
mutant21
mutation_info.xlsx


title: Gentamicin-induced mutation 23

description:
mutant23
mutation_info.xlsx


title: Gentamicin-induced mutation 20

description:
mutant20
mutation_info.xlsx


title: H1299_Y47A_RNA-seq_rep3

value: TIP60 KO1/TIP60 OE Y47A


title: Gentamicin-induced mutation 19

description:
mutant19
mutation_info.xlsx


title: H1299_Y47A_RNA-seq_rep1


title: Gentamicin-induced mutation 27

description:
mutant27
mutation_info.xlsx


title: H1299 KAT5 Y47A OE KAT5 rep2


title: H1299 KAT5 FL OE KAT5 rep3


title: H1299_WT_RNA-seq_rep3

value: TIP60 KO1/TIP60 OE FL


title: H1299_Y47A_RNA-seq_rep2


title: Gentamicin-induced mutation 17

description:
mutant17
mutation_info.xlsx


title: H1299_WT_RNA-seq_rep2


title: H1299_WT_RNA-seq_rep1


title: Gentamicin-induced mutation 15

description:
mutant15
mutation_info.xlsx


title: H1299_KO2_RNA-seq_rep2

value: TIP60 KO2


title: Gentamicin-induced mutation 13

description:
mutant13
mutation_info.xlsx


title: Gentamicin-induced mutation 16

description:
mutant16
mutation_info.xlsx


title: Gentamicin-induced mutation 12

description:
mutant12
mutation_info.xlsx


title: H1299_NTT_RNA-seq_rep2


title: H1299_KO2_RNA-seq_rep1


title: Gentamicin-induced mutation 11

description:
mutant11
mutation_info.xlsx


title: Gentamicin-induced mutation 10

description:
mutant10
mutation_info.xlsx


title: H1299_KO1_RNA-seq_rep2

value: TIP60 KO1


title: Gentamicin-induced mutation 18

description:
mutant18
mutation_info.xlsx


title: H1299_KO1_RNA-seq_rep1


title: Gentamicin-induced mutation 8

description:
mutant8
mutation_info.xlsx


title: Gentamicin-induced mutation 9

description:
mutant9
mutation_info.xlsx


title: H1299_KO1_RNA-seq_rep3


title: H1299_ctl_RNA-seq_rep3

value: sgGFP


title: Gentamicin-induced mutation 14

description:
mutant14
mutation_info.xlsx


title: Gentamicin-induced mutation 7

description:
mutant7
mutation_info.xlsx


title: H1299_ctl_RNA-seq_rep2


title: H1299_KO2_RNA-seq_rep3


title: Gentamicin-induced mutation 5

description:
mutant5
mutation_info.xlsx


title: Gentamicin-induced mutation 4

description:
mutant4
mutation_info.xlsx


title: H1299_ctl_RNA-seq_rep1


title: Gentamicin-induced mutation 6

description:
mutant6
mutation_info.xlsx


title: Gentamicin-induced mutation 3

description:
mutant3
mutation_info.xlsx


title: A549 KAT8 R98W OE rep3

growth_protocol: A549 is cultured in DMEM with 10% FBS.

value: KAT8 R98W OE


title: A549 KAT8 WT OE rep2

value: KAT8 WT OE


title: A549 KAT8 R98W OE rep1

value: Human lung cancer


title: A549 KAT8 R98W OE rep2


title: Gentamicin, 60 min, 3'-end-seq, Δmfd

description:
Gentamicin_60min_3end_seq_mfd
PRSE_end_CPM.xlsx

value: {delta}mfd

value: 6 mg/L, gentamicin


title: Gentamicin-induced mutation 1

description:
mutant1
mutation_info.xlsx


title: A549 KAT8 WT OE rep3


title: Gentamicin, 110 min, 3'-end-seq, Δmfd

description:
Gentamicin_110min_3end_seq_mfd
PRSE_end_CPM.xlsx


title: A549 KAT8 WT OE rep1


title: A549 KAT8 R98W OE KAT8 rep3

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to hg38 by HISAT2 (v2.1.0).
Bigwig is generated with Danpos2 (v2.2.2).
Assembly: hg38
Supplementary files format and content: bigwig file, ChIP density profiles for genome browser.

tag: antibody


title: A549 KAT8 R98W OE KAT8 rep1


title: Gentamicin, 110 min, 3'-end-seq, wildtype

description:
Gentamicin_110min_3end_seq_wt
PRSE_end_CPM.xlsx

value: wildtype


title: A549 KAT8 R98W OE KAT8 rep2


title: A549 KAT8 WT OE KAT8 rep3


title: Gentamicin, 60 min, 3'-end-seq, wildtype

description:
Gentamicin_60min_3end_seq_wt
PRSE_end_CPM.xlsx


title: Gentamicin-induced mutation 2

description:
mutant2
mutation_info.xlsx


title: Gentamicin, 40 min, 3'-end-seq, wildtype

description:
Gentamicin_40min_3end_seq_wt
PRSE_end_CPM.xlsx


title: Gentamicin, 74 min, 3'-end-seq, wildype

description:
Gentamicin_74min_3end_seq_wt
PRSE_end_CPM.xlsx


title: A549 KAT8 WT OE KAT8 rep2


title: Gentamicin, 20 min, 3'-end-seq, wildtype

description:
Gentamicin_20min_3end_seq_wt
PRSE_end_CPM.xlsx


title: Gentamicin, 13 min, 3'-end-seq, wildtype

description:
Gentamicin_13min_3end_seq_wt
PRSE_end_CPM.xlsx


title: A549 KAT8 R98W OE H4K16ac rep3


title: A549 KAT8 R98W OE H4K16ac rep2


title: 0 min, replicate 2, 3'-end-seq, wildtype

description:
0min_replicate_2_3end_seq_wt
PRSE_end_CPM.xlsx


title: 12hpf_embryo_H2A.Z,rep2

city: Rochester

first: Fanju

last: Meng

state: NY

address: 601 Elmwood Avenue

department: Biomedical Genetics

institute: University of Rochester Medical Center

data_processing:
Adapters were trimmed from raw reads using cutadapt
Trimmed reads were aligned to zebrafish genome (GRCz11) using Bowtie2, and then PCR duplicates were marked and removed using Picard
Read count normalized genome browser tracks were generated using bamCoverage from merged Sam files of triplicates with the following parameters: --normalizeUsing RPKM --binSize 10
Assembly: Zv11
Supplementary files format and content: bigWig files

organism: Danio rerio

source_name: whole embryo

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

extract_protocol:
Embryos were manuallly dechorionated, dissociated by pipetting, and around 100,000 cells were used for nuclei isolation and CUT&Tag
CUT&Tag libraries were generated using NEBNext High-Fidelity 2X PCR Master Mix (M-541S) according to standard method.

value: whole embryo

tag: developmental stages

value: 12hour post fertilization

value: wild type


title: 12hpf_embryo_H2A.Z,rep3


title: A549 input

value: input


title: 0 min, replicate 1, 3'-end-seq, wildtype

description:
0min_replicate_1_3end_seq_wt
PRSE_end_CPM.xlsx


title: 12hpf_embryo_Anp32e,rep3


title: Gentamicin, 110 min, RNA-seq, Δmfd

description:
Gentamicin_110min_RNA_seq_mfd
qualified_gene_TPM.csv


title: 12hpf_embryo_H2A.Z,rep1


title: A549 KAT8 WT OE H4K16ac rep2


title: 12hpf_embryo_Anp32e,rep2


title: A549 KAT8 WT OE H4K16ac rep3


title: 12hpf_embryo_Anp32e,rep1


title: PA1_DRIP_RNaseH_plus_rep2

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

data_processing:
First filtered by using Trimmomatic v0.38; Next removed rRNA by bowtie v1.1.2;
Analyses by Bowtie2 v2.3.5;  Duplicated reads were removed by Picard v2.22.1
Assembly: GRCh38/hg38 human reference genome with the GENCODE gene annotation (v28)
Supplementary files format and content: bigwig files include the mapping information

extract_protocol:
Genomic DNAs (containing RNAs in the hybrid state) were extracted by phenol/chloroform extraction and ethanol precipitation gently. Then the extracted DNAs were fragmented by treatment with restriction enzymes cocktail (HindIII, EcoRI, BsrGI, XbaI, and SspI) overnight. Fragmented DNAs were recovered by phenol/chloroform extraction and ethanol precipitation gently, and dissolved into 200 μL water. Half of recovered DNAs were treated with RNase H enzyme (Thermo) to eliminate RNAs in the hybrids overnight at 37 ℃ as DRIP control sample, while the remaining half were treated with water as DRIP sample. Digested DNAs were extracted by phenol/chloroform extraction and ethanol precipitation gently, and dissolved into 100 μL water. 10 μg total DNAs in the DRIP sample or DRIP control sample was used for immunoprecipitation (IP) using 5μg S9.6 antibody (Karafast) overnight at 4 ℃, followed by incubation with 50 μL Dynabeads Protein G. The beads were then washed two times with binding buffer (100 mM NaPO4 pH 7.0, 1.4 M NaCl, 0.5% Triton X-100) and eluted by elution buffer (50 mM Tris pH 8.0, 10 mM EDTA, 0.5% SDS) with Proteinase K at 55 ℃ for 1hr. At last, DNAs in the DNA:RNA hybrids were extracted by phenol/chloroform extraction and ethanol precipitation for qPCR. For DRIP-seq, extracted DNAs were further digested with 0.1 mg/mL RNase A at 37 ℃ for 1 hr and recovered by phenol/chloroform extraction and ethanol precipitation.
Ribominus RNA libraries were prepared using Illumina TruSeq Stranded Total RNA LT Sample Prep Kit. All libraries were size-selected with AmpureXP beads (Agencourt) and quantified. using Agilent Bio analyzer 2100 and Qubit high-sensitivity dsDNA assay. Size-selected libraries were subjected to deep sequencing with Illumina NextSeq 500
1×100bp single-end Ribominus RNA-seq

treatment_protocol: At least 5×106 cultured cells were washed with DPBS, collected and resuspended into 1.6 mL 1×TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). Then 83 μL 10% SDS was added to lyse cells at 37 ℃ for 1hr, and 20 μL 20 mg/mL proteinase K were added to digest proteins at 55 ℃ for at least 10hr.

value: RNase H1


title: Gentamicin, 60 min, RNA-seq, Δmfd

description:
Gentamicin_60min_RNA_seq_mfd
qualified_gene_TPM.csv


title: 0 min, 3'-end-seq, Δmfd

description:
0min_3end_seq_mfd
PRSE_end_CPM.xlsx


title: A549 KAT8 WT OE KAT8 rep1


title: 6hpf_embryo_Anp32e,rep3

value: 6hour post fertilization


title: 6hpf_embryo_Anp32e,rep2


title: PA1_DRIP_RNaseH_minus_rep2


title: PA1_DRIP_RNaseH_minus_rep1


title: Gentamicin, 6 min, 3'-end-seq, wildtype

description:
Gentamicin_6min_3end_seq_wt
PRSE_end_CPM.xlsx


title: U251 cells, STING-OE3

city: guangzhou

first: xinrou

last: lin

address: yanjiang Road

institute: Sun Yat-sen Memorial Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: U251 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells were transfected with negative control plasmids or the STING overexpression plasmids for three days (1ug/well)

value: glioblastoma cells

value: WT

value: cells were transfected with STING overexpression plasmids

tag: time

value: Day 3


title: 6hpf_embryo_Anp32e,rep1


title: A549 KAT8 WT OE H4K16ac rep1


title: 0 min, RNA-seq, Δmfd

description:
0min_RNA_seq_mfd
qualified_gene_TPM.csv


title: Gentamicin, 110 min, RNA-seq, wildtype

description:
Gentamicin_110min_RNA_seq_wt
qualified_gene_TPM.csv


title: A549 KAT8 R98W OE H4K16ac rep1


title: PA1_DRIP_RNaseH_plus_rep1


title: U251 cells, STING-OE2


title: U251 cells, STING-OE1


title: WT_484_rep4

city: Brno

first: Vaclav

last: Hejret

address: Kamenice 5

country: Czech Republic

institute: Masaryk University

data_processing:
bcl2fastq v. 2.20.0.422 software used for basecalling
6-nt long barcode sequence related to Lexogen QuantSeq Library Prep Kit were trimmed using seqtk 1.3-r106, the adapters and quality trimming of raw fastq reads was performed using Trimmomatic v. 0.36
Trimmed RNA-Seq reads were mapped against the human genome (hg38) reference genome using STAR v. 2.7.3a with default parameters default parameters except -outFilterMismatchNoverLmax 0.1 and -twopassMode Basic
Gene counts were produced using featureCounts tool v2.0.1
The differential gene expression analysis was performed using Bioconductor package DESeq2 v1.20.0. Genes were considered as differentially expressed based on a cut-off of adjusted p-value<0.05 and log2(fold-change) ≥1 or ≤-1
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts values for each sample

growth_protocol: Standard HEK293TREx growth conditions

extract_protocol:
Total RNA was extratced from cells using standard Trizol Rna isolation method.
500 nanograms of total RNA per sample was used as an input for library preparation using QuantSeq FWD 3’mRNA Library Prep Kit (Lexogen). Briefly, RNA was transcribed into cDNA using oligodT primer (FS1) at half volume compared to the manufacturer's instructions to minimize the off-target products. Following the first strand synthesis, RNA removal and second strand synthesis were performed using the UMI Second Strand Synthesis Mix (USS) containing Unique Molecular Identifiers (UMIs) that allow detection and removal of PCR duplicates. Finally, sequencing libraries were created by PCR with i5 Unique Dual Indexing Add-on Kit for Illumina (Lexogen). The quality and quantity of libraries was determined using Fragment Analyzer by DNF-474 High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies) and QuantiFluor dsDNA System (Promega). Final library pool was sequenced on Illumina NextSeq 500 with 75 bp single-ends

treatment_protocol: HEK293TREx cells at ~40% confluency were transfected with AntimiRs for 24hrs for the respective miRNAs at final concentration of 30nM, using RNAimax following the manufacturer's protocol.

value: Human embryonic kidney

value: Wildtype


title: Gentamicin, 74 min, RNA-seq, wildype

description:
Gentamicin_74min_RNA_seq_wt
qualified_gene_TPM.csv


title: K562 Ponatinib PCHiC

data_processing:
PCHiC data was processed as described in Freire-Pritchett et al. (doi: 10.1038/s41596-021-00567-5).
Raw fastq files were aligned to the human genome (hg38) using the HiCUP package (v0.7.3), with the range di-tags set between 100 - 850 bp.
The Capture Hi-C Analysis of Genomic Organisation (CHiCAGO) (v1.18.0) was utilised to process HiCUP-generated bam files to produce interaction files, with a score threshold of 5.
Assembly: hg38
Supplementary files format and content: Significant PCHiC interactions (Bait chromosome, bait start, bait end, other-end chromosome coordinate and CHiCAGO score, CHiCAGO score)

source_name: Cell line

growth_protocol: K562 cells were maintained at a density of 0.5-2 million cells/mL in RPMI-1640 media supplemented with 20% FBS, 1% Pen/Strep and 1X Glutamax.

extract_protocol:
Cells were counted and a total of 20 million cells were harvested to be processed with the promoter-capture HiC protocol as described in Schoenfelder et al. (doi:10.3791/57320). Briefly, paraformaldehyde crosslinked nuclei were digested with HindIII, with the ends labelled with biotin and subsequently ligated. Reverse crosslink was performed and the DNA was sonicated and subsequently purified with streptavidin beads.
Library construction was prepared according to the protocol described in Schoenfelder et al (doi:10.3791/57320). Briefly, xGen Stubby Adapter and UDI primer set was utilised to index each HiC library using the Phusion polymerase. Following sequencing adapter ligation, the library was purified with SPRI beads. To generate PCHiC library, biotinylated RNA probes were used to capture promoter sequences from the HiC library and amplified by PCR and subsequently purified. PCHiC library was sequenced by paired-end sequencing.

treatment_protocol: Cells were treated with either DMSO (vehicle control), or Ponatinib (100 nM) for 24 hours before harvesting the cells.

value: Cell line

value: Chronic Myelogenous leukaemia

value: Ponatinib


title: Gentamicin, 60 min, RNA-seq, wildtype

description:
Gentamicin_60min_RNA_seq_wt
qualified_gene_TPM.csv

value: 6 mg/L, gentamicin


title: WT_484_rep3


title: K562 DMSO PCHiC

value: DMSO


title: U251 cells, NC3

value: cells were transfected with negative control plasmids


title: Gentamicin, 40 min, RNA-seq, wildtype

description:
Gentamicin_40min_RNA_seq_wt
qualified_gene_TPM.csv

value: wildtype


title: U251 cells, NC2


title: Gentamicin, 20 min, RNA-seq, wildtype

description:
Gentamicin_20min_RNA_seq_wt
qualified_gene_TPM.csv


title: WT_484_rep2


title: U251 cells, NC1


title: Gentamicin, 13 min, RNA-seq, wildtype

description:
Gentamicin_13min_RNA_seq_wt
qualified_gene_TPM.csv


title: M126 H3K27ac

data_processing:
Fastq were converted to uBAM and adapters marked with Picard v2.6.0, before aligning with BWA MEM v0.7.17 to the GRCh38 genome, Gencode v36
Duplicates marked with Picard, and filtering sorting and indexing performed with Samtools v1.2
Tracks were generated with DeepTools v3.5.1 using RPKM nomalization, peaks called with MACS2 v2.2.7.1
Assembly: hg38
Supplementary files format and content: RPKM normalised bedGraph files for track visualisation by genome browsers.

source_name: CML patient leukaemia cells

growth_protocol: Leukaemia cells from patients were isolated from peripheral blood/bone marrow or leukopheresis using density gradient separation and erythrocyte lysis, and then subjected to ChIP-Seq.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10min, and quenched and lysed as described (Boulianne et al, doi:10.1016/j.celrep.2017.01.057). Chromatin was sonicated using an S220 sonicator (Covaris). Pulldown of H3K27ac-bound DNA was performed using H3K27ac antibodies (abcam ab4729) as described in Boulianne et al.
ChIP-Seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB).

value: CML patient leukaemia cells


title: WT_484_rep1


title: M124 H3K27ac


title: RNA-Seq; of homo sapiens; SNU449 cells; depletion of RBM39 by indisulam treatmend and RBM39_siRNA experiment_3

city: Basel

first: Dirk

last: Mossmann

state: BS

address: Spitalstrasse 41

department: Biocenter

country: Switzerland

institute: University of Basel

description:
RBM39depletion_RBM_3
RBM39depletion_RBM_3

data_processing:
RBM39_KDandDepletion_ASEs_contrasts_20230307.xlsx:
align fastq-files on unix cluster: STAR/2.7.9a-GCC-7.3.0-2.30
generating differential alternative splicing data in Rstudio: using library <NxtIRFcore> , filter data using default filters. The function <limma_ASE> was used to generate statistics for differential ASE analysis
RBM39_KDandDepletion_contrasts_20230307.xlsx:
align fastq-files on unix cluster: Subread/2.0.2-foss-2018b using the function <subread-align>
feature count on unix cluster: Subread/2.0.2-foss-2018b using the function <featureCounts>
generating linear fitted normalized counts in Rstudio: using library <EdgeR> , filter data for abundance higher than cpm = 2 in at least 2 samples using the function <rowSums>; calculate the normalization factors with the function <calcNornFactors> then <voom> and finally <lmFit>
Assembly: RBM39_KDandDepletion_ASEs_contrasts_20230307.xlsx:  Ensemble: Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa
Assembly: RBM39_KDandDepletion_contrasts_20230307.xlsx:  Homo_sapiens.GRCh38.106
Supplementary files format and content: RBM39_KDandDepletion_ASEs_contrasts_20230307.xlsx: Columns A-E: Annotations: UniProt_ACC; GeneName; EventName; EventType; NMD_direction; Columns F-K: PSI values (percent sliced in): RBM39depletion_Ctrl_1; RBM39depletion_Ctrl_2; RBM39depletion_Ctrl_3; RBM39depletion_RBM_1; RBM39depletion_RBM_2; RBM39depletion_RBM_3; Columns L-S: ASE_statistics: AvgPSI_CTR; AvgPSI_RBM; logFC; negLog.adj.P.Val; Inc.logFC; negLog.Inc.adj.P.Val; Exc.logFC ; negLogExc.adj.P.Value
Supplementary files format and content: RBM39_KDandDepletion_contrasts_20230307.xlsx:  Columns A-F: Annotation: Symbol; Length; GeneID; Chr_Loc; description; Gene_Type; Columns G-L: normalized abundance (Log2): RBM39depletion_Ctrl_1; RBM39depletion_Ctrl_2; RBM39depletion_Ctrl_3; RBM39depletion_RBM_1; RBM39depletion_RBM_2; RBM39depletion_RBM_3; Columns M-N: LFC (RBMvsCTRL); negLog p-value (RBMvsCTRL)

extract_protocol:
Total RNA was extracted using the Rneasy kit (Qiagen) following the manufacturers protocol
Starting from 200 ng of total RNA, library preparation was performed using the TruSeq Stranded mRNA Library Kit (Illumina (USA), Cat# 20020595) and the TruSeq RNA Unique Dual (UD) Indexes (Illumina (USA), Cat# 20022371) with 15 cycles of PCR
Libraries were sequenced paired-end 51 bases bases (in addition: 8 bases for index 1 and 8 bases for index 2) using the NovaSeq 6000 instrument (Illumina (USA)) and the SP Flow-Cell loaded at a final concentration in Flow Lane of 380 pM and including 1% PhiX. Primary data analysis was performed with the Illumina real-time analysis (RTA) version 3.4.4.  On average per sample: 39±3 millions pass-filter reads were collected on 1 SP Flow-Cell.
Sequencing depth: 51 cycles

value: primary hepatocellular carcinoma

value: siRBM39 KD

value: Indisulam


title: RNA-Seq; of homo sapiens; SNU449 cells; depletion of RBM39 by indisulam treatmend and RBM39_siRNA experiment_2

description:
RBM39depletion_RBM_2
RBM39depletion_RBM_2


title: WT_320_rep4


title: 0 min, replicate 2, RNA-seq, wildtype

description:
0min_replicate_2_RNA_seq_wt
qualified_gene_TPM.csv


title: RNA-Seq; of homo sapiens; SNU449 cells; depletion of RBM39 by indisulam treatmend and RBM39_siRNA experiment_1

description:
RBM39depletion_RBM_1
RBM39depletion_RBM_1


title: WT_320_rep2


title: Gentamicin, 6 min, RNA-seq, wildtype

description:
Gentamicin_6min_RNA_seq_wt
qualified_gene_TPM.csv


title: WT_320_rep3


title: WT_320_rep1


title: M125 H3K27ac


title: RNA-Seq; homo sapiens; SNU449 cells; DMSO and nonTarget_siRNA control experiment_3

description:
RBM39depletion_Ctrl_3
RBM39depletion_Ctrl_3

value: Control non-targeting siRNA

value: Control DMSO


type: genomic

city: Bologna

first: Maria Giulia

last: Bacalini

address: Via Altura 3

department: Brain Aging Laboratory

country: Italy

institute: IRCCS Istituto delle Scienze Neurologiche di Bologna

description: genomic DNA from fibroblasts from donor CS816VI, CS type II, csb

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Infinium BeadChip using standard Illumina protocol

scan_protocol: HiScan scanner (Illumina)

data_processing: Signal intensities files were extracted using the minfi Bioconductor package. The preprocessNoob function implemented in minfi was applied to normalize raw data.

label: Cy3 and Cy5

source_name: donor CS816VI

label_protocol: Standard Illumina Protocol

growth_protocol: Patient fibroblasts were derived from skin biopsies excised from unexposed body sites by dermatologists. Healthy, UVSS and CS cells initially thawed at passage number (PN) 12 were cultured in Dulbecco's modified eagle medium (DMEM; Gibco) supplemented with 2mM L-glutamine (GlutaMAX™; Gibco), 10% foetal bovine serum (FBS; Gibco), 1% Penicillin-streptomycin (Gibco) in 20% O2/5% CO2 at 37 °C. Cells were harvested at PN14 for further experiments.

extract_protocol: Total genomic DNA (gDNA) from WT, UVSS and CS primary skin fibroblasts was isolated using the QIamp® DNA mini kit (Qiagen) and used for microarray-based analysis of genome wide DNA methylation levels in two different sets. For the first set, extracted gDNA was quantified by NanoDrop (ND-1000; Thermo Fisher Scientific) and 1µg was bisulfite-treated using the EZ DNA Methylation™ kit (Zymo Research), according to manufacturer instructions. Genone-wide DNA methylation analysis was performed on this material by Aros Applied Biotechnology A/S (Eurofins Genomics; Denmark) using the Infinium HumanMethylation450 BeadChip (Illumina). For the second set, extracted gDNA was directly send to Aros Applied Biotechnology A/S for bisulfite conversion and genome-wide DNA methylation using the Infinium MethylationEPIC BeadChip (Illumina) following manufacturer's instructions.

tag: donor

tag: disease

value: Cockayne syndrome (CS)

tag: diagnosis

value: CS type II

tag: mutation

value: csb

tag: group

value: CS

tag: csa/csb

value: truncated forms

tag: Sex

value: Male

tag: age at skin biopsy (yrs)

tag: age at death or latest report (yrs)


title: 0 min, replicate 1, RNA-seq, wildtype

description:
0min_replicate_1_RNA_seq_wt
qualified_gene_TPM.csv


title: M110 H3K27ac

tag: cell type


title: RNA-Seq; homo sapiens; SNU449 cells; DMSO and nonTarget_siRNA control experiment_2

description:
RBM39depletion_Ctrl_2
RBM39depletion_Ctrl_2

tag: cell line

tag: genotype


description: genomic DNA from fibroblasts from donor CS797VI, CS type II, csb

source_name: donor CS797VI

value: 50 CSB loss

value: Female


title: Antimir_320_rep4

value: Human embryonic kidney

tag: treatment

value: Anti miR-320 assay


title: M128 H3K27ac, repeat


title: M105 H3K27ac


title: Antimir_320_rep3


title: RNA-Seq; homo sapiens; SNU449 cells; DMSO and nonTarget_siRNA control experiment_1

description:
RBM39depletion_Ctrl_1
RBM39depletion_Ctrl_1


description: genomic DNA from fibroblasts from donor UVSS1VI, UVSS, csa

source_name: donor UVSS1VI

value: UV-sensitivity syndrome (UVSS)

value: UVSS

value: csa

value: NonAGED


description: genomic DNA from fibroblasts from donor CS548VI, CS type I, csb

source_name: donor CS548VI

value: CS type I

value: abscence of CSB


title: Antimir_320_rep2


title: RNA-Seq; homo sapiens; SNU449 cells; empty vector control experiment_3

data_processing:
AAOE_ASEs_contrasts_20230307.xlsx:
align fastq-files on unix cluster: STAR/2.7.9a-GCC-7.3.0-2.30
generating differential alternative splicing data in Rstudio: using library <NxtIRFcore> , filter data using default filters. The function <limma_ASE> was used to generate statistics for differential ASE analysis
AAOE_RNA_SEQ_contrasts_20230307.xlsx:
Primary data analysis was performed with the Illumina real-time analysis (RTA) version 3.4.4
On average per sample: 39±3 millions pass-filter reads were collected on 1 SP Flow-Cell
Assembly: Ensemble: Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa
Supplementary files format and content: AAOE_ASEs_contrasts_20230307.xlsx: Columns A-E: Annotations: UniProt_ACC; GeneName; EventName; EventType; NMD_direction; Columns F-K: PSI values (percent sliced in): RBM39depletion_Ctrl_1; AAOE_CTRL_1; AAOE_CTRL_2; AAOE_CTRL_3; AAOE_AA_1; AAOE_AA_2; AAOE_AA_3; Columns L-S: ASE_statistics: AvgPSI_CTR; AvgPSI_RBM; logFC; negLog.adj.P.Val; Inc.logFC; negLog.Inc.adj.P.Val; Exc.logFC ; negLogExc.adj.P.Value
Supplementary files format and content: AAOE_RNA_SEQ_contrasts_20230307.xlsx: Columns A-E:Annotation:  Gene Name; EntrezGene ID; Ensemble GeneID Human; Genetic Location; Genomic Coordinates; Columns F-K: normalized abundance (Log2):  AAOE_AA_1; AAOE_AA_2; AAOE_AA_3; AAOE_CTRL_1; AAOE_CTRL_2; AAOE_CTRL_3; Columns L-M: Statistics: LFC AA vs CTRL_1R; negLog p_value AA vs CTRL

value: primary hepatocellular carcinoma

value: Control empty vector

value: medium restricted to 1% arginine


title: M128 H3K27ac

value: CML patient leukaemia cells


title: M101 input ctrl


title: Antimir_320_rep1


title: RNA-Seq; homo sapiens; SNU449 cells; empty vector control experiment_2


title: M101 H3K27ac


description: genomic DNA from fibroblasts from donor CS466VI, CS type I, csa

source_name: donor CS466VI

value: Cockayne syndrome (CS)

value: CS

value: abscence of CSA


title: Antimir_484_rep4

value: Anti miR-484 assay


description: genomic DNA from fibroblasts from donor CS539VI, CS type I, csb

source_name: donor CS539VI

value: csb

value: Female


title: Kasumi-4 ATAC

data_processing:
Fastq were converted to uBAM and adapters marked with Picard v2.6.0, before aligning with BWA MEM v0.7.17 to the GRCh38 genome, Gencode v36
Duplicates marked with Picard, and filtering sorting and indexing performed with Samtools v1.2
Tracks were generated with DeepTools v3.5.1 using RPKM nomalization, peaks called with MACS2 v2.2.7.1
Assembly: hg38
Supplementary files format and content: RPKM normalised bigwig files for track visualisation by genome browsers.

growth_protocol: Cells were grown at a density 0.5-3mio/ml in RPMI1640 media with 20% FBS, 1% Pen/Strep and 1X Glutamax.

extract_protocol:
Cells were washed with PBS, counted and subjected to the ATAC-Seq protocol.
ATAC-Seq was performed according to the Omni-ATAC-seq protocol (https://doi.org/10.1038/protex.2017.096). In brief, cells were lysed using NP40, Tween-20 and Digitonin, and nuclei were treated with transposase followed by PCR-amplification of transposed fragments using NEBNext 2x MasterMix.


description: genomic DNA from fibroblasts from donor CS333VI, CS type I, csa

source_name: donor CS333VI

value: Male


title: RNA-Seq; homo sapiens; SNU449 cells; empty vector control experiment_1


title: Antimir_484_rep2

value: Human embryonic kidney


description: genomic DNA from fibroblasts from donor 198VI, Healthy, Wild type (WT)

source_name: donor 198VI

value: Healthy

value: Wild type (WT)


title: HL60 ATAC


title: RNA-Seq; homo sapiens; SNU449 cells; arginase and agmatinase overexpression experiment_1

value: Arginase1/Agmatinase overexpression


description: genomic DNA from fibroblasts from donor 194VI, Healthy, Wild type (WT)

source_name: donor 194VI

value: NonAGED


title: KCL22 ATAC


title: M102 H3K27ac


title: K562 ATAC


title: LBUB3

data_processing:
bcl2fastq v. 2.20.0.422 software used for basecalling
The adapters and quality trimming of raw fastq reads was performed using Trimmomatic v. 0.36
Trimmed CLASH reads were mapped against the human genome (hg38) and using STAR v. 2.5.3 with default parameters default parameters except --outFilterMismatchNoverReadLmax 0.1  --outFilterMismatchNoverLmax 0.1  --outFilterScoreMinOverLread 0.85 –outFilterMatchNminOverLread 0.85 to detect and separate single genomic reads
Remaining reads were mapped against the in-house database of noncoding RNAs using STAR v. 2.5.3 with default parameters default parameters except --outFilterMismatchNoverReadLmax 0.1 --outFilterMismatchNoverLmax 0.1 –outFilterScoreMinOverLread 0.25 --outFilterMatchNminOverLread 0.25 to detect both single noncoding RNA and noncoding RNA parts of chimeric reads.
Softclipped parts of chimeric reads were extracted and mapped against the human genome (hg38) using STAR v. 2.5.3 with default parameters default parameters except --outFilterMismatchNoverReadLmax 0.1 --outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.75 --outFilterMatchNminOverLread 0.75 to specify genomic parts of chimeric reads.
Obtained chimeric reads were further deduplicated, collapsed and filtered using in-house script.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include obtained chimeric interactions for each sample
Library strategy: CLASH-seq

growth_protocol: Standard HEK293 TREx growth conditions

extract_protocol:
Ago2-PTH CLASH-seq in HEK293 TREx
Library preparation was executed based on CLASH-seq protocol by Helwak et al 2014 with minor modifications

treatment_protocol: Ago2-PTH expression was induced using doxycyclin for 36 hours

value: AGO2 overexpression


title: RNA-Seq; homo sapiens; SNU449 cells; arginase and agmatinase overexpression experiment_2

value: primary hepatocellular carcinoma


description: genomic DNA from fibroblasts from donor CS177VI, CS type II, csb

source_name: donor CS177VI

value: CS type II

value: abscence of CSB


title: HEL ATAC

value: HEL


title: LBUB2


description: genomic DNA from fibroblasts from donor 911VI, Healthy, Wild type (WT)

source_name: donor 911VI


title: K562 4C-Seq bait A, repeat #1

data_processing:
Bait and adapter sequencer were trimmed from raw reads using cutadapt v3.0 with -e 0.2 flag
Reads were aligned to the GRCh38 genome with Bowtie v2.3 or BWA MEM v0.7.17
Downstream analysis was done following the Pipe4C pipeline described by Krijger et al. 2019 Methods (doi:10.1016/j.ymeth.2019.07.014).
Assembly: hg38
Supplementary files format and content: RPKM normalised bigwig files for track visualisation by genome browsers.


title: LBUB1


title: K562, H3K4me3

data_processing:
Raw MChIP-C reads were mapped to the hg19 genome build with BWA-MEM (with -SP5M flags).
Mapped reads were parsed, uniquely mapped distal read pairs (>5,000 bp apart; cis) were selected and deduplicated with the pairtools package (v.0.3.0).
Binary BAM files were produced from pairtools output and reads mapping to the H3K4me3 ChIP-seq peaks were selected with the samtools (v.1.15.1).
BigWig proximity ligation profiles (merged or separated by individual viewpoints) were generated with the deeptools (v.3.5.1).
Assembly: hg19
Supplementary files format and content: bigWig: viewpoint specific and merged MChIP-C proximity ligation coverage in 100bp and 250bp genomic bins, ChIP-seq occupancy coverage in 50bp genomic bins
Supplementary files format and content: bed: genomic intervals corresponding to the positions of MChIP-C viewpoints
Supplementary files format and content: bedpe: pairs of genomic interval representing MChIP-C identified physical genomic interactions

value: Human erythroleukemia


title: Antimir_484_rep3


title: spleen, Cy3+HA+, Smart-seq, cell 62

status: Public on Dec 25 2023

city: Stanford

first: Yueh-hsiu

last: Chien

state: CA

address: Stanford University

department: Microbiology and Immunology

institute: Stanford University

library_source: transcriptomic single cell

data_processing:
FASTQ files for each cell were extracted and generated, distinguished by the unique dual index adaptors. Reads were aligned to the mm10 genome using STAR v2.6.1d. Transcript abundance was quantified using HTSeq v0.5.4p5.
Assembly: mm10
Supplementary files format and content: csv file including counts for each cell

source_name: spleen

extract_protocol:
Spleen Cy3+HA+ gdT cells (Live Cy3+HA+CD3+TCRgd+TCRb-CD19-F4/80-CD11b-CD11c-TER119- cells) were sorted into 96-well plates and cDNA synthesis was performed using the Smart-seq protocol.
Illumina sequencing libraries were prepared as described previously using a Mosquito HTS liquid handler (TTP Labtech). In brief, the tagmentation was carried out on 0.4 μl double-stranded cDNA using the Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096). Each well was mixed with 0.8 μl Nextera tagmentation DNA buffer (Illumina) and 0.4 μl Amplicon Tagment Mix (Illumina), then incubated at 55 °C for 10 min. The reaction was stopped by adding 0.4 μl Neutralize Tagment Buffer (Illumina) and centrifuging at room temperature at 3,000 g for 5 min. Indexing PCR reactions were performed by adding 0.8 μl of pre-mixed 5 μM i5 and i7 unique dual indexing primers (IDT, customized) and 1.2 μl of Nextera NPM mix (Illumina). PCR amplification was carried out on a C1000 Touch™ Thermal Cycler with 384-Well Reaction Module (Bio-rad) using the following program: 1) 72 °C for 3 min, 2) 95 °C for 30 s, 3) 12 cycles of 95 °C for 10 s, 55 °C for 30 s and 72 °C for 1 min, and 4) 72 °C for 5 min.

tag: tissue

value: spleen

tag: strain

value: Cy3+HA+ gdT

value: female

value: No (wild-type, naive)


title: SRA-/- bio rep1

status: Public on Dec 23 2023

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

data_processing:
To manage data quality using FastQC.
To trim adapter sequences using a trimming tool named "BBDuk".
To align the reads to reference genome using the tool named "STAR".
For counting reads to genomic features using tool named "FeatureCounts".
Assembly: mm39/vM26 annotation
Supplementary files format and content: Tab-separated values files which store read counts for genomic features.

source_name: liver

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Total RNA sample preparation Kit with HMR rRNA depletion module following manufacturer's protocols.

value: liver

value: primary non-parenchymal cells

value: SRA-/-

value: male

value: Acetaminophen (400 mg/kg, i.p.)


title: SRA-/- bio rep3


title: SRA-/- bio rep2


title: RNA-Seq; homo sapiens; SNU449 cells; arginase and agmatinase overexpression experiment_3

value: Arginase1/Agmatinase overexpression

value: medium restricted to 1% arginine


title: Antimir_484_rep1

value: Human embryonic kidney

value: Anti miR-484 assay


title: Wild type bio rep1

value: wild type


title: Wild type bio rep2


title: Wild type bio rep3


title: 205310780042_R06C01 Case

city: Baltimore

first: Rasika

middle: M

last: Mathias

state: MD

address: 5501 Bayview Cir

department: Allergy and Clinical Immunology

institute: Johns Hopkins University

description: Case

hyb_protocol: bisulphite conversion was performed using the EZ DNA Methylation kit (Zymo Research)

scan_protocol: DNA methylation quantification was performed using Illumina Infinium protocol

data_processing:
minfi R-package
Final_methylation_matrix_processed.txt (Average Beta)
Final_methylation_signals.txt (Unmethylated and methylated signal intensities)

label: Cy5 and Cy3

source_name: nasal epithelium, 163723

extract_protocol: genomic DNA was extracted from nasal airway epithelial cells

value: nasal epithelium

tag: site

value: Washington DC

tag: age

value: Female

tag: plate number

tag: ancestry pc1

tag: ancestry pc2

tag: asthma

value: Case


title: 205332910161_R07C01 Control

description: Control

source_name: nasal epithelium, 225803

value: Control


title: 205332910009_R01C01 NA

source_name: nasal epithelium, 212534

value: Male


title: 205332910115_R06C01 NA

value: Hypo-Methylated Control


title: 205332910017_R02C01 NA


title: 205332910191_R03C01 NA


title: 205332910124_R04C01 Control

description: Control

source_name: nasal epithelium, 908105


title: 205332910082_R01C01 NA

source_name: nasal epithelium, 562895


title: 205332910047_R07C01 Case

description: Case

source_name: nasal epithelium, 742413


title: 205310780026_R05C01 NA

value: Hyper-Methylated Control


title: 205332910157_R04C01 NA

source_name: nasal epithelium, 464453


title: 205332910057_R05C01 NA


title: 205332910131_R01C01 NA


title: 205332910056_R06C01 Case

description: Case

source_name: nasal epithelium, 913750


title: 205332910120_R02C01 NA


title: 205332910178_R03C01 Control

description: Control

source_name: nasal epithelium, 424087


title: 205332910171_R05C01 Control

description: Control

source_name: nasal epithelium, 526200


title: 205332910056_R04C01 Control

description: Control

source_name: nasal epithelium, 451623


title: 205332910171_R02C01 NA


title: 205332910062_R01C01 NA

source_name: nasal epithelium, 139478


title: 205332910137_R07C01 Control

description: Control

source_name: nasal epithelium, 392634


title: 205332910131_R02C01 Control

description: Control

source_name: nasal epithelium, 329074


title: 205332910138_R01C01 Control

description: Control

source_name: nasal epithelium, 327681


title: 205332910009_R04C01 Control

description: Control

source_name: nasal epithelium, 732804


title: 205310780026_R04C01 Control

description: Control

source_name: nasal epithelium, 582483


title: 205332910181_R05C01 NA

source_name: nasal epithelium, 903098


title: 205332910116_R02C01 NA

source_name: nasal epithelium, 489439


title: 205332910090_R02C01 NA

source_name: nasal epithelium, 146064


title: 205310780034_R03C01 Control

description: Control

source_name: nasal epithelium, 404552


title: 205332910137_R05C01 Control

description: Control

source_name: nasal epithelium, 668166


title: 205332910087_R02C01 Control

description: Control

source_name: nasal epithelium, 930128


title: 205332910120_R03C01 Control

description: Control

source_name: nasal epithelium, 693783


title: 205332910118_R08C01 Case

description: Case

source_name: nasal epithelium, 680724


title: 205310780049_R02C01 Control

description: Control

source_name: nasal epithelium, 134880


title: 205332910184_R08C01 Control

description: Control

source_name: nasal epithelium, 187245


title: 205310780043_R01C01 Control

description: Control

source_name: nasal epithelium, 759165


title: 205332910057_R01C01 Case

description: Case

source_name: nasal epithelium, 481550


title: 205332910155_R03C01 NA

source_name: nasal epithelium, 744393


title: 205332910082_R07C01 Control

description: Control

source_name: nasal epithelium, 965888


title: 205332910161_R08C01 NA

source_name: nasal epithelium, 805847


title: 205332910120_R06C01 Control

description: Control

source_name: nasal epithelium, 821361


title: 205310780003_R06C01 NA

source_name: nasal epithelium, 976267


title: 205332910124_R05C01 Case

description: Case

source_name: nasal epithelium, 422662


title: 205332910123_R04C01 Control

description: Control

source_name: nasal epithelium, 770063


title: 205332910046_R07C01 Control

description: Control

source_name: nasal epithelium, 971000


title: 205332910111_R08C01 Case

description: Case

source_name: nasal epithelium, 654730


title: 205332910111_R02C01 Control

description: Control

source_name: nasal epithelium, 158702


title: 205332910157_R08C01 Control

description: Control

source_name: nasal epithelium, 377622


title: 205332910123_R05C01 Control

description: Control

source_name: nasal epithelium, 736647


title: 205332910088_R03C01 Case

description: Case

source_name: nasal epithelium, 186072


title: 205310780049_R01C01 Case

description: Case

source_name: nasal epithelium, 951563


title: 205332910131_R05C01 Control

description: Control

source_name: nasal epithelium, 533068


title: 205332910144_R03C01 Control

description: Control

source_name: nasal epithelium, 543278


title: 205332910172_R05C01 Case

description: Case

source_name: nasal epithelium, 321646


title: 205310780042_R03C01 Control

description: Control

source_name: nasal epithelium, 147132


title: 205332910115_R07C01 Case

description: Case

source_name: nasal epithelium, 340870


title: 205332910144_R06C01 Control

description: Control

source_name: nasal epithelium, 761251


title: 205332910171_R08C01 NA

source_name: nasal epithelium, 750370


title: 205332910021_R03C01 Control

description: Control

source_name: nasal epithelium, 127901


title: 205332910062_R07C01 Control

description: Control

source_name: nasal epithelium, 961086


title: 205332910085_R05C01 Control

description: Control

source_name: nasal epithelium, 329058


title: 205310780054_R06C01 Case

description: Case

source_name: nasal epithelium, 548925


title: 205332910085_R06C01 Case

description: Case

source_name: nasal epithelium, 683334


title: 205332910109_R07C01 Control

description: Control

source_name: nasal epithelium, 653272


title: 205332910172_R04C01 Control

description: Control

source_name: nasal epithelium, 367305


title: 205310780003_R08C01 Control

description: Control

source_name: nasal epithelium, 903689


title: 205332910078_R03C01 Control

description: Control

source_name: nasal epithelium, 823055


title: 205332910039_R04C01 Control

description: Control

source_name: nasal epithelium, 889103


title: 205332910047_R04C01 Control

description: Control

source_name: nasal epithelium, 171234


title: 205332910087_R05C01 Control

description: Control

source_name: nasal epithelium, 204531


title: 205310780043_R06C01 Case

description: Case

source_name: nasal epithelium, 796482


title: 205332910146_R07C01 Case

description: Case

source_name: nasal epithelium, 123884


title: 205332910017_R06C01 NA

source_name: nasal epithelium, 695630


title: 205332910090_R05C01 Control

description: Control

source_name: nasal epithelium, 157395


title: 205332910119_R05C01 NA

source_name: nasal epithelium, 201266


title: 205332910173_R04C01 Case

description: Case

source_name: nasal epithelium, 340148


title: 205332910102_R04C01 Case

description: Case

source_name: nasal epithelium, 312945


title: 205332910191_R05C01 Case

description: Case

source_name: nasal epithelium, 500940


title: 205332910191_R07C01 Control

description: Control

source_name: nasal epithelium, 929889


title: 205332910088_R06C01 Control

description: Control

source_name: nasal epithelium, 642866


title: 205310780026_R07C01 Control

description: Control

source_name: nasal epithelium, 121658


title: 205310780054_R03C01 Control

description: Control

source_name: nasal epithelium, 668288


title: 205310780011_R06C01 Case

description: Case

source_name: nasal epithelium, 850284


title: 205332910109_R08C01 Case

description: Case

source_name: nasal epithelium, 659979


title: 205332910115_R03C01 Control

description: Control

source_name: nasal epithelium, 611874


title: 205332910078_R02C01 NA

source_name: nasal epithelium, 963760


title: 205310780011_R02C01 Case

description: Case

source_name: nasal epithelium, 788880

value: Baltimore


title: 205332910021_R06C01 Control

description: Control

source_name: nasal epithelium, 453694


title: 205332910155_R01C01 NA

source_name: nasal epithelium, 472921


title: 205332910181_R01C01 Control

description: Control

source_name: nasal epithelium, 585564


title: 205332910039_R05C01 Control

description: Control

source_name: nasal epithelium, 593787


title: 205332910161_R06C01 Case

description: Case

source_name: nasal epithelium, 900634


title: 205332910146_R08C01 Control

description: Control

source_name: nasal epithelium, 318849


title: 205332910172_R08C01 Case

description: Case

source_name: nasal epithelium, 672934


title: 205332910046_R01C01 Control

description: Control

source_name: nasal epithelium, 875950


title: 205310780026_R02C01 Control

description: Control

source_name: nasal epithelium, 182132


title: 205332910090_R04C01 Control

description: Control

source_name: nasal epithelium, 292316


title: 205332910085_R03C01 Control

description: Control

source_name: nasal epithelium, 887064


title: 205332910181_R02C01 Control

description: Control

source_name: nasal epithelium, 822235


title: 205310780034_R01C01 Control

description: Control

source_name: nasal epithelium, 583516


title: 205332910120_R05C01 Control

description: Control

source_name: nasal epithelium, 987105


title: 205332910184_R05C01 Control

description: Control

source_name: nasal epithelium, 640459


title: 205332910056_R05C01 Control

description: Control

source_name: nasal epithelium, 819062


title: 205332910138_R06C01 NA

source_name: nasal epithelium, 182666


title: 205332910078_R05C01 Control

description: Control

source_name: nasal epithelium, 906537


title: 205332910102_R02C01 Case

description: Case

source_name: nasal epithelium, 739383


title: 205332910021_R04C01 Control

description: Control

source_name: nasal epithelium, 613147


title: 205310780042_R07C01 Case

description: Case

source_name: nasal epithelium, 259704


title: 205332910116_R08C01 Control

description: Control

source_name: nasal epithelium, 884075


title: 205332910178_R01C01 Control

description: Control

source_name: nasal epithelium, 261680


title: 205332910191_R01C01 Case

description: Case

source_name: nasal epithelium, 540484


title: 205310780011_R01C01 Control

description: Control

source_name: nasal epithelium, 670619


title: 205332910109_R01C01 Control

description: Control

source_name: nasal epithelium, 740939


title: 205332910118_R04C01 Control

description: Control

source_name: nasal epithelium, 970590


title: 205332910157_R06C01 Control

description: Control

source_name: nasal epithelium, 659790


title: 205332910184_R06C01 Case

description: Case

source_name: nasal epithelium, 372742


title: 205332910173_R06C01 Control

description: Control

source_name: nasal epithelium, 497401


title: 205332910062_R03C01 Control

description: Control

source_name: nasal epithelium, 562892


title: 205332910144_R02C01 Control

description: Control

source_name: nasal epithelium, 349883


title: 205332910062_R05C01 NA

source_name: nasal epithelium, 646317


title: 205332910171_R06C01 Control

description: Control

source_name: nasal epithelium, 184802


title: 205310780054_R01C01 Case

description: Case

source_name: nasal epithelium, 250170


title: 205332910118_R02C01 Case

description: Case

source_name: nasal epithelium, 838090


title: 205332910155_R07C01 NA

source_name: nasal epithelium, 709203


title: 205332910137_R06C01 Case

description: Case

source_name: nasal epithelium, 162630


title: 205332910146_R06C01 Control

description: Control

source_name: nasal epithelium, 705813


title: 205332910131_R06C01 Control

description: Control

source_name: nasal epithelium, 242744


title: 205332910088_R05C01 Case

description: Case

source_name: nasal epithelium, 146520


title: 205332910161_R04C01 Control

description: Control

source_name: nasal epithelium, 746366


title: 205310780043_R08C01 Case

description: Case

source_name: nasal epithelium, 910004


title: 205332910056_R08C01 Case

description: Case

source_name: nasal epithelium, 341050


title: 205310780054_R05C01 Control

description: Control

source_name: nasal epithelium, 601110


title: 205332910047_R01C01 Case

description: Case

source_name: nasal epithelium, 786811


title: 205332910118_R05C01 Case

description: Case

source_name: nasal epithelium, 750185


title: 205332910087_R06C01 Case

description: Case

source_name: nasal epithelium, 187945


title: 205332910017_R07C01 Control

description: Control

source_name: nasal epithelium, 185058


title: 205332910111_R06C01 Case

description: Case

source_name: nasal epithelium, 358504


title: 205310780003_R03C01 NA

source_name: nasal epithelium, 388836


title: 205332910057_R07C01 Control

description: Control

source_name: nasal epithelium, 524872


title: 205332910046_R05C01 Case

description: Case

source_name: nasal epithelium, 714648


title: 205332910039_R06C01 Case

description: Case

source_name: nasal epithelium, 371760


title: 205332910181_R06C01 Case

description: Case

source_name: nasal epithelium, 315866


title: 205332910157_R02C01 Case

description: Case

source_name: nasal epithelium, 958312


title: 205332910115_R05C01 Control

description: Control

source_name: nasal epithelium, 494540


title: 205332910088_R02C01 NA

source_name: nasal epithelium, 977125


title: 205332910039_R07C01 Control

description: Control

source_name: nasal epithelium, 197500


title: 205332910116_R04C01 Case

description: Case

source_name: nasal epithelium, 380774


title: 205332910111_R01C01 Control

description: Control

source_name: nasal epithelium, 682222


title: 205332910085_R04C01 Case

description: Case

source_name: nasal epithelium, 970097


title: 205332910057_R08C01 Case

description: Case

source_name: nasal epithelium, 961485


title: 205332910124_R03C01 Case

description: Case

source_name: nasal epithelium, 939029


title: 205332910021_R05C01 Case

description: Case

source_name: nasal epithelium, 406700


title: 205332910137_R04C01 Control

description: Control

source_name: nasal epithelium, 381964


title: 205332910109_R03C01 Case

description: Case

source_name: nasal epithelium, 952898


title: 205332910047_R08C01 Control

description: Control

source_name: nasal epithelium, 617140


title: 205332910138_R04C01 Control

description: Control

source_name: nasal epithelium, 512060


title: 205332910123_R08C01 Case

description: Case

source_name: nasal epithelium, 561010


title: 205310780042_R02C01 Control

description: Control

source_name: nasal epithelium, 937114


title: 205332910090_R08C01 Case

description: Case

source_name: nasal epithelium, 748488


title: 205332910115_R04C01 Case

description: Case

source_name: nasal epithelium, 283400


title: 205332910172_R07C01 Control

description: Control

source_name: nasal epithelium, 834571


title: 205332910102_R01C01 NA

source_name: nasal epithelium, 263787


title: 205310780049_R07C01 Control

description: Control

source_name: nasal epithelium, 350808


title: 205332910173_R05C01 Case

description: Case

source_name: nasal epithelium, 975840


title: 205332910144_R01C01 Case

description: Case

source_name: nasal epithelium, 577594


title: 205310780003_R04C01 Control

description: Control

source_name: nasal epithelium, 231517


title: 205332910082_R06C01 NA

source_name: nasal epithelium, 562965


title: 205332910017_R08C01 Case

description: Case

source_name: nasal epithelium, 127000


title: 205332910146_R05C01 Case

description: Case

source_name: nasal epithelium, 398552


title: 205310780026_R08C01 Case

description: Case

source_name: nasal epithelium, 509779


title: 205332910087_R03C01 Control

description: Control

source_name: nasal epithelium, 723720


title: 205332910009_R05C01 Case

description: Case

source_name: nasal epithelium, 388758


title: 205332910178_R02C01 Case

description: Case

source_name: nasal epithelium, 992487


title: 205332910191_R04C01 Control

description: Control

source_name: nasal epithelium, 983772


title: 205310780042_R05C01 NA

source_name: nasal epithelium, 314946

value: Chicago


title: 205332910078_R07C01 Control

description: Control

source_name: nasal epithelium, 404297


title: 205332910021_R07C01 Control

description: Control

source_name: nasal epithelium, 849126


title: 205310780034_R04C01 NA

source_name: nasal epithelium, 962884


title: 205332910138_R08C01 NA

source_name: nasal epithelium, 698056


title: 205332910046_R08C01 Control

description: Control

source_name: nasal epithelium, 208963


title: 205310780049_R08C01 Case

description: Case

source_name: nasal epithelium, 916037


title: 205332910123_R03C01 Control

description: Control

source_name: nasal epithelium, 613079


title: 205332910082_R04C01 Case

description: Case

source_name: nasal epithelium, 912562


title: 205332910056_R02C01 Control

description: Control

source_name: nasal epithelium, 227173


title: 205332910124_R01C01 Control

description: Control

source_name: nasal epithelium, 767804


title: 205332910088_R04C01 Control

description: Control

source_name: nasal epithelium, 539687


title: 205310780049_R05C01 Control

description: Control

source_name: nasal epithelium, 602185


title: 205332910057_R02C01 Case

description: Case

source_name: nasal epithelium, 349987


title: 205332910157_R03C01 Control

description: Control

source_name: nasal epithelium, 261148


title: 205332910116_R07C01 Control

description: Control

source_name: nasal epithelium, 925429


title: 205332910009_R02C01 Control

description: Control

source_name: nasal epithelium, 344472


title: 205332910118_R06C01 Control

description: Control

source_name: nasal epithelium, 969225


title: 205332910111_R03C01 Control

description: Control

source_name: nasal epithelium, 955250


title: 205332910171_R01C01 Control

description: Control

source_name: nasal epithelium, 114982


title: 205332910039_R08C01 Control

description: Control

source_name: nasal epithelium, 345691


title: 205332910123_R02C01 Control

description: Control

source_name: nasal epithelium, 106439


title: 205310780011_R05C01 Control

description: Control

source_name: nasal epithelium, 380176


title: 205332910173_R07C01 Case

description: Case

source_name: nasal epithelium, 663753


title: 205332910181_R03C01 Control

description: Control

source_name: nasal epithelium, 653062


title: 205332910131_R07C01 Case

description: Case

source_name: nasal epithelium, 858660


title: 205332910184_R01C01 Control

description: Control

source_name: nasal epithelium, 910527


title: 205332910131_R08C01 Control

description: Control

source_name: nasal epithelium, 570411


title: 205310780003_R07C01 Case

description: Case

source_name: nasal epithelium, 835041


title: 205332910120_R04C01 Control

description: Control

source_name: nasal epithelium, 512903


title: 205332910102_R06C01 Control

description: Control

source_name: nasal epithelium, 187045


title: 205332910138_R05C01 Case

description: Case

source_name: nasal epithelium, 426136


title: 205310780026_R03C01 Case

description: Case

source_name: nasal epithelium, 584099


title: 205310780042_R01C01 Case

description: Case

source_name: nasal epithelium, 919873


title: 205332910039_R01C01 Case

description: Case

source_name: nasal epithelium, 781476


title: 205332910078_R04C01 Case

description: Case

source_name: nasal epithelium, 745230


title: 205332910172_R03C01 Case

description: Case

source_name: nasal epithelium, 512700


title: 205310780043_R03C01 Control

description: Control

source_name: nasal epithelium, 901190


title: 205332910118_R03C01 Case

description: Case

source_name: nasal epithelium, 345849


title: 205332910171_R04C01 Case

description: Case

source_name: nasal epithelium, 702340


title: 205332910155_R04C01 Case

description: Case

source_name: nasal epithelium, 185178


title: 205332910009_R06C01 Case

description: Case

source_name: nasal epithelium, 358402


title: 205332910184_R02C01 Case

description: Case

source_name: nasal epithelium, 538092


title: 205332910056_R03C01 Case

description: Case

source_name: nasal epithelium, 477803


title: 205332910021_R02C01 Case

description: Case

source_name: nasal epithelium, 921102


title: 205332910116_R01C01 NA

source_name: nasal epithelium, 819271


title: 205332910181_R08C01 Case

description: Case

source_name: nasal epithelium, 215444


title: 205332910090_R03C01 Case

description: Case

source_name: nasal epithelium, 707831


title: 205310780043_R07C01 Control

description: Control

source_name: nasal epithelium, 436163


title: 205332910144_R05C01 Control

description: Control

source_name: nasal epithelium, 791016


title: 205332910046_R04C01 Case

description: Case

source_name: nasal epithelium, 706259


title: 205332910115_R01C01 Case

description: Case

source_name: nasal epithelium, 234097


title: 205332910157_R01C01 Case

description: Case

source_name: nasal epithelium, 666800


title: 205332910017_R03C01 Case

description: Case

source_name: nasal epithelium, 935378


title: 205332910109_R06C01 Control

description: Control

source_name: nasal epithelium, 239067


title: 205332910137_R02C01 Control

description: Control

source_name: nasal epithelium, 107687


title: 205332910082_R05C01 Control

description: Control

source_name: nasal epithelium, 928810


title: 205332910178_R08C01 Case

description: Case

source_name: nasal epithelium, 648829


title: 205332910120_R07C01 Case

description: Case

source_name: nasal epithelium, 510286


title: 205332910082_R08C01 NA

source_name: nasal epithelium, 892115


title: 205332910137_R01C01 Case

description: Case

source_name: nasal epithelium, 123162


title: 205332910191_R08C01 Case

description: Case

source_name: nasal epithelium, 481302


title: 205332910146_R04C01 Case

description: Case

source_name: nasal epithelium, 113230


title: 205310780011_R08C01 Case

description: Case

source_name: nasal epithelium, 977825


title: 205310780034_R06C01 Control

description: Control

source_name: nasal epithelium, 736148


title: 205332910062_R06C01 Case

description: Case

source_name: nasal epithelium, 237325


title: 205332910144_R07C01 Case

description: Case

source_name: nasal epithelium, 906477


title: 205332910102_R07C01 Case

description: Case

source_name: nasal epithelium, 277677


title: 205332910161_R01C01 Case

description: Case

source_name: nasal epithelium, 716595


title: 205310780049_R06C01 NA

source_name: nasal epithelium, 657308


title: 205332910120_R08C01 NA

source_name: nasal epithelium, 731958


title: 205332910090_R06C01 Control

description: Control

source_name: nasal epithelium, 821473


title: 205332910124_R02C01 Case

description: Case

source_name: nasal epithelium, 727704


title: 205332910087_R07C01 Case

description: Case

source_name: nasal epithelium, 163297


title: 205332910123_R06C01 Case

description: Case

source_name: nasal epithelium, 347175


title: 205332910085_R07C01 Control

description: Control

source_name: nasal epithelium, 722046


title: 205332910161_R03C01 Control

description: Control

source_name: nasal epithelium, 752990


title: 205310780034_R08C01 Case

description: Case

source_name: nasal epithelium, 270436


title: 205332910047_R05C01 Case

description: Case

source_name: nasal epithelium, 492250


title: 205332910046_R06C01 Control

description: Control

source_name: nasal epithelium, 108994


title: 205332910017_R05C01 Control

description: Control

source_name: nasal epithelium, 807903


title: 205332910191_R06C01 Control

description: Control

source_name: nasal epithelium, 182286


title: 205332910173_R01C01 Control

description: Control

source_name: nasal epithelium, 636342


title: 205332910109_R04C01 Case

description: Case

source_name: nasal epithelium, 289085


title: 205332910146_R02C01 Control

description: Control

source_name: nasal epithelium, 581487


title: 205310780054_R07C01 Control

description: Control

source_name: nasal epithelium, 708768


title: 205332910172_R02C01 Control

description: Control

source_name: nasal epithelium, 658979


title: 205332910088_R01C01 Case

description: Case

source_name: nasal epithelium, 794388


title: 205332910178_R07C01 Control

description: Control

source_name: nasal epithelium, 723142


title: 205332910062_R04C01 Control

description: Control

source_name: nasal epithelium, 908637


title: 205332910047_R06C01 Control

description: Control

source_name: nasal epithelium, 581375


title: 205332910057_R04C01 Control

description: Control

source_name: nasal epithelium, 895834


title: 205332910087_R04C01 Control

description: Control

source_name: nasal epithelium, 724136


title: 205332910085_R08C01 Case

description: Case

source_name: nasal epithelium, 226750


title: 205310780003_R01C01 Control

description: Control

source_name: nasal epithelium, 730854


title: 205332910111_R05C01 Case

description: Case

source_name: nasal epithelium, 622911


title: 205332910138_R03C01 Control

description: Control

source_name: nasal epithelium, 845423


title: 205310780054_R08C01 Case

description: Case

source_name: nasal epithelium, 889980


title: 205332910102_R03C01 Control

description: Control

source_name: nasal epithelium, 241786

value: Denver


title: 205310780043_R02C01 Case

description: Case

source_name: nasal epithelium, 220887


title: 205332910009_R03C01 Case

description: Case

source_name: nasal epithelium, 475110


title: 205310780011_R04C01 Case

description: Case

source_name: nasal epithelium, 760312


title: 205332910172_R01C01 NA

source_name: nasal epithelium, 680730


title: 205332910057_R06C01 NA

source_name: nasal epithelium, 494211


title: 205332910137_R08C01 Case

description: Case

source_name: nasal epithelium, 554529


title: 205332910056_R07C01 Control

description: Control

source_name: nasal epithelium, 366700


title: 205332910178_R05C01 Case

description: Case

source_name: nasal epithelium, 306300


title: 205332910116_R05C01 Control

description: Control

source_name: nasal epithelium, 952199


title: 205332910009_R07C01 Case

description: Case

source_name: nasal epithelium, 548963


title: 205332910046_R02C01 Case

description: Case

source_name: nasal epithelium, 186360


title: 205332910118_R07C01 Control

description: Control

source_name: nasal epithelium, 367100


title: 205332910111_R04C01 Control

description: Control

source_name: nasal epithelium, 955144


title: 205332910171_R07C01 Control

description: Control

source_name: nasal epithelium, 889140


title: 205332910184_R03C01 Case

description: Case

source_name: nasal epithelium, 254466


title: 205310780034_R07C01 Control

description: Control

source_name: nasal epithelium, 152053


title: 205332910009_R08C01 Control

description: Control

source_name: nasal epithelium, 836570


title: 205332910039_R02C01 Control

description: Control

source_name: nasal epithelium, 970199


title: 205332910115_R02C01 Control

description: Control

source_name: nasal epithelium, 906069


title: 205332910116_R06C01 Control

description: Control

source_name: nasal epithelium, 714009


title: 205332910157_R07C01 Control

description: Control

source_name: nasal epithelium, 755306


title: 205332910078_R06C01 Control

description: Control

source_name: nasal epithelium, 541243


title: 205332910087_R08C01 Control

description: Control

source_name: nasal epithelium, 850104


title: 205332910062_R08C01 Control

description: Control

source_name: nasal epithelium, 289084


title: 205332910131_R03C01 Case

description: Case

source_name: nasal epithelium, 419158


title: 205310780026_R01C01 Control

description: Control

source_name: nasal epithelium, 696378


title: 205310780049_R03C01 Control

description: Control

source_name: nasal epithelium, 496463


title: 205332910181_R07C01 Control

description: Control

source_name: nasal epithelium, 695499


title: 205332910178_R06C01 Case

description: Case

source_name: nasal epithelium, 766563


title: 205332910057_R03C01 Control

description: Control

source_name: nasal epithelium, 230419


title: 205332910017_R04C01 Control

description: Control

source_name: nasal epithelium, 111671


title: 205332910184_R07C01 Control

description: Control

source_name: nasal epithelium, 761467


title: 205310780011_R07C01 Control

description: Control

source_name: nasal epithelium, 211401


title: 205310780042_R04C01 NA

source_name: nasal epithelium, 631932


title: 205332910047_R02C01 Control

description: Control

source_name: nasal epithelium, 702288


title: 205332910178_R04C01 Control

description: Control

source_name: nasal epithelium, 680250


title: 205332910078_R01C01 Control

description: Control

source_name: nasal epithelium, 293993


title: 205332910137_R03C01 Control

description: Control

source_name: nasal epithelium, 774819


title: 205332910109_R02C01 Control

description: Control

source_name: nasal epithelium, 319221


title: 205332910116_R03C01 Case

description: Case

source_name: nasal epithelium, 229680


title: 205332910155_R02C01 NA

source_name: nasal epithelium, 556731


title: 205332910173_R02C01 Control

description: Control

source_name: nasal epithelium, 666259


title: 205310780042_R08C01 Control

description: Control

source_name: nasal epithelium, 792185


title: 205332910090_R07C01 Control

description: Control

source_name: nasal epithelium, 822772


title: 205332910021_R01C01 Control

description: Control

source_name: nasal epithelium, 719799


title: 205332910144_R04C01 Control

description: Control

source_name: nasal epithelium, 986020


title: 205332910102_R05C01 Case

description: Case

source_name: nasal epithelium, 265510


title: 205332910131_R04C01 Control

description: Control

source_name: nasal epithelium, 985385


title: 205332910161_R02C01 Control

description: Control

source_name: nasal epithelium, 536350


title: 205332910124_R08C01 Control

description: Control

source_name: nasal epithelium, 508860


title: PsMETTL16_IP

first: Fan

last: Zhang

address: No.2 Yuanmingyuan West Road, Haidian District, Beijing

institute: China Agricultural University

description:
genes_expression.xlsx
PsMETTL16_call_peak.xlsx

data_processing:
Illumina Casava1.8 software used for basecalling.
fastp software (https://github.com/OpenGene/fastp) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter, and sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome. Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak). And Called called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all transcripts from input libraries by calculating FPKM . The differentially expressed mRNAs were selected by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: Phytophthora sojae Ensembl release-101
Supplementary files format and content: .xlsx files include gene expression and methylation level

organism: Phytophthora sojae

source_name: hyphae

growth_protocol: The mycelium was cultured in liquid, then RNA was collected and extracted

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification. The poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to create the final cDNA library in accordance with the protocol for the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, cat.e7530L, USA).

treatment_protocol: RNA was extracted directly without treatment

value: hyphae

value: PsMETTL16 knockout mutant

value: Liquid culture was performed and mycelium was collected for RNA extraction


title: 205310780043_R05C01 Control

description: Control

source_name: nasal epithelium, 869640


title: PsMETTL3B_IP

data_processing:
Illumina Casava1.8 software used for basecalling.
fastp software (https://github.com/OpenGene/fastp) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter, and sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome. Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak). And Called called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all transcripts from input libraries by calculating FPKM . The differentially expressed mRNAs were selected by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: Phytophthora sojae Ensembl release-101
Supplementary files format and content: .xlsx files include gene expression and methylation level
Library strategy: MeRIP-seq

value: PsMETTL3B knockout mutant


title: PsMETTL16_input


title: 205332910046_R03C01 Case

description: Case

source_name: nasal epithelium, 706417


title: 205310780011_R03C01 Control

description: Control

source_name: nasal epithelium, 454922


title: 205332910155_R05C01 Control

description: Control

source_name: nasal epithelium, 251593


title: PsMETTL3A_IP

value: PsMETTL3A knockout mutant


title: PsMETTL3A_input

description:
genes_expression.xlsx
PsMETTL3A_call_peak.xlsx


title: 205332910191_R02C01 Control

description: Control

source_name: nasal epithelium, 460697


title: 205332910111_R07C01 Case

description: Case

source_name: nasal epithelium, 287592


title: 205332910138_R07C01 Case

description: Case

source_name: nasal epithelium, 359995


title: WT_IP

value: WT


title: 205310780003_R02C01 Control

description: Control

source_name: nasal epithelium, 255440

value: nasal epithelium


title: 205310780054_R02C01 Control

description: Control

source_name: nasal epithelium, 595900


title: WT_input

description:
genes_expression.xlsx
WT_call_peak.xlsx


title: 205332910123_R07C01 Control

description: Control

source_name: nasal epithelium, 966333


title: 205332910173_R03C01 Case

description: Case

source_name: nasal epithelium, 668110


title: EDC response-treated c57b6l,repeated2

first: fei

last: sun

state: Shanghai

address: Laboratory of Biotechnology, School of Life Science, Baoshan Campus, Shanghai University, Dachang Town, Baoshan District, Shanghai

institute: Shanghai University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequences reads were mapped to mm10 using CLC genomic benchwork(parameters-mismath cost:2 insertion cost:3 deletion cost:3 length fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchworl
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: muscle

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1 µg of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols

value: muscle

tag: agent

value: EDC


title: click response-treated c57b6l mice,repeated3

value: click


title: EDC response-treated c57b6l,repeated3


title: click response-treated c57b6l mice,repeated2


title: 205332910062_R02C01 Case

description: Case

source_name: nasal epithelium, 974464

value: Case


title: EDC response-treated c57b6l,repeated1


title: Eomes-KO CD4 T cells (replicat 2) [CnR]

city: Toulouse

first: Anne

middle: S

last: Dejean

state: Midi-Pyrenees

address: CHU Purpan – BP 3028

country: France

institute: Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)

data_processing:
Adapter trimming and quality controls were performed using Trimgalore v0.6.5. and FastQC v0.11.7.
Reads were aligned to the mm10 reference genome by using Bowtie2 v2.2.9. with the splicing alignment feature switched off.
Assembly: mm10 reference genome
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

source_name: CD4 T cells

growth_protocol: Naive CD4+ T cells were isolated from spleen and lymph nodes by negative selection using the « Naive CD4 T Cell Isolation Kit » according to the manufacturer’s instructions (Miltenyi Biotec, Cat: 130-104-453). Cells were cultured in RPMI 1640 media supplemented with 10% FCS, 2 mM L-glutamine, 100 U/mL penicillin/streptomycin and 50 μM β-mercaptoethanol in 96 well plates at a seeding concentration of 2x105 cells per well. Polyclonal naïve CD4+ T cells were stimulated with 2 ug/mL anti-CD3 antibody (Biolegend) and 1 ug/mL anti-CD28 (BD Biosciences) under non-polarizing conditions.

extract_protocol:
CUT&RUN was performed as previously described (Krzywinska et al., 2022) with some modifications. Briefly, 50,000 cells were harvested and processed with the CUT&RUN (Cleavage Under Targets & Release Using Nuclease) Assay Kit (86652; Cell Signaling Technology) following the supplier’s instructions. Eomes monoclonal antibody (Dan11mag, Thermofisher, 14-4875-82) was used at 2 µg. DNA was purified using the QIAGEN MinElute kit (QIAGEN) and its quality was assessed on a 2100 Bioanalyzer (Agilent Technologies).
Paired-end libraries have been prepared according to Active Motif's protocol with some adjustments, using the Next Gen DNA Library Kit (Active Motif, Carlsbad, USA), assuming a starting input of 100 pg of dsDNA. Briefly, DNA first underwent a 2-phases reparation. Then, Illumina compatible adaptors were ligated, allowing the barcoding of the samples with single indices, and the addition of molecular identifiers (MIDs) composed of 9-bases random sequence. These MIDs will enable to distinguish PCR duplicates from fragmentation duplicates, and the removal of true PCR duplicates from the subsequent sequencing analysis. The libraries were then amplified using 15 cycles of PCR, and an additional 2-sides purification step was finally performed, allowing to obtain 250-1000 pb fragments.

value: CD4 T cells


title: PsMETTL3B_input

description:
genes_expression.xlsx
PsMETTL3B_call_peak.xlsx


title: 205332910088_R08C01 Case

description: Case

source_name: nasal epithelium, 324673

value: Male


title: 205332910146_R03C01 Case

description: Case

source_name: nasal epithelium, 226779

value: Female