title: Gr4_CDAA_HFD_90mpk_L_286_EC014_71_Liver_S11_L001


title: TT04_subj3_V3

status: Public on Nov 25 2023

type: SRA

city: Hoerholm

first: Niels Peter

last: Hell Knudsen

address: Bøge Alle 3

country: Denmark

institute: ALK-Abello

library_source: transcriptomic single cell

data_processing:
Cellranger 6.1.2
Seurat v4
Assembly: GRCh38-2020-A
Supplementary files format and content: Cellranger filtered and raw bc matrix counts
Supplementary files format and content: Integrated Seurat object with UMAP

molecule: polyA RNA

organism: Homo sapiens

source_name: blood

extract_protocol: Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium 5’ Single Cell Gene Expression assay and Chromium Controller Instrument according to the manufacturer’s published protocol

tag: tissue

value: blood

tag: cell type

value: PBMCs

tag: group

value: allergic


title: Gr2_CDAA_HFD_EC014_39_Liver_S9_L001

city: Riverside

first: Brendan

last: Gongol

state: Ca

address: 900 University Ave

country: USA

institute: University of California, Riverside

library_source: transcriptomic

data_processing:
Following DNA sequencing and read mapping to the mouse GRCm39 genome, reads aligning to coding regions were retained and the number of read counts per gene were calculated.
Assembly: GRCm39
Supplementary files format and content: Excel files include FPKM or values for each sample.

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA was extracted using QIAzol reagent followed by chloroform extraction followed by an additional purification step using RNeasy mini kit with a DNAse digestion (Qiagen).
For each sample, total RNA was normalized to 100 ng before undergoing library preparation using the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit per manufacturer’s instructions. The Agilent Bioanalyzer and Qubit Fluorometer were used to libraries were qualified and quantified using the the Agilent Bioanalyzer and Qubit Fluorometer prior to pooling samples. Samples were sequenced on the Illumina Novaseq 6000 using 2x100 cycles, per manufacturer’s instructions.

tag: strain

tag: Sex

value: Male

tag: age

value: 20 wk

tag: diet

value: CDAA-HFD


title: TT04_subj5_V3


title: TT04_subj4_V2


title: Gr2_CDAA_HFD_EC014_37_Liver_S7_L001


title: Gr2_CDAA_HFD_EC014_36_Liver_S6_L002


title: TT04_subj2_V2


title: Gr2_CDAA_HFD_EC014_38_Liver_S8_L002


title: Gr2_CDAA_HFD_EC014_37_Liver_S7_L002


title: TT04_subj2_V3


title: Gr2_CDAA_HFD_EC014_36_Liver_S6_L001


title: Gr2_CDAA_HFD_EC014_40_Liver_S10_L002


title: TT04_subj1_V3


title: non_allergic_5

value: non-allergic


title: Gr2_CDAA_HFD_EC014_35_Liver_S5_L002


title: Gr2_CDAA_HFD_EC014_35_Liver_S5_L001


title: non_allergic_4


title: Gr2_CDAA_HFD_EC014_34_Liver_S4_L002


title: TT04_subj3_V2


title: T50

city: Shenyang

first: Yibei

last: Wang

state: Liaoning

address: No.77 Puhe Road

country: China

institute: China Medical University

description: FPKM.txt

data_processing:
The raw reads were further processed with a bioinformatic pipeline tool, BMKCloud(www.biocloud.net) online platform.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
The number of fragments from a transcript is affected by sequencing data volume (or number of mapped reads), length of the transcript, expression level of transcripts. In order to reveal the expression level of each transcript more accurately, the number of mapped reads needs to be normalized by the length of its transcripts. FPKM(Fragments Per Kilobase of transcript per Million fragments mapped) was applied to measure the expression level of a gene or transcript by StringTie using maximum flow algorithm.
Assembly: hg18
Supplementary files format and content: .txt
Supplementary files format and content: gene expression quantification (FPKM value)

molecule: total RNA

source_name: tumor tissue

extract_protocol:
RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: tumor tissue


title: T45

description: FPKM.txt


title: non_allergic_3


title: non_allergic_2


title: T41

description: FPKM.txt


title: T43

description: FPKM.txt


title: T44

description: FPKM.txt


title: Gr2_CDAA_HFD_EC014_34_Liver_S4_L001


title: T42

description: FPKM.txt


title: T39

description: FPKM.txt


title: T38

description: FPKM.txt


title: non_allergic_1


title: T37

description: FPKM.txt


title: Gr2_CDAA_HFD_EC014_33_Liver_S3_L002


title: T47

description: FPKM.txt


title: Gr2_CDAA_HFD_EC014_33_Liver_S3_L001


title: allergic_4


title: T35

description: FPKM.txt


title: T34

description: FPKM.txt


title: T31

description: FPKM.txt


title: Gr2_CDAA_HFD_EC014_32_Liver_S2_L002


title: T30

description: FPKM.txt


title: Gr2_CDAA_HFD_EC014_32_Liver_S2_L001


title: T29

description: FPKM.txt


title: T27

description: FPKM.txt


title: Gr2_CDAA_HFD_EC014_31_Liver_S1_L002


title: T26

description: FPKM.txt


title: allergic_3


title: allergic_2


title: T21

description: FPKM.txt


title: T24

description: FPKM.txt


title: T36

description: FPKM.txt


title: T20

description: FPKM.txt


title: T28

description: FPKM.txt


title: T22

description: FPKM.txt


title: Gr2_CDAA_HFD_EC014_31_Liver_S1_L001


title: BIU87_INPUT

first: Shutao

last: Tan

address: No.36 Sanhao Street

institute: Shengjing Hospital of China Medical University

library_source: genomic

data_processing:
Raw sequencing data was first filtered by fastp (version 0.23.4), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to the reference genome of GRCh38 using STAR software (version 2.5.3a) with default parameters.
The MACS2 software（Version 2.1.1）was used for peak calling. The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis.
The differentially binding peaks were identified by csaw(version 1.30.1).
The Homer（version 4.10）was used for motifs analysis.
Assembly: GRCh38
Supplementary files format and content: Bigwig

molecule: genomic DNA

growth_protocol: BIU-87 cells were maintained in DMEM supplemented with 10% Fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
The cell was fixed in 1% formaldehyde for 10 min at room temperature. After quenching cell was treated with cell lysis buffer and nucleus was collected by centrifuging at 2000g for 5min. Then, nucleus was treated with nucleus lysis buffer and sonicated to fragment chromatin DNA.
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bp were enriched and quantified.

tag: cell line

value: Bladder cancer cells

tag: chip antibody


title: BIU87_AATF_IP

value: AATF


title: T13

description: FPKM.txt


title: T09

description: FPKM.txt


title: MDA-MB-453_Input_D11-8_2

city: ADELAIDE UNIVERSITY

first: Geraldine

last: Laven-Law

state: South Australia

address: Adelaide Health & Med Sci Bldg, Corner George St & North Terrace

country: Australia

institute: The University of Adelaide

data_processing:
Reads were aligned to human assembly GRCh37 (hg19) using Bowtie2 (Langmead & Salzberg 2012, Nature Methods).
Pol II peaks were called with MACS2 (Zhang et al. 2008, Genome Biology) against the corresponding total chromatin input for each replicate and condition.
Peaks were annotated to UCSC.hg19.knownGene. Peaks called in both replicates per condition which intersected promoters (+/- 300 bp of a transcription start site) were subject to differential enrichment analysis using DiffBind (Ross-Innes et al. 2012, Nature; Stark & Brown 2011, Bioconductor). In case of multiple transcripts, peaks associated with the longest isoform were retained. Peaks with a false discovery rate (FDR) of q < 0.05 were considered differentially enriched.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: MACS2 Pol II ChIP-seq peak files are also provided for each replicate and condition.
Supplementary_files_format_and_content: A UCSC.hg19.knownGene-annotated DiffBind output table is also provided, containing all consensus Pol II peaks which intersect promoters, regardless of differential enrichment status.
Supplementary_files_format_and_content: Bigwig files are provided, which were generated from a merge of the two Pol II ChIP-seq replicates for each condition using deepTools (Ramirez et al. 2016, Nucleic Acids Res.). ENCODE blacklisted regions have been subtracted from deposited bigwig files.

source_name: Breast cancer cell line

growth_protocol: MDA-MB-453 cells were cultured for three days in their normal culture media (DMEM High Glucose + 10% FBS) until reaching ~80% confluence

extract_protocol:
MDA-MB-453 cells were fixed with 1% formaldehyde for 10 min prior to quenching. Chromatin was prepared and subsequently sheared as previously described (Mohammed et al. 2015, Nature). Sheared chromatin was immunoprecipitated with 10 µg of RNA Polymerase II (Pol II) antibody (Santa Cruz, SC-47701), after coupling to Protein A Dynabeads (10002D).
Recovered DNA was amplified using the NEBNext Ultra IIDNA Library Prep Kit (NEB) following manufacturer's protocols.
DNA libraries were sequenced on the Illumina Novaseq 6000 to a minimumof 60 million 150 bp paired-end reads per sample.

treatment_protocol: MDA-MB-453 cells were treated for 4 hours with either a vehicle or 600 nM CDK9 inhibitor D11-8. Two replicates per condition were collected, representing independent passages of cells.

value: Breast cancer cell line

value: Input DNA

tag: treatment

tag: replicate


title: Day 6, replicate 1, Multiome scRNAseq

city: Stanford

first: Jingxue

last: Xin

state: California

address: JAMES CLARK CENTER E100A

institute: Stanford University

description: 10x Genomics

data_processing:
10x Genomics Cell Ranger arc v2.0.0 was used to process the raw fastq files for each multiome single-cell dataset separately. The reference genome and transcriptome for alignment and annotation was version arc-mm10-2020-A-2.0.0. To integrate all filtered count matrices for scRNA-seq and scATAC-seq from different replicates and time points, the cellranger-arc aggr command was applied with default depth normalization method.
Assembly: mm10
Supplementary files format and content: feature barcode matrix HDF5 files, and ATAC Per fragment information file and index

molecule: nuclear RNA

growth_protocol: mESCs were differentiated using the hanging drop method. Trypsinized cells were suspended in chemically defined medium CDM to a concentration of 37,500 cells/mL. 20 μL drops (∼750 cells per drop) were then placed on the lid of a bacterial plate and the lid was upside down. After 48 h incubation at 37◦C incubator with 5% CO2, Embryoid bodies (EBs) formed at the bottom of the drops were collected and placed in the well of a 6-well ultra-low attachment plate (Corning) with fresh CDM medium containing 50 ng/mL Activin A (R&D Systems, 338-AC-050/CF) and 2 mM Lithium Chloride (LiCl,Sigma-Aldrich) for up to 6 days, with the medium being changed daily.

extract_protocol:
The EBs were collected at Day 2, 4, and 6 after Activin A/Lithium Chloride treatment. For each time point,the cells were first treated with StemPro Accutase Cell Dissociation Reagent (Thermo Fisher) at 37◦C for 10-15 min with pipetting. Single cell suspension was obtained by passing through 37 μM cell strainer (STEMCELL Technologies) twice. After measuring cell concentration, approximately 1 million of cells were centrifuged at 300 rcf for 5 min. Nuclei were isolated by following the protocol provided by 10x Genomics (Nuclei isolation for single cell multiome ATAC + Gene expression sequencing, CG00365, Rev A). The final nuclei concentration was adjusted to 3000 cell/μL in 1X Nuclei Buffer (10x Genomics). The sample was immediately submitted to Stanford Genomics Service Center (SGSC) for single cell sorting using 10x Chromium Controller (target cells: 5000 per replicate, total 2-3 replicates per time point).
The singe cell multiome library was generated using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle Kit (10x Genomics, PN-1000283).
Single cell multiome

value: Mouse embryonic stem cell

value: Activin A/Lithium Chloride

value: Day 6


title: T08

description: FPKM.txt


title: T19

description: FPKM.txt


title: MDA-MB-453_Input_D11-8_1


title: Day 4, replicate 2, Multiome scRNAseq

description: 10x Genomics

value: Day 4


title: T07

description: FPKM.txt


title: Day 4, replicate 1, Multiome scRNAseq

description: 10x Genomics


title: T04

description: FPKM.txt


title: Day 2, replicate 3, Multiome scRNAseq

description: 10x Genomics

value: Day 2


title: N50

description: FPKM.txt

source_name: paracancerous tissue

value: paracancerous tissue


title: N47

description: FPKM.txt


title: Day 6, replicate 2, Multiome scRNAseq

description: 10x Genomics


title: N44

description: FPKM.txt


title: N45

description: FPKM.txt


title: N43

description: FPKM.txt


title: Day 2, replicate 1, Multiome scRNAseq

description: 10x Genomics


title: MDA-MB-453_PolII_ChIP_D11-8_2

value: Pol II (CTD4H8); Santa Cruz SC-47701


title: allergic_1

value: blood

value: PBMCs

value: allergic


title: T05

description: FPKM.txt


title: MDA-MB-453_PolII_ChIP_Veh_2

value: Veh


title: N42

description: FPKM.txt


title: N41

description: FPKM.txt


title: N39

description: FPKM.txt


title: N38

description: FPKM.txt


title: MDA-MB-453_Input_Veh_2


title: Day 6, replicate 1, Multiome scATACseq

description: 10x Genomics


title: Day 4, replicate 2, Multiome scATACseq

description: 10x Genomics


title: N36

description: FPKM.txt


title: N35

description: FPKM.txt


title: Rad2gray_3_Lane2

city: Philadelphia

first: Andrei

last: Georgescu

state: Pennsylvania

address: 315 Skirkanich Hall, 210 S. 33rd Street

institute: University of Pennsylvania

description: All samples merged in same final count matrix

data_processing:
Basecalls performed using RTA3 software
STAR was used for alignment and feature quantification; DESeq1 was run directly on the data in the .TSV file provided to quantify differential mRNA expression between samples
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Hematopoietic niche in vitro model

extract_protocol:
RNA was isolated by dissolving the tissues whole in Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: radiation dose (gy)

tag: biological replicate id


title: MDA-MB-453_Input_Veh_1


title: Day 4, replicate 1, Multiome scATACseq

description: 10x Genomics


title: Day 2, replicate 2, Multiome scRNAseq

description: 10x Genomics


title: Rad2gray_3_Lane1


title: N34

description: FPKM.txt


title: Day 2, replicate 3, Multiome scATACseq

description: 10x Genomics


title: MDA-MB-453_PolII_ChIP_D11-8_1


title: Rad2gray_2_Lane2


title: N29

description: FPKM.txt


title: N30

description: FPKM.txt


title: N28

description: FPKM.txt


title: Day 6, replicate 2, Multiome scATACseq

description: 10x Genomics


title: Day 2, replicate 2, Multiome scATACseq

description: 10x Genomics


title: N37

description: FPKM.txt


title: Rad2gray_2_Lane1


title: Day 2, replicate 1, Multiome scATACseq

description: 10x Genomics


title: MDA-MB-453_PolII_ChIP_Veh_1


title: N24

description: FPKM.txt


title: N26

description: FPKM.txt


title: Fhl2 KO primary graunolosa cells #3

city: Wuhan

first: Guohua

last: Hua

state: China

address: No. 1, Shizishan Street

institute: Huazhong Agricultural University

data_processing:
fastq data were filtered using fastp software with "-r" parameter.
The filtered reads were mapped to the mouse reference genome (mm10) using hisat2 aligner (v 2.2.1) with “—dta-cufflinks” parameter.Aligned sam files were sorted and transferred to bam format by using samtools.
Based ne the genome annotate file from gencode (vM23), raw read count and FPKM at gene-level were produced by featureCounts (v 1.6.4) and cufflinks (v 2.2.1), respectively.
Raw reads count matrix of all samples was used for differentially expressed gene identification by DEseq2 (v 1.28.1) with default pamameters
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each sample

source_name: ovary

extract_protocol:
Total RNAs were extracted from  ovarian graunolosa cells using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).
RNA libraries for RNA-seq were prepared using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China)  following manufacturer's protocols.

value: ovary

value: primary graunolosa cells

tag: genotype

value: Fhl2 KO

value: no treatment


title: N20

description: FPKM.txt


title: Rad2gray_1_Lane2


title: N13

description: FPKM.txt


title: N19

description: FPKM.txt


title: Fhl2 KO primary graunolosa cells #2


title: Rad2gray_1_Lane1


title: N22

description: FPKM.txt


title: Fhl2 KO primary graunolosa cells #1


title: N09

description: FPKM.txt


title: Rad20gray_3_Lane2


title: N31

description: FPKM.txt


title: N08

description: FPKM.txt


title: N27

description: FPKM.txt


title: Rad20gray_2_Lane2


title: N05

description: FPKM.txt


title: Rad20gray_3_Lane1


title: Rad20gray_2_Lane1


title: WT mice primary  graunolosa cells #4

value: WT


title: WT mice primary  graunolosa cells #3


title: N04

description: FPKM.txt


title: WT mice primary  graunolosa cells #2


title: Aged CTRL #6

city: Baton Rouge

first: John

middle: P

last: Kirwan

state: LA

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V3.4.3, Rstudio V1.3.1056 and biomaRt V2.24.1
DESeq2  V1.18.1 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Genome_build: mouse- GRCm38.84
Supplementary_files_format_and_content: tab-delimited text containing DESeq2 normalized counts

source_name: inguinal white adipose tissue

extract_protocol:
iWAT depots were removed at necropsy and flash frozen in liquid nitrogen. Approximately 150-200mg tissue was homogenized in Trizol, and RNA was extracted per manufacturer's protocol using chlorofom phase separation
Lexogen Quant-Seq

value: C57BL/6J WT

value: 92 weeks

value: CTRL

tag: ID


title: N07

description: FPKM.txt


title: WT mice primary  graunolosa cells #1


title: Aged CTRL #5


title: N21

description: FPKM.txt


title: Rad20gray_1_Lane1


title: Aged BAM15 #4


title: Aged CTRL #4


title: Rad02gray_3_Lane2


title: Aged BAM15 #5


title: Aged BAM15 #3


title: Aged BAM15 #2


title: Rad02gray_3_Lane1


title: Aged CTRL #3


title: HaCaT-FLI1

city: Guiyang

first: Maoting

last: Hu

state: Guizhou

address: Baiyun District, Guiyang City, Guizhou Province, China.

institute: Guizhou Medical University

data_processing:
Sequencing data is called raw reads or raw data, and quality control (QC) is then performed on the raw reads to determine whether the sequencing data is suitable for subsequent analysis. After quality control, the filtered clean reads were aligned to the reference sequence. After the alignment, the statistics of the mapping rate and the distribution of reads on the reference sequence are used to determine whether the alignment result passes the second QC of alignment. If it passes, we perform gene quantification analysis and other analysis based on gene expression (principal component, correlation, differential gene screening, etc.), and perform significant enrichment analysis of GO function on differentially expressed genes among the screened samples, significance enrichment analysis of pathway, clustering, protein interaction networks, and transcription factors, and more in-depth mining analysis. SNP & InDel, differential splicing gene detection can also be done.
Assembly: Reference Genome Version: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited xls file includes FPKM values for each sample
Supplementary files format and content: tab-delimited xls file includes counts for each sample

source_name: epithelial skin

growth_protocol: The spontaneously immortalized human epidermal keratinocytes HaCaT was maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% Fetal Bovine Serum (FBS) and antibiotics. Cells were trypsinized (0.25% trypsin-EDTA solution; Invitrogen, US) and sub-cultured when attained 70–80% confluence. All these cells cultured in incubator with 5% CO2 at 37 °C and maintained mycoplasma free used in all experiments.

extract_protocol:
Total RNA was extracted fusing TRIzol reagent kit (Life Technologies; Thermo Fisher Scientific, USA).
In this project, we sequence 2 samples used BGISEQ platform, averagely generating about 6.61G Gb bases per sample. The average mapping ratio with reference genome is 97.23%, the average mapping ratio with gene is 66.23%; 15159 genes were identified

treatment_protocol: DNA was diluted in TE buffer to a final concentration of 4 μg (MigR1; MigR1-Fli1). Lipofectamine transduction of cells was performed according to the manufacturer’s protocol (Invitrogen). Transduction of samples at a final concentration of 4 μg was made in 250 μL of Dulbecco modified Eagle medium (serum free) and incubated at room temperature for 5 minutes. Lipofectamine 2000 reagent was diluted to 10μL of 250μL of media (serum free). Diluted DNA was then added to the lipofectamine 2000 reagent, mixed gently, and incubated for 15 minutes at room temperature to allow for the DNA-lipofectamine complexes to develop. After incubation, DNA-lipofectamine mixture was added to the 70%-80% confluent HaCaT and A431 cell culture in dishes. Transduced cells were left to incubate at 37°C. After 6 hours, the medium was changed. Two days after transfection, cells were checked for GFP expression and RNA extracted for further analysis.

value: epithelial skin

value: HaCaT

value: immortalized human keratinocytes cell

value: FLI1 overexpression

value: Transfection


title: LPS-treated MTX-M-MØ macrophage donor3 rep3

city: Madrid

first: Amaya

middle: Rocío

last: Puig Kröger

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

country: Spain

institute: Hospital General Universitario Gregorio Marañón

data_processing:
BGISEQ-500 platform
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads. Sequences were mapped to GRCh38 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

source_name: macrophages

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 10^6 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 10 ng/ml M-CSF to generate M-CSF-polarized macrophages (M-MØ).

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Freshly isolated CD14+ monocytes were cultured for 7 days in RPMI 10% FBS containing M-CSF after an initial exposure (at day 0) to 5 micromolar of the antifolate methotrexate (MTX). 7 days later, fully-differentiated macrophages (untreated or MTX-treated) were exposed to 10 ng/ml LPS ( 0111:B4 strain) for 3 hours and total RNA was extracted.

tag: cell

value: Monocyte-derived M-CSF macrophages

value: LPS (10 ng/ml) for 3 hours.

tag: agent


title: HaCaT-control

tag: tissue

value: Vector


title: Aged CTRL #2


title: Rad02gray_2_Lane2


title: Aged CTRL #1


title: LPS-treated MTX-M-MØ macrophage donor2 rep2

value: 5 micromolar of the antifolate methotrexate


title: Rad20gray_1_Lane2


title: Rad02gray_2_Lane1


title: Aged BAM15 #1


title: Young CTRL #7

value: 16 weeks


title: LPS-treated MTX-M-MØ macrophage donor1 rep1


title: Young BAM15 #6


title: LPS-treated M-MØ macrophage donor3 rep3


title: Young CTRL #6


title: Rad02gray_1_Lane1


title: Rad02gray_1_Lane2


title: LPS-treated M-MØ macrophage donor2 rep2


title: Young BAM15 #4


title: ControlA_3_Lane2


title: LPS-treated M-MØ macrophage donor1 rep1


title: eds1_rep3

city: Nanjing

first: Yiming

last: wang

address: No. 1 Weigang Rd., Nanjing, Jiangsu 210095, China

department: Department of Plant Pathology

institute: Nanjing Agricultural University

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml).
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: IRGSP-1.0
Supplementary files format and content: tab-delimited text file includes TPM value for each Sample

organism: Oryza sativa

source_name: leaf

growth_protocol: The seeds of wild-type (Oryza sativa L. ZH11) and transgenic plant (Oseds1) were surface sterilized by 10% NaClO, washed with ddH2O, and imbibed in 4℃ overnight. The imbibed seeds were germinated on soil at 28°C. The germinal seedlings at 3 days were transformed into pots filled with nutrient soil, and then grown in a growth chamber under the conditions of 14-h day, 28°C, 80% relative-humidity (RH) followed by 10-h night, 26°C, 80% RH.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Thermo Fisher Scientific, 15596026) from leaf tissues.
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq 6000 sequencer (2 × 150bp read length).

treatment_protocol: For the Xoo infection assay, bacterial strain PXO99A was grown on nutrient broth agar (NA) medium at 28°C for 2 days, bacterial pellets were washed twice and resuspended in sterile water to generate inoculum suspensions with an optical density of OD600 = 0.5. The Xoo suspension was directly inoculated on leaves of two-week-old rice seedlings by infiltration with needleless syringes with three sites per leaf. Three leaves were collected as one sample for RNA extraction.

value: leaf

value: Oseds1 mutant

value: Inoculation with PXO99A


title: Young BAM15 #3


title: ControlA_3_Lane1


title: eds1_rep2


title: eds1_rep1


title: ControlA_2_Lane1


title: Young CTRL #3


title: ControlA_2_Lane2


title: OVCAR8-pladienolide B-2

city: Jinan

first: shourong

address: No. 107, Wenhua West Road, Lixia District, Jinan City, Shandong Province

institute: Qilu Hospital，Shandong University

data_processing:
Raw fastq sequences were treated with Trimmomatictools(v 0.36) using the following options: :TRAILING:20,SLIDINGWINDOW:4:15 MINLEN:52, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes.
Clean reads were aligned to the hg19 with HISAT2. HTSeq v0.12.4 was used to count the reads numbers mapped to each gene.
Differential expression was assessed by DESeq2 using read counts as input
Assembly: hg19/
Supplementary files format and content: spreadsheet file include RPKM values for each sample

extract_protocol:
Total RNA was isolated from cells using the Magzol Reagent (Magen, China)according to the manufacturer' s protocol. mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary

tag: cell type

value: ovarian cancer cell

value: wild type

value: pladienolide B


title: ZH11_rep3

value: wildtype


title: ZH11_rep2


title: Young BAM15 #1

value: C57BL/6J WT


title: ControlA_1_Lane2


title: ControlA_1_Lane1


title: OVCAR8-DMSO-3

value: DMSO


title: Young BAM15 #2


title: ZH11_rep1


title: Young CTRL #5

value: CTRL


title: OVCAR8-DMSO-2


title: Young BAM15 #5


title: Young CTRL #2


title: OVCAR8-DMSO-1


title: Young CTRL #1


title: human non-diabetic ulcer

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr

data_processing:
Base calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation mkfastq and then aligned against  the Cell Ranger GRCh38 v3.0.0 human reference genome, available at: http://cf.10xgenomics.com/supp/cell-exp/, or using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample.
Base calls were converted to reads using the Cell Ranger (10X Genomics, Pleasanton, CA, USA; version 3.1) implementation mkfastq and then aligned against the GRCh38 v3.0.0 (human) genome using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample. Cell barcodes representative of quality cells were delineated from barcodes of apoptotic cells or background RNA based on a threshold of having at least 300 unique transcripts profiled, less than 100,000 total transcripts, and less than 10% of their transcriptome of mitochondrial origin. Unique molecular identifiers (UMIs) from each cell barcode were retained for all downstream analysis. Raw UMI counts were normalized with a scale factor of 10,000 UMIs per cell and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1)
Aggregated data were then evaluated using uniform manifold approximation and projection (UMAP) analysis over the first 15 principal components [21]. Cell annotations were ascribed using SingleR (version 3.11) against the Human Primary Cell Atlas (HPCA) reference dataset.

source_name: plantar foot ulcer

extract_protocol:
Debrided diabetic foot ulcer (DFU) tissue was collected from one patient and immediately placed into a solution of Dulbecco’s Modified Eagle Medium (DMEM; Sigma-Aldrich, St. Louis, MO, USA) with 10% fetal bovine serum (FBS; ThermoFisher, Waltham, MA, USA) and stored on normal ice (to keep samples at 4 °C). Then, debrided non-diabetic foot ulcer (NFU) tissue was collected from a second patient in the same fashion 1.5 h later. Samples remained on ice at the wound clinic for 1.5 to 3 h following debridement before transfer to the laboratory for processing. At the laboratory, samples were rinsed three times with 1x phosphate buffered saline (PBS; Fisher Scientific, Waltham, MA, USA) to cleanse samples of media and FBS that would quench the enzymatic digest solutions added next. Samples were cut into ~2–3 mm3 pieces with a scalpel and finely minced with fine scissors until a sludge-like consistency (<~0.1 mm3 pieces). Although samples were already small prior to mincing (<100 mm3), effort was made to ensure that a fine a consistency was reached, as finer tissue pieces have superior cellular yields. The resulting tissue was placed into a 50 mL conical tube containing 20 mL Liberase (Sigma-Aldrich) in PBS at a concentration of 0.5 mg/mL for enzymatic digest. The cell-digest suspensions were constantly agitated (rotated) for a total of 1.5 h at 37 °C. Every half hour, the sample was subjected to maximum speed on a vortex mixer (VWR) for 30 s to physically disrupt any tissue that had clumped together and thus maximize the tissue surface area exposed to enzymatic digestion at all times. The cellular and enzymatic solution was then pipetted through a 100 µm Nylon cell filter (Fisher-Scientific) into a new conical tube, and 20 mL of 10% FBS DMEM was added through the filter to quench the enzymatic reaction and release any cells trapped within the filter, maximizing downstream cell yield. Solutions were then spun at 300× g for 8 min at 4 °C in a centrifuge to pellet the cells, resuspended in 20 mL 10% FBS DMEM, and passed through a 70 µm Nylon cell filter. A 20 mL solution of 10% FBS DMEM was added through the filter to collect the remaining cells, and the solution was re-spun to obtain a final cell pellet. This pellet was resuspended to a final cellular concentration of 1200 cells/µL in 0.04% Bovine Serum Albumin (BSA; Sigma-Aldrich) in PBS in accordance with the maximum capture, concentration short of overloading, per specifications from 10X Genomics (Pleasanton, CA, USA).
Single-cell RNA-seq (scRNA-seq) was performed at the Stanford Functional Genomics Facility (SFGF) for droplet-based microfluidic single cell RNA sequencing (scRNA-seq) using the 10x Chromium Single Cell platform (Single Cell 3′ v3, 10X Genomics, Pleasanton, CA, USA). A droplet of the cell suspensions, reverse transcription master mix, and partitioning oil was loaded onto a single cell chip and processed on the Chromium Controller. Reverse Transcription was performed at 53 °C for 45 min. cDNA was amplified for 12 cycles total (BioRad C1000 Touch thermocycler) with cDNA size selected using SpriSelect beads (Beckman Coulter, Indianapolis, IN, USA) and a ratio of SpriSelect reagent volume to sample volume of 0.6. cDNA was analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. cDNA was fragmented using the proprietary fragmentation enzyme blend for 5 min at 32 °C, followed by end repair and A-tailing at 65 °C for 30 min. cDNA were double-sided size selected using SpriSelect beats. Sequencing adaptors were ligated to the cDNA at 20 °C for 15 min. cDNA was amplified using a sample-specific index oligo as primer, followed by another round of double-sided size selection using SpriSelect beads.
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell.

value: plantar foot ulcer

value: all cells (unsorted)


title: Young CTRL #4


title: RP-3

status: Public on Nov 24 2023

city: Lanzhou

first: Chen

last: Lv

address: No.1 Yingmen Village

institute: Gansu Agricultural University

data_processing:
Using two software models, CIRCExplorer2 and CIRI, to predict circRNA, and integrating the results of the two software based on the start and end positions of circRNA. The following are the criteria for circRNA identification:
1.mismatch less than or equal 2; 2.Back-spliced junctions reads  greater than or equal 1; 3. The distance between two splice sites on the genome is less than 100kb.
Assembly: After the construction of the sequencing library is completed, Qubit is used for preliminary quantification and the library is diluted to 1ng/ul. Then, Agilent 2100 Bioanalyzer is used to detect the insert size of the sequencing library. Once the insert size meets expectations, qPCR method is used to accurately determine the effective concentration of the library (the effective concentration of the library is>2nM) to ensure the quality of the library.
Supplementary files format and content: txt,expression profiles

organism: Bos taurus

source_name: caudal vein blood

extract_protocol:
Total RNA from the NC and RP groups was isolated and purified using TRIzol reagentt (Thermo Fisher Scientific, Waltham, MA, USA).
After the construction of the sequencing library is completed, Qubit is used for preliminary quantification and the library is diluted to 1ng/ul. Then, Agilent 2100 Bioanalyzer is used to detect the insert size of the sequencing library. Once the insert size meets expectations, qPCR method is used to accurately determine the effective concentration of the library (the effective concentration of the library is>2nM) to ensure the quality of the library.

value: caudal vein blood

tag: breed

value: Holstein

tag: group

value: retained


title: HematopoieticNiche - Donor1

data_processing:
Basecalls performed using RTA3 software
Raw reads were processed using CellRanger count (to generate the BAM file) and CellRanger aggr (to generate the processed data) using CellRanger v3.1
Genome_build: GRCh38 Ensembl 93
Supplementary_files_format_and_content: Processed data provided as filtered feature/barcode matrix which includes a triplet of barcodes, features, and the count matrix files, each gzipped, as outputted by `CellRanger aggr`, all using Cell Ranger pipeline v3.1

extract_protocol:
Cells were isolated by degrading the engineered tissue constructs with 0.05% Trypsin until disaggregated, followed by filtration through a 50 µm filter and resuspension in PBS
Libraries were constructed using the 10X Chromium platform, using the Single Cell 3' v3 chemistry/kit to all manufacturer specifications.

tag: donor


title: RP-2


title: human diabetic foot ulcer


title: OVCAR8-pladienolide B-3


title: RP-1


title: OVCAR8-pladienolide B-1


title: NC-3

value: discharged normally


title: NC-2


title: NC-1


title: Pool5

city: Madison

first: Hasan

last: Khatib

state: WI

address: 1675 Observatory Dr

department: Animal and Dairy Sciences

institute: University of Wisconsin Madison

description: Sample 5 pool 5 (WMS normal - lesion free)

data_processing:
Paired-end reads were mapped to the swien genome (Sus Scrofa 10.2)
Transcript abundance was estimated using RSEM v1.3.0.
Differential expression was carried using EdgeR of the Bioconductor package.
Assembly: Sus Scrofa 10.2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Sus scrofa

source_name: Abdominal aortic tissue

extract_protocol:
RNA was extracted from each tissue using RNeasy mini kit (QIAGEN., Valencia, CA). Briefly, ?3 mg of tissue was lyophilized and reduced to powder using liquid nitrogen. Then, pulverized tissues were transferred to a QIAshred column to homogenize and reduce sample viscosity. Subsequent steps followed manufacturer instructions. RNA quality and quantity was assessed using NanodropONE (Thermofisher Scientific, DE, USA) and Bioanalyzer 2100 Eukaryote Total RNA Nano (Agilent Technologies, CA, USA).
LC sciences prepared the library  using illumina truseq-stranded-total-rna-kit (Part#-15031048-e)

value: aorta

tag: lesion status

value: Lesion free


title: Pool4

description: Sample 4 pool 4 (WMS normal - lesion free)


title: Pool3

description: Sample 3 pool 3 ( WMS FH - with lesion)

value: With atherosclerotic lesion


title: Pool2

description: Sample 2 pool 2 (WMS FH- With lesion)


title: +Dox, replicate 1, scRNAseq

city: Pohang

first: Somi

last: Kim

address: 47, Jigok-ro

department: Life Sciences

country: South Korea

institute: POSTECH

description: 10x Genomics

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Technical artifacts were eliminated using the remove-background function of the CellBender (v0.2.0) python package
Assembly: GRCm38.102
Supplementary files format and content: h5 files including filtered cells with filtered gene expression by CellBender

source_name: Small intestine

extract_protocol:
To prepare single cells, whole epithelial segments were isolated with 2mM EDTA for 30 min, washed with PBS, and then dissociated to single cells with TrypLE (Invitrogen) at 37℃ for 30 min, with mixing every 10 min. Dissociated cells were filtered through a 40-𝜇m cell strainer on ice and washed three times with cold DMEM/F12.
Single-cell suspensions with 90% cell viability were processed on the 10x Chromium Controller using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics) according to the manufacturer’s instructions. Cells were partitioned into nanoliter-scale Gel Beads-in-Emulsion (GEMs) with target recovery of 10,000 cells. The single-cell 3 prime mRNA seq library was generated by reverse transcription, cDNA amplification, fragmentation, and ligation with adaptors followed by sample index PCR. Resulting libraries were quality checked by Bioanalyzer and sequenced on an Illumina NovaSeq 6000 (index = 8 bases, read 1 = 26 bases, and read 2 = 91 bases).

treatment_protocol: 0.15mg/ml doxycycline and 5% sucrose in drinking water was administrated for 4 days. 5% sucrose in drinking water was administrated to control mice for 4 days.

value: Small intestine

value: Epithelial cells

value: 0.15mg/ml Doxycycline


title: -Dox, replicate 1, scRNAseq

description: 10x Genomics

value: Cont


title: HematopoieticNiche - Donor2

description: Processed files pooled with Donor1


title: BBN-ATM-KO tumor, sample 5

city: Lodz

first: Konrad

last: Stawiski

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

data_processing:
The Nextflow RNA-seq pipeline (nf-core/rnaseq; version 3.9) was used to perform quality control and STAR aligner and Salmon were used for quantification.  Counts were normalized using the median of ratios method and differential expression analysis was performed with DESeq2.
Assembly: CGRm39
Supplementary files format and content: DESeq2 normalized counts for all samples

source_name: Urothelial tumor

growth_protocol: We established a second cohort of BBN and BBN-ATM-KO tumor-bearing mice.  When tumors reached 500 mm3 in size, mice were sacrificed and tumors harvested with half of the tumor snap-frozen for RNA sequencing.

extract_protocol:
Snap frozen tumors were sent to Novogene (Durham, NC) for RNA extraction. Standard Novogene protocol was used.
RNA libraries for RNA-seq were prepared by NovoGene following manufacturer's protocols.

value: Urothelial tumor

value: ATM-KO


title: BBN-ATM-KO tumor, sample 3


title: BBN-ATM-KO tumor, sample 2


title: BBN-ATM-KO tumor, sample 1


title: BBN-ATM-WT tumor, sample 5

value: ATM-WT


title: BBN-ATM-WT tumor, sample 4


title: BBN-ATM-WT tumor, sample 3


title: BBN-ATM-WT tumor, sample 2


title: BBN-ATM-WT tumor, sample 1


title: Pool6

description: Sample 6 pool 6 (WMS normal - lesion free)


title: Sap_pEx3_RESC_BR2: N2a Flp-In rtTA (Sap30bp_withEx3), siSap30bp +Dox (Sap30bp_pEx3 isoform rescue), Biological rep 2

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

data_processing:
RTA 3.4.4
AS analysis for RNA-seq data was performed using the vast-tools analysis pipeline, version 2.2 https://github.com/vastgroup/vast-tools with VastDB version Mmu released Feb. 16, 2018 (Braunschweig et al., 2014; Irimia et al., 2014; Tapial et al., 2017). Events with poor coverage or junction balance were filtered out (vast-tools quality column score 3 other than SOK/OK/LOW for cassette exon [CE], microexon [MIC], and alternative 5' or 3' splice site [Alt5/3] events or coverage less than 15 reads for intron retention [IR] events; score 4 other than OK/B1 for CE and MIC events and score 5 of less than 0.05 for IR events). Differential splicing was assessed using a combination of the change in average “percent spliced in” (avgPSI) or percent intron retention (avgPIR) levels along with vast-tool’s diff module. For Sap30bp RNA-seq experiments, AS events showing changing splicing upon Sap30bp knockdown were defined as those with at least a 15% change in avgPSI/PIR (∆PSI/∆PIR) between the siRNA knockdown and NTC treated samples for both Sap30bp +Ex3 and ∆Ex3 expressing N2a Flp-In rtTA cell lines with maximum of 10% ∆PSI difference between cell lines and called as a significant change by the vast-tools diff module (minimum value for change with a likelihood of 0.95, MV[abs(dPSI)] at 0.95, > 0). Events showing Sap30bp mediated rescue by either the +Ex3 or ∆Ex3 isoforms were defined as those events showing significant Sap30bp knockdown in both cell lines (as described above) and for which the siRNA treated samples induced with Doxycycline showed at least a 10% avgPSI change compared to the siRNA knockdown samples (-Dox) and showed a significant change according to the vast-tools diff module (MV[abs(dPSI)] at 0.95 > 0). An event was called as showing isoform specific rescue if the change in the ∆PSI (∆∆PSI/∆∆PIR) between the rescue and knockdown samples was greater than 7% between the Sap30bp isoforms rescued cell lines. AS events showing Sap30bp regulation according to these criteria are listed in Supplementary table 5.
Gene expression changes were analyzed by pseudo-aligning pre-trimmed reads to GENCODE vM21 transcripts using Salmon v0.14.1 (Patro et al., 2017) and aggregated per gene using the R package tximport (Soneson et al., 2015). Differential expression was assessed using the classic mode (exactTest) in edgeR (McCarthy et al., 2012). Lowly expressed genes (<5 RPKM) were removed from the analysis. For Sap30bp knockdown, a gene was considered to show differential expression if it had at least a 0.6 log2FC (~50% change) between the siRNA knockdown and NTC control samples with an FDR < 0.1. For Sap30bp rescue samples, a gene was considered to be rescued by either Sap30bp isoform if it had at least a 0.4 log2FC between the Sap30bp rescue (+Dox) and siRNA knockdown samples in either +EX3 or ∆EX3 cell line with an FDR < 0.1.
Assembly: mm9
Supplementary files format and content: All files are in tab-delimited format. “vast.tools_INCLUSION_LEVELS_Altsplicing_Sap30bp_Mmu12-mm9.tab” contains vast-tools output showing the percent spliced in (PSI) values for each splicing events across samples. “AS.DiffEvents_Sap30bp_dPSI.15.tab” contains ∆PSI (dPSI) values and vast-tools diff module annotations for AS events showing differential inclusion between any of the NTC, Knockdown, or Rescue conditions (minimum ∆PSI of 15% with a likelihood of 0.95, MV[abs(dPSI)] at 0.95, > 0 [annotated as “TRUE” in signif. columns]). “DE_Sap30bp.tab” contains edgeR-estimated average RPKM, fold change and FDR values assessing differential RNA expression changes between conditions. (General Note: Sap.mEx.siNTC = ∆Exon3 isoform line_NTC, Sap.mEx.siSap = ∆Exon3 isoform line_Knockdown, Sap.mEx.siSap.dox = ∆Exon3 isoform line_Isoform Rescue, Sap.pEx.siNTC = +Exon3 isoform line_NTC, Sap.pEx.siSap = +Exon3 isoform line_Knockdown, Sap.pEx.siSap.dox = +Exon3 isoform line_Isoform Rescue)

source_name: N2a Flp-In rtTA

growth_protocol: Mouse neuroblastoma (N2a/N2a Flp-In rtTA) cells were grown in DMEM (high glucose; Sigma-Aldrich) supplemented with 10% FBS, sodium pyruvate, non-essential amino acids, and penicillin/streptomycin. Cell lines were maintained at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN) as recommended by the manufacturer. For RT-PCR and RT-qPCR experiments, cDNA was synthesized for each sample for ~500ng - 1 µg of RNA using the Maxima H Minus First Strand cDNA Synthesis Kit (Thermo Fischer Scientific, K1651) and diluted in water to a concentration of 5 ng/µL. qPCR reactions were performed using the SensiFAST SYBR No-ROX Kit (Meridian Bioscience, BIO-98005) and analyzed using a CFX96 Real-Time PCR Detection System (BIO-RAD).
1000 ng per sample was used in the library preparation. To obtain larger insert size (540 nt on average after size selection), Illumina’s TruSeq Stranded mRNA sample preparation protocol was modified as follows: 1) fragmentation time and temperature was reduced from 8 minutes at 98°C to 2 minutes at 80°C. Average size distribution prior to library preparation was 232 nt versus 740 nt, respectively; 2) after the final library was generated, the samples were loaded onto a 2% agarose gel (Cat # 1613101, BioRad) and run for 1 hour at 100 V. The libraries were size selected between 400 and 600 bp. Excised gel fragments were purified using the Qiagen MinElute Gel Extraction kit (Cat # 28604, Qiagen). The rest of the protocol was adapted as described in Illumina’s TruSeq Stranded mRNA sample preparation guide (Part# 15031047 Rev. E, Illumina).

treatment_protocol: For siRNA knockdown and rescue experiments, N2a Flp-In rtTA cells (~1.2x105) were grown for 24 hours in two (Control) or three (Knockdown/Rescue) 6-well dishes and transfected with siGENOME siRNA (Dharmacon) using RNAiMax (Life Technologies) as recommended by the manufacturer. The siGENOME siRNA used for the transfections was Sap30bp (D-055094-01-0002) with a non-targeting control (NTC) pool (D-001810-10) used for the controls. Media was changed 24 hours post transfection with or without Doxycycline to induce isoform expression, with cells from all matching condition wells harvested and combined at 72 hours. Two-thirds of the total sample was stored for western blot analysis and one-third stored for RNA extraction.

value: N2a Flp-In rtTA

value: Mouse neuroblastoma

tag: cdna expressed_(n2a_flp-in_line)

tag: condition

value: Sap30bp siRNA knockdown, Sap30bp pEx3 isoform rescue (+Dox)


title: Sap_pEx3_NTC_BR2: N2a Flp-In rtTA (Sap30bp_withEx3), NT-control, Biological rep 2

tag: cell line

value: NT-control


title: Sap_pEx3_KD_BR2: N2a Flp-In rtTA (Sap30bp_withEx3), siSap30bp, Biological rep 2

value: Sap30bp siRNA knockdown


title: Sap_pEx3_KD_BR1: N2a Flp-In rtTA (Sap30bp_withEx3), siSap30bp, Biological rep 1


title: Sap_pEx3_RESC_BR1: N2a Flp-In rtTA (Sap30bp_withEx3), siSap30bp +Dox (Sap30bp_pEx3 isoform rescue), Biological rep 1


title: Sap_mEx3_RESC_BR2: N2a Flp-In rtTA (Sap30bp_withoutEx3), siSap30bp +Dox (Sap30bp_mEx3 isoform rescue), Biological rep 2

value: Sap30bp siRNA knockdown, Sap30bp mEx3 isoform rescue (+Dox)


title: Sap_mEx3_KD_BR2: N2a Flp-In rtTA (Sap30bp_withoutEx3), siSap30bp, Biological rep 2


title: Sap_mEx3_RESC_BR1: N2a Flp-In rtTA (Sap30bp_withoutEx3), siSap30bp +Dox (Sap30bp_mEx3 isoform rescue), Biological rep 1


title: Pool1

description: Sample 1 pool 1 (WMS FH- With lesion)


title: Sap_mEx3_KD_BR1: N2a Flp-In rtTA (Sap30bp_withoutEx3), siSap30bp, Biological rep 1


title: Sap_pEx3_NTC_BR1: N2a Flp-In rtTA (Sap30bp_withEx3), NT-control, Biological rep 1


title: TT04_subj1_V2

city: Hoerholm

first: Niels Peter

last: Hell Knudsen

address: Bøge Alle 3

institute: ALK-Abello

data_processing:
Cellranger 6.1.2
Seurat v4
Assembly: GRCh38-2020-A
Supplementary files format and content: Cellranger filtered and raw bc matrix counts
Supplementary files format and content: Integrated Seurat object with UMAP

source_name: blood

extract_protocol: Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium 5’ Single Cell Gene Expression assay and Chromium Controller Instrument according to the manufacturer’s published protocol

value: blood

value: PBMCs

value: allergic


title: BBN-ATM-KO tumor, sample 4


title: Sap_mEx3_NTC_BR2: N2a Flp-In rtTA (Sap30bp_withoutEx3), NT-control, Biological rep 2


title: Cyto_Chtop_pEx5_RESC_BR4: N2a Flp-In rtTA (Chtop_w/Exon5), siChtop, +Dox (Chtop pEx5 isof resc), cytop frac, Bio rep 1

data_processing:
RTA 3.4.4
Pre-trimmed reads from total, nuclear, and cytoplasmic samples were pseudo-aligned to GENCODE vM21 transcripts using Salmon v0.14.1 (Patro et al., 2017) and gene-level abundances calculated using tximport (Soneson et al., 2015). Differential analysis comparing the nuclear/cytoplasmic ratios in the Chtop knockdown and rescue fractions was performed using DESeq2 (Love et al., 2014) as per Lee et al., 2020 with a minimum of 3 RPKM required across all samples. Gene-level changes in the knockdown vs control and rescue vs knockdown samples were calculated by comparing nuclear/cytoplasmic ratios across samples using the formula log2(Nuclear/Cytoplasmic)kd/resc – log2(Nuclear/Cytoplasmic)ntc/kd). Changes in nuclear (formula: log2(Nuclear/Total)kd/resc - log2(Nuclear/Total)ntc/kd) and cytoplasmic (formula: log2(Cytoplasmic/Total)kd/resc– log2(Cytoplasmic/Total)ntc/kd) fractions were similarly analyzed using DESeq2 normalized by the totals. For knockdown (kd vs ntc) comparisons, a transcript was considered to show an altered nuclear/cytoplasmic ratio in the siRNA knockdown samples compared to controls if the change in nuclear/cytoplasmic ratios was greater than 0.3 (~20% change) with a similar change (>0.3) in either the nuclear or cytoplasmic fractions. For Chtop rescue (resc vs kd) samples, a transcript was considered to be rescued by either Chtop isoform (Chtop +Ex5 or Chtop ∆Ex5) if it showed a change in the knockdown samples (as described above) and had at least a 0.25 change in nuclear/cytoplasmic ratio between the Chtop rescue (+Dox) and matching siRNA knockdown samples from the same expression line in the opposite direction as the knockdown. A transcript was annotated as showing better rescue upon re-expression of either Chtop isoform if the difference in the change in nuclear/cytoplasmic ratios between the Chtop isoform expressing lines was greater than 0.25 (∆∆log2(Nuclear/Cytoplasm) ratio).
Assembly: mm10 (GENCODE vM21)
Supplementary files format and content: All files are in tab-delimited format. “NCFracts_Chtop_COUNTS.txt.gz” and “NCFracts_Chtop_RPKM.tab.gz” contains the raw count and RPKM values for genes expressed (3 RPKM) across all conditions (NTC/Kd/Resc) and fractions (Total/Nuclear/Cyto). “NCFracts_Chtop_DESeq2_normCOUNTS_CytovsTotal_wAnnotations.txt.gz”, “NCFracts_Chtop_DESeq2_normCOUNTS_NucvsCyto_wAnnotations.txt.gz” and “NCFracts_Chtop_DESeq2_normCOUNTS_NucvsTotal_wAnnotations.txt.gz” contains the normalized count information as calculated by DESeq2 along with the Nuclear/Cytoplasmic, Nuclear/Total and Cytoplasmic/Total log2FC values used to assess changes in RNA expression between the fractions. Genes showing changing ratios in the knockdown (KD vs NTC) or isoform rescue (RES vs KD; mEX5/pEX5) samples are highlighted in the “Annotation” columns (“BOTH” = consistent regulation with both isoform rescue samples [>0.25 ∆log2FC and <0.25 ∆∆log2FC_pEXvsmEX], mEX_Up/Dn = increased or decreased [>0.25 ∆log2FC and >0.25 ∆∆log2FC_pEXvsmEX] nuclear/cytoplasmic expression with the ∆Ex5 isoform, pEX_Up/Dn = increased or decreased [>0.25 ∆log2FC and >0.25 ∆∆log2FC_pEXvsmEX] nuclear/cytoplasmic expression with the +Ex5 isoform).

extract_protocol:
For nuclear/cytoplasmic fractionation experiments N2a Flp-In rtTA cells were grown for 72 hours in a 6-well dish as described above. After 72 hours, N2a cells were harvested through addition of 200 µL Trypsin (0.05%) for ~10 minutes until most cells could be dislodged from the plate with gentle shaking. After trypsinization, cells were resuspended in 500 µL of DMEM growth media and the total volume transferred to a 1.5 mL microcentrifuge tube. To ensure similar number of cells in each sample for lysis, cells were then counted using an automated cell counter (Millipore, Scepter Handheld Automated Cell Counter) and equal number of cells transferred to a new microcentrifuge tube corresponding to the lowest cell count within each experiment. Next, cells were pelleted by centrifugation (300 rcf for 3 minutes) and then washed two times with 500 µL PBS and samples placed on ice for all remaining steps. 20% (100 µL) of the sample was removed as a “total” sample, centrifuged (300 rcf for 3 mins at 4 °C), and cell pellets resuspended in 200 µL of pre-chilled RIPA buffer containing freshly added 1mM DTT and 1mM PMSF and stored on ice. The remaining sample (400 µL) was pelleted (300 rcf for 3 mins at 4 °C), and 200 µL pre-chilled RLN buffer (recipe from QIAGEN: “Purification of cytoplasmic RNA from animal cells using the RNeasy Mini Kit”) containing 50 mM Tris·Cl (pH 8.0), 140 mM NaCl, 1.5 mM MgCl2 and 0.5% (v/v) Nonidet P-40 with freshly added 1mM DTT and 1mM PMSF was added slowly, and mixed by carefully inverting the tube and gentle pipetting. Samples were left for 5 minutes until homogenous and then centrifuged (300 rcf for 3 mins at 4 °C) to pellet the nuclei and cell debris. The lysate (~200 µL total) was removed and centrifuged at maximum speed (17,000 rcf for 3 mins at 4 °C) to remove any undigested cell debris and lysate transferred to a new tube (the “cytoplasmic” fraction). The remaining pellet (containing nuclei) were gently washed again with pre-chilled 200 µL RLN buffer as described above and pelleted again by centrifugation (300 rcf for 3 minutes at 4 °C). Pellets were then resuspended in 200 µL of RIPA buffer (the “nuclear” fraction). All samples were sonicated (2x15 pulses) to help sample homogenization before the lysates were divided with approximately one-third of the sample (~80 µL) taken for protein analysis and approximately two-thirds (~120 µL) taken for RNA analysis. For protein samples, Laemmli buffer was added and samples stored at -80 °C until western blots performed as described above. RNA was purified directly (same day) from the RLN buffer lysates using the RNeasy Mini Kit (QIAGEN) as recommended by the manufacturer and samples prepared for sequencing.
RNA samples (250 ng) were enriched for mRNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490L, NEB) and subsequent libraries obtained using the NEBNext Ultra II Directional RNA library prep kit (E7760L, NEB) with some modifications. Specific modifications include; 1) fragmentation time was reduced from 15 minutes at 94°C to 7.5 minutes, 2) During the first strand cDNA synthesis reaction, the incubation times were increased from from 15 to 50 minutes at 42°C and 3) fragments were size selected using Ampure XP Beads (17.5ul for removing large fragments and 10ul to retain fragments without dimers).

treatment_protocol: For siRNA knockdown and rescue experiments, N2a Flp-In rtTA cells (~1.2x105) were grown for 24 hours in two (Control) or three (Knockdown/Rescue) 6-well dishes and transfected with siGENOME siRNA (Dharmacon) using RNAiMax (Life Technologies) as recommended by the manufacturer. The siGENOME siRNA used for the transfections was Chtop/2500003M10Rik (D-063383-02) with a non-targeting control (NTC) pool (D-001810-10) used for the controls. Media was changed 24 hours post transfection with or without Doxycycline to induce isoform expression, with cells from all matching condition wells harvested and combined at 72 hours. Two-thirds of the total sample was stored for western blot analysis and one-third stored for RNA extraction.

tag: fraction

value: Cytoplasmic

value: Chtop siRNA knockdown, Chtop pEx5 isoform rescue (+Dox)


title: Cyto_Chtop_pEx5_KD_BR4: N2a Flp-In rtTA (Chtop_w/Exon5), siChtop, cytop frac, Bio rep 1

value: Chtop siRNA knockdown


title: Cyto_Chtop_pEx5_KD_BR6: N2a Flp-In rtTA (Chtop_w/Exon5), siChtop, cytop frac, Bio rep 2


title: Cyto_Chtop_pEx5_NTC_BR4: N2a Flp-In rtTA (Chtop_w/Exon5), NT-control, cytop frac, Bio rep 1


title: Cyto_Chtop_mEx5_KD_BR4: N2a Flp-In rtTA (Chtop_w/oExon5), siChtop, cytop frac, Bio rep 1


title: Cyto_Chtop_mEx5_RESC_BR4: N2a Flp-In rtTA (Chtop_w/oExon5), siChtop, +Dox (Chtop mEx5 isof resc), cytop frac, Bio rep 1

value: Chtop siRNA knockdown, Chtop mEx5 isoform rescue (+Dox)


title: Cyto_Chtop_mEx5_KD_BR6: N2a Flp-In rtTA (Chtop_w/oExon5), siChtop, cytop frac, Bio rep 2


title: Cyto_Chtop_mEx5_RESC_BR6: N2a Flp-In rtTA (Chtop_w/oExon5), siChtop, +Dox (Chtop mEx5 isof resc), cytop frac, Bio rep 2


title: Nuc_Chtop_pEx5_RESC_BR6: N2a Flp-In rtTA (Chtop_w/Exon5), siChtop, +Dox (Chtop pEx5 isof resc), nuc frac, Bio rep 2

value: Nuclear


title: Cyto_Chtop_mEx5_NTC_BR4: N2a Flp-In rtTA (Chtop_w/oExon5), NT-control, cytop frac, Bio rep 1


title: Nuc_Chtop_pEx5_RESC_BR4: N2a Flp-In rtTA (Chtop_w/Exon5), siChtop, +Dox (Chtop pEx5 isof resc), nuc frac, Bio rep 1


title: Nuc_Chtop_pEx5_KD_BR6: N2a Flp-In rtTA (Chtop_w/Exon5), siChtop, nuc frac, Bio rep 2


title: Nuc_Chtop_pEx5_NTC_BR6: N2a Flp-In rtTA (Chtop_w/Exon5), NT-control, nuc frac, Bio rep 2


title: Nuc_Chtop_pEx5_NTC_BR4: N2a Flp-In rtTA (Chtop_w/Exon5), NT-control, nuc frac, Bio rep 1


title: Nuc_Chtop_mEx5_RESC_BR6: N2a Flp-In rtTA (Chtop_w/oExon5), siChtop, +Dox (Chtop mEx5 isof resc), nuc frac, Bio rep 2


title: Nuc_Chtop_pEx5_KD_BR4: N2a Flp-In rtTA (Chtop_w/Exon5), siChtop, nuc frac, Bio rep 1


title: Sap_mEx3_NTC_BR1: N2a Flp-In rtTA (Sap30bp_withoutEx3), NT-control, Biological rep 1


title: Cyto_Chtop_pEx5_RESC_BR6: N2a Flp-In rtTA (Chtop_w/Exon5), siChtop, +Dox (Chtop pEx5 isof resc), cytop frac, Bio rep 2


title: Nuc_Chtop_mEx5_RESC_BR4: N2a Flp-In rtTA (Chtop_w/oExon5), siChtop, +Dox (Chtop mEx5 isof resc), nuc frac, Bio rep 1


title: Nuc_Chtop_mEx5_KD_BR6: N2a Flp-In rtTA (Chtop_w/oExon5), siChtop, nuc frac, Bio rep 2


title: Total_Chtop_pEx5_KD_BR6: N2a Flp-In rtTA (Chtop_w/Exon5), siChtop, Total frac, Bio rep 2

value: Total


title: Total_Chtop_pEx5_NTC_BR6: N2a Flp-In rtTA (Chtop_w/Exon5), NT-control, Total frac, Bio rep 2


title: Nuc_Chtop_mEx5_NTC_BR6: N2a Flp-In rtTA (Chtop_w/oExon5), NT-control, nuc frac, Bio rep 2


title: Nuc_Chtop_mEx5_KD_BR4: N2a Flp-In rtTA (Chtop_w/oExon5), siChtop, nuc frac, Bio rep 1


title: Total_Chtop_pEx5_RESC_BR4: N2a Flp-In rtTA (Chtop_w/Exon5), siChtop, +Dox (Chtop pEx5 isof resc), Total frac, Bio rep 1


title: Total_Chtop_pEx5_RESC_BR6: N2a Flp-In rtTA (Chtop_w/Exon5), siChtop, +Dox (Chtop pEx5 isof resc), Total frac, Bio rep 2


title: Total_Chtop_pEx5_NTC_BR4: N2a Flp-In rtTA (Chtop_w/Exon5), NT-control, Total frac, Bio rep 1


title: Total_Chtop_pEx5_KD_BR4: N2a Flp-In rtTA (Chtop_w/Exon5), siChtop, Total frac, Bio rep 1


title: Total_Chtop_mEx5_RESC_BR4: N2a Flp-In rtTA (Chtop_w/oExon5), siChtop, +Dox (Chtop mEx5 isof resc), Total frac, Bio rep 1


title: Total_Chtop_mEx5_RESC_BR6: N2a Flp-In rtTA (Chtop_w/oExon5), siChtop, +Dox (Chtop mEx5 isof resc), Total frac, Bio rep 2


title: Total_Chtop_mEx5_KD_BR4: N2a Flp-In rtTA (Chtop_w/oExon5), siChtop, Total frac, Bio rep 1


title: bo scRNAseq

city: changsha

first: Hui

last: Xie

state: hunan

address: #87 Xiangya Road

department: Orthopedics

institute: Central South University

data_processing:
Reads from single-cell RNA sequencing were aligned to mm10 and collapsed into unique molecular identifier (UMI) counts using the 10x Genomics Cell Ranger software (version 4.0.0) with default parameters.
Further analyses were performed using Seurat 3.0 in the R Statistical language.
Cells with more than 20% mitochondrial gene expression were removed.
Doublets were identified using the ScDblFinder package.
Hematopoietic clusters and small clusters without clear BMSC lineage or EC characteristics were removed from visualization and analyses.
Genome_build: mm10
Supplementary_files_format_and_content: TAR (of barcodes.tsv, features.tsv,matrix.mtx)

source_name: Tibiae and femurs, bone

extract_protocol:
Tibiae and femurs were collected from 5-week-old mice (n = 3), then bone chips (bo) and bone marrow (bm) cells were digested in aMEM medium containing 2% FBS, 1 mg/mL type II collagenase (17101015, Gibco), 1 mg/mL Dispase II (04942078001, Sigma-Alderich) and 1 mg/mL DNase (10104159001, Roche), then shaken at 120 r.p.m. at 37 ℃ for 45 minutes. After erythrocytes lysis and filtering through 40-μm cell strainers, a lineage cell depletion kit (130-090-858, Miltenyi Biotec) was used to enrich non-hematopoietic cells of bm by MACS, followed by FACS sorting of live single Lin/CD45/CD71/CD3/CD19 negative cells. The bo sample was directly sorted by FACS for live single Lin/CD45/CD71/CD3/CD19  negative cells. If the cell viability was higher than 85%, the cell concentration was adjusted to 700-1200 /L. The prepared cell suspension was carried out using microflow control chip, and the bead and cells with cell Barcode sequence (cell Barcode) were wrapped in the droplets, where the cells burst, and the released mRNA are connected with the cell tag sequence on the Gel beads to form single-cell GEMs structures (Gel Bead in Emulsions). Cell mRNAs undergo a reverse transcriptional reaction in the droplet to form cDNA, followed by demulsification and cDNA library construction.
single cell mRNA libraries were prepared for sequencing using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1(#1000121)

tag: strain

value: Tibiae and femurs, bone

tag: age

value: 5 weeks


title: Cyto_Chtop_mEx5_NTC_BR6: N2a Flp-In rtTA (Chtop_w/oExon5), NT-control, cytop frac, Bio rep 2

value: N2a Flp-In rtTA


title: bm scRNAseq

source_name: Tibiae and femurs, bone marrow

value: Tibiae and femurs, bone marrow


title: Total_Chtop_mEx5_NTC_BR6: N2a Flp-In rtTA (Chtop_w/oExon5), NT-control, Total frac, Bio rep 2

value: Mouse neuroblastoma


title: Total_Chtop_mEx5_KD_BR6: N2a Flp-In rtTA (Chtop_w/oExon5), siChtop, Total frac, Bio rep 2


title: Total_Chtop_mEx5_NTC_BR4: N2a Flp-In rtTA (Chtop_w/oExon5), NT-control, Total frac, Bio rep 1

value: NT-control


title: pole1WT_mat2aWT 2

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

description: bisulfite-treated genomic DNA

data_processing:
base calling: HiSeq Analysis Software
trimming: reads were adapter-, quality- and end- trimmed using snakePipes 1.2.3, which uses cutadapt 2.1, using -a AGATCGGAAGAGC -A AGATCGGAAGAGC -q 10 -m 30 -j 8 as parameters
alignment: reads were aligned to the bisulfite-converted GRCz11 genome using snakePipes 1.2.3 which uses bwa-meth version 0.2.2 using --read-group as a parameter
PCR duplicate removal: mapped reads were weeded for PCR duplicates using snakePipes 1.2.3 which uses sambamba version 0.6.6 using --remove-duplicates as a parameter
CpG methylation extraction and coverage generation: methylation coverages were generated using snakePipes 1.2.3 which uses methyl_extract version 1.9 using default parameters
Differential methylation analysis was performed using snakePipes 1.2.3 which uses metilene 0.2.6 using default parameters
Genome_build: GRCz11
Supplementary_files_format_and_content: bigwig format

organism: Danio rerio

source_name: 5dpf zebrafish embryos

growth_protocol: WT, dnmt1 mutant (N1391K), pole1 mutant (I633K), mat2aa knockout (Y101X), mcm10 mutant (L246R) zebrafish were crossed to obtain dnmt1/pole1 single or double mutant fish, mat2a/pole1 single or double mutant fish or mcm10 single mutant fish

extract_protocol:
Genomic DNA was extracted from 5dpf zebrafish embryos using the DNeasy blood and tissue kit (Qiagen).
0.5µg of DNA was used for bisulfite reactions and library construction using the EpiGnome Methyl-Seq kit (Epicentre).

value: 5dpf zebrafish embryos

tag: mutational status


title: pole1WT_mat2aWT 1

description: bisulfite-treated genomic DNA


title: Nuc_Chtop_mEx5_NTC_BR4: N2a Flp-In rtTA (Chtop_w/oExon5), NT-control, nuc frac, Bio rep 1


title: pole1WT_mat2aWT 4

description: bisulfite-treated genomic DNA


title: pole1WT_mat2aMUT 1

description: bisulfite-treated genomic DNA


title: pole1WT_mat2aMUT 4

description: bisulfite-treated genomic DNA


title: pole1WT_mat2aMUT 3

description: bisulfite-treated genomic DNA


title: pole1WT_mat2aMUT 2

description: bisulfite-treated genomic DNA


title: pole1MUT_mat2aMUT 3

description: bisulfite-treated genomic DNA


title: pole1MUT_mat2aMUT 2

description: bisulfite-treated genomic DNA


title: pole1MUT_mat2aMUT 1

description: bisulfite-treated genomic DNA


title: pole1MUT_mat2aMUT 4

description: bisulfite-treated genomic DNA


title: mcm10_WT1 1

description: bisulfite-treated genomic DNA


title: mcm10_WT3 1

description: bisulfite-treated genomic DNA


title: mcm10_WT2 1

description: bisulfite-treated genomic DNA


title: mcm10_MUT4 1

description: bisulfite-treated genomic DNA


title: mcm10_WT4 1

description: bisulfite-treated genomic DNA


title: pole1WT_mat2aWT 3

description: bisulfite-treated genomic DNA


title: mcm10_MUT1 1

description: bisulfite-treated genomic DNA


title: dnmt1WT_pole1WT 4

description: bisulfite-treated genomic DNA


title: mcm10_MUT3 1

description: bisulfite-treated genomic DNA


title: mcm10_MUT2 1

description: bisulfite-treated genomic DNA


title: dnmt1WT_pole1WT 2

description: bisulfite-treated genomic DNA


title: dnmt1WT_pole1WT 3

description: bisulfite-treated genomic DNA


title: dnmt1WT_pole1WT 1

description: bisulfite-treated genomic DNA


title: dnmt1WT_pole1MUT 4

description: bisulfite-treated genomic DNA


title: dnmt1WT_pole1MUT 2

description: bisulfite-treated genomic DNA


title: dnmt1WT_pole1MUT 1

description: bisulfite-treated genomic DNA


title: dnmt1WT_pole1MUT 3

description: bisulfite-treated genomic DNA


title: dnmt1MUT_pole1WT 2

description: bisulfite-treated genomic DNA


title: 6 (diabetic macrosomia)

type: RNA

city: Shenyang

first: guiyu

last: song

address: Sanhao Street

institute: Shengjing Hospital affilited to China Medical University

description: Gene expression of diabetic macrosomia placenta.

hyb_protocol: One microgram of each labelled cRNA was fragmented by adding 5 μl of 10 × blocking agent and 1 μl of 25 × fragmentation buffer, the mixture was then heated at 60°C for 30 min and finally, 25 μl of 2 × GE hybridization buffer was added to dilute the labelled cRNA. Hybridization solution (50 μl) was dispensed into a gasket slide, which was then assembled with the lncRNA expression microarray slide. The slides were incubated for 17 h at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyse the acquired array images.

source_name: placenta2, diabetic macrosomia2, replicate 1

label_protocol: The global profiling of human lncRNAs and protein-coding transcripts were performed using Arraystar Human LncRNA Microarray V3.0. Sample labelling and array hybridization were performed according to the Agilent One-Colour Microarray Based Gene Expression Analysis protocol (Agilent Technology, Santa Clara, USA) with minor modifications. Briefly, mRNA was purified from total RNA after removing of ribosomal RNA (rRNA) (mRNA-ONLYTM Eukaryotic mRNA Isolation Kit; Epicentre, Wisconsin, USA). Then, each sample was amplified and transcribed into fluorescent complementary RNA (cRNA) along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit; Arraystar, Rockville, USA). The labelled cRNAs were purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany). The concentration and specific activity of the labelled cRNAs (pmol Cy3/μg cRNA) were measured using a NanoDrop ND-1000 instrument.

extract_protocol: Total RNA was isolated from the placenta samples using TRIZOL reagent according to the manufacturer’s protocol. RNA quantity and quality were measured using a NanoDrop ND-1000 instrument. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Human placenta was collected from patients who were delivered by operation. The inclusion criteria is: 1) full-term, singleton patients; 2) delivered by caesarean section; 3) to exclude patients with hypertension, thyroid disorder, placenta previa, multiple pregnancy, assisted reproductive treatment, fetal malformation, premature of membrane rupture and other complications. The diagnosis criteria of GDM: 75g OGTT was conducted in pregnancy patients during 24-28 weeks, fasting plasma glucose, 1h blood glucose and 2h blood glucose were 5.1mmol/L, 10.0mmol/L, 8.5.mmol/L, the patients was diagnosed as GDM, if any of blood glucoses is higher than this criteria. Diabetic macrosomia group (DM group) is defined as patients with GDM and newborn birth weight above 4000g. Control group is defined as patients without GDM and newborn birth weight is between 2500-4000g. Placenta was collected from the maternal side of the placenta 2 cm away from the umbilical cord insertion site within 30 min after delivery, and was divided into 1 cm3 samples, and then frozen in liquid nitrogen and stored at −80°C.

value: placenta

tag: gravidity

tag: parity

tag: gestational week

tag: ogtt fasting blood glucose

tag: ogtt 1h glucose

tag: ogtt 2h glucose

tag: pre-pregnancy bmi

tag: newborn birth weight

tag: newborn body length

tag: newborn chest circumference

tag: newborn abdominal circumference


title: 5 (diabetic macrosomia)

source_name: placenta1, diabetic macrosomia1, replicate 1

tag: tissue


title: SCD -AID_DCP2_replicate2_t45

city: Zürich

first: Mostafa

last: Zedan

address: Otto-Stern-Weg 3

country: Switzerland

institute: ETH-Zurich

data_processing:
The SLAM-DUNK software was used for reads alignment, filtration, calling SNP, and calculating the relevant statistics of SLAMSeq reads for each given 3’ UTR.
Assembly: The FASTA file of the Yeast Genome was downloaded from the Saccharomyces Genome Database "SGD"
Supplementary files format and content: A tab-separated tcount file per sample containing the SLAMSeq statistics

organism: Saccharomyces cerevisiae

extract_protocol:
Yeast cells were lysed and RNA was extracted using Phenol-Chlorform
Quantseq
3’mRNA-Seq

tag: cell line

tag: cell type

value: Yeast cells

tag: time after_chase

value: 45 min

tag: genotype

tag: biological replicate

value: replicate 2

tag: treatment

value: plus Ethanol


title: 15 (diabetic macrosomia)

source_name: placenta3, diabetic macrosomia3, replicate 1

tag: age

tag: gravidity

tag: parity


title: SCD -AID_DCP2_replicate2_t55

value: 55 min


title: SCD -AID_DCP2_replicate2_t50

value: 50 min


title: dnmt1MUT_pole1WT 4

description: bisulfite-treated genomic DNA

tag: mutational status


title: 16 (diabetic macrosomia)

source_name: placenta4, diabetic macrosomia4, replicate 1

tag: gestational week

tag: ogtt fasting blood glucose

tag: ogtt 1h glucose

tag: ogtt 2h glucose


title: SCD -AID_DCP2_replicate2_t35

value: 35 min


title: SCD -AID_DCP2_replicate2_t40

value: 40 min


title: 29 (control)

description: Gene expression of normal birth weight newborn's placenta.

source_name: placenta4, normal birth weight4, replicate 1

tag: pre-pregnancy bmi

tag: newborn birth weight

tag: newborn body length

tag: newborn chest circumference


title: 22 (control)

source_name: placenta3, normal birth weight3, replicate 1

tag: tissue

tag: newborn abdominal circumference


title: dnmt1MUT_pole1WT 3

description: bisulfite-treated genomic DNA


title: SCD -AID_DCP2_replicate2_t25

tag: cell line

tag: cell type

tag: time after_chase

value: 25 min

tag: genotype


title: 21 (control)

source_name: placenta2, normal birth weight2, replicate 1

tag: age

tag: gravidity


title: SCD -AID_DCP2_replicate2_t30

value: 30 min

tag: biological replicate

tag: treatment


title: dnmt1MUT_pole1WT 1

description: bisulfite-treated genomic DNA

tag: mutational status


title: dnmt1MUT_pole1MUT 4

description: bisulfite-treated genomic DNA


title: dnmt1MUT_pole1MUT 3

description: bisulfite-treated genomic DNA


title: SCD -AID_DCP2_replicate2_t20

value: 20 min


title: 18 (control)

source_name: placenta1, normal birth weight1, replicate 1

tag: parity

tag: gestational week

tag: ogtt fasting blood glucose

tag: ogtt 1h glucose


title: dnmt1MUT_pole1MUT 2

description: bisulfite-treated genomic DNA


title: dnmt1MUT_pole1MUT 1

description: bisulfite-treated genomic DNA


title: SCD -AID_DCP2_replicate2_t15

value: 15 min


title: SCD -AID_DCP2_replicate2_t10

value: 10 min


title: MCM10WT_4

data_processing:
base calling: HiSeq Analysis Software
alignment: reads were aligned to the GRCz11 genome using snakePipes 2.4.2 which uses STAR version 2.4.7a using --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outSAMunmapped Within--sjdbGTFfile --sjdbOverhang 100 as parameters
PCR duplicate removal: mapped reads were weeded for PCR duplicates using snakePipes 2.4.2 which uses sambamba version 1.0.0 using --sort-buffer-size=6000 --overflow-list -size 600000 as a parameter
count retrieval: counts were obtained using snakePipes 2.4.2 which uses featureCounts from the subread package 2.0.0 using -p -B -C -Q 10 --primary -T 8 -s 2 -a as parameters
coverage generation: read coverages were obtained using snakePipes 2.4.2 which uses bamCoverage version 3.3.2, with --binSize 25 --normalizeRPKM --effectiveGenomeSize 1679186873 --maxFragmentLength 1000 --scaleFactor as parameters following multiBamSummary version 3.3.2 using bins --scalingFactors as parameters
differential gene expression analysis: differentially expressed genes were obtained using snakePipes 2.4.2 which uses DESEq2 version 1.26.0 using alpha = 0.05 as a parameter
Genome_build: GRCz11
Supplementary_files_format_and_content: bigWig format
Supplementary_files_format_and_content: Tab-delimited text file containing raw featureCount counts

extract_protocol:
Total RNA was extracted from whole zebrafish larvae at 5 dpf using TRI Reagent (Sigma) following the manufacturer’s instructions. After treatment with Cloned DNaseI (Takara), RNA extraction using TRI Reagent was repeated.
Libraries were prepared via the TruSeq® mRNA library preparation protocol according to manufacturer's instructions


title: SCD -AID_DCP2_replicate2_t5

value: 5 min


title: MCM10WT_3


title: SCD -AID_DCP2_replicate2_t0

value: 0 min


title: SCD +AID_DCP2_replicate2_t55

value: plus Auxin and Estradiol


title: MCM10WT_1

value: 5dpf zebrafish embryos


title: MCM10WT_2


title: SCD +AID_DCP2_replicate2_t45

value: Yeast cells


title: MCM10MUT_3


title: MCM10MUT_4


title: SCD +AID_DCP2_replicate2_t40


title: SCD +AID_DCP2_replicate2_t30


title: MCM10MUT_1


title: Mat2aWT_Pole1WT_4


title: MCM10MUT_2


title: SCD +AID_DCP2_replicate2_t25


title: SCD +AID_DCP2_replicate2_t50


title: SCD +AID_DCP2_replicate2_t35


title: SCD +AID_DCP2_replicate2_t20


title: 35-36 weeks distal intestine 4

city: Amsterdam

first: Vanesa

last: Muncan

address: Meibergdreef 69-71

department: Tytgat institute

country: Netherlands

institute: AMC

hyb_protocol: Fragmented cDNA was hybridized on human Clariom S HTassay platform following standard hybridisation protocol (Thermofisher)

scan_protocol: Gene Titan instrument

data_processing: Data were analysed using Affimetrix expression console, RMA as normalization method

label: Biotin

source_name: whole intestinal tissue of extremely premature 28 weeks operated at 7 weeks postnatal

label_protocol: Samples were labeled using 3′ IVT Pico Kit (Affymetrix) and RNA Amplification Kit (Nugene) according to manufacturer's protocols

extract_protocol: Bioline Isolate II RNA mini kit

treatment_protocol: Resections specimes were cut into small tissue peaces.

tag: diagnosis

value: NEC


title: 35-36 weeks distal intestine 1

source_name: whole intestinal tissue of extremely premature 27 weeks operated at 8 weeks postnatal


title: 35-36 weeks distal intestine 2

source_name: whole intestinal tissue of extremely premature 24 weeks operated at 12 weeks postnatal


title: 35-36 weeks distal intestine 3

source_name: whole intestinal tissue of extremely premature 24 weeks operated at 11 weeks postnatal


title: 20 weeks distal intestine 2

source_name: whole intestinal tissue at 20 weeks of gestation distal segment

value: normal


title: 20 weeks proximal intestine 5

source_name: whole intestinal tissue at 20 weeks of gestation proximal segment


title: SCD +AID_DCP2_replicate2_t15

value: replicate 2


title: 20 weeks proximal intestine 2


title: 20 weeks distal intestine 4


title: 20 weeks proximal intestine 3


title: 20 weeks distal intestine 3


title: 20 weeks proximal intestine 1


title: 20 weeks proximal intestine 4


title: 35-36 weeks distal intestine 5


title: 20 weeks distal intestine 5


title: 18 weeks distal intestine 5

source_name: whole intestinal tissue at 18 weeks of gestation distal segment


title: 20 weeks distal intestine 1


title: Mat2aWT_Pole1WT_2


title: Mat2aWT_Pole1WT_1


title: SCD +AID_DCP2_replicate2_t10


title: Mat2aWT_Pole1MUT_4


title: SCD +AID_DCP2_replicate2_t5


title: 18 weeks distal intestine 3


title: Mat2aWT_Pole1MUT_3


title: 18 weeks distal intestine 4


title: SCD +AID_DCP2_replicate2_t0


title: 18 weeks distal intestine 2


title: SCD -AID_POP2/CCR4_replicate2_t55

value: 55 min

value: plus Ethanol


title: Mat2aWT_Pole1MUT_1


title: 18 weeks proximal intestine 5

source_name: whole intestinal tissue at 18 weeks of gestation proximal segment


title: SCD -AID_POP2/CCR4_replicate2_t50

value: 50 min


title: 18 weeks proximal intestine 4


title: Mat2aMUT_Pole1WT_4

source_name: 5dpf zebrafish embryos


title: 18 weeks distal intestine 1


title: 18 weeks proximal intestine 3


title: 18 weeks proximal intestine 1


title: SCD -AID_POP2/CCR4_replicate2_t45

value: 45 min


title: 16 weeks distal intestine 5

source_name: whole intestinal tissue at 16 weeks of gestation distal segment


title: Mat2aMUT_Pole1WT_3


title: Mat2aWT_Pole1MUT_2


title: SCD -AID_POP2/CCR4_replicate2_t40

value: 40 min


title: Mat2aMUT_Pole1WT_2


title: 16 weeks distal intestine 4


title: 16 weeks distal intestine 3


title: Mat2aMUT_Pole1WT_1


title: 18 weeks proximal intestine 2


title: SCD -AID_POP2/CCR4_replicate2_t30

value: 30 min


title: 16 weeks distal intestine 2


title: 16 weeks distal intestine 1


title: Mat2aMUT_Pole1MUT_4


title: 16 weeks proximal intestine 5

source_name: whole intestinal tissue at 16 weeks of gestation proximal segment


title: SCD -AID_POP2/CCR4_replicate2_t25

value: 25 min


title: Mat2aMUT_Pole1MUT_3


title: 16 weeks proximal intestine 3


title: 16 weeks proximal intestine 4


title: SCD -AID_POP2/CCR4_replicate2_t35

value: 35 min


title: WT iPSC

type: genomic

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

hyb_protocol: Bisulfite conversion and hybridization to the array was carried out by Life&Brain (Bonn, Germany). Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium EPIC Beadchip using the standard protocol from Illumina.

scan_protocol: Standard protocols from Illumina

data_processing: Analysis was performed on RAW idat filed using the R package SeSAMe and the ssNoob normalization. Detection p-values were calculated using the SeSAMe package and the pOOBAH apporach.

label: Cy3 and Cy5

label_protocol: Standard protocols from Illumina

growth_protocol: iPSCs were cultured on tissue culture plastic coated with vitronectin in StemMACS iPS-Brew XF

extract_protocol: Genomic DNA was isolated with the NucleoSpin Tissue Kit (Macherey-Nagel, Düren, Germany).

treatment_protocol: CRISPR-cas 9 mediated CTCF deletion. Transfection of complexed crRNA-tracrRNA and Cas9 using the NEON transfection system using standard protocols.

tag: gender

value: Female


title: SCD -AID_POP2/CCR4_replicate2_t20

value: 20 min


title: 13 weeks distal intestine 5

source_name: whole intestinal tissue at 13 weeks of gestation distal segment


title: Mat2aMUT_Pole1MUT_2

tag: tissue


title: 16 weeks proximal intestine 1


title: SCD -AID_POP2/CCR4_replicate2_t15

value: 15 min


title: Mat2aMUT_Pole1MUT_1


title: 13 weeks distal intestine 3


title: 13 weeks distal intestine 2


title: 16 weeks proximal intestine 2


title: SCD -AID_POP2/CCR4_replicate2_t10

value: 10 min


title: dnmt1WT_pole1WT_4

value: 5dpf zebrafish embryos


title: dnmt1WT_pole1WT_3


title: SCD -AID_POP2/CCR4_replicate2_t5

value: Yeast cells

value: 5 min


title: 13 weeks proximal intestine 5

source_name: whole intestinal tissue at 13 weeks of gestation proximal segment

value: normal


title: SCD -AID_POP2/CCR4_replicate2_t0

value: 0 min

value: replicate 2


title: 13 weeks distal intestine 1


title: human adipocyte, H3K9me3 CUT&Tag, ZNF189 depletion replicate 1

city: Huddinge

first: Niklas

last: Mejhert

address: Blickagången 16

country: Sweden

institute: Karolinska Institute

data_processing:
Sequencing files (FASTQ) were aligned to the GRCh38/hg38 version of the human reference genome, using Bowtie2 on the Galaxy platform
Peak calling was done using MACS2
Assembly: hg38
Supplementary files format and content: bedGraph, bed
Library strategy: CUT&Tag

source_name: adipocyte

extract_protocol:
Nuclear isolation by hypotonic buffer and mechanical lysis followed by centrifugation in 0.3M sucrose buffer. CUT&Tag was then performed following the protocol from Kaya-Okur et al. (https://doi.org/10.1038/s41596-020-0373-x).
IDT primers (Illumina, 20027213) and PCR enzyme mix (NEB, M0541S) were used for library preparation, and AMPure beads (Beckman Coulter, A63881) were used for PCR cleanup
CUT&Tag with DNA-sequencing

value: adipocyte

value: ZNF189 depletion

tag: antibody


title: human adipocyte, H3K9me3 CUT&Tag, ZNF189 depletion replicate 2


title: CTCF-del iPSC 1


title: dnmt1WT_pole1WT_2


title: SCD +AID_POP2/CCR4_replicate2_t55

tag: cell line

value: 55 min

value: plus Auxin and Estradiol


title: human adipocyte, H3K27ac CUT&Tag, ZNF189 depletion replicate 3

tag: cell type


title: 13 weeks proximal intestine 3


title: human adipocyte, H3K27ac CUT&Tag, ZNF189 depletion replicate 1


title: human adipocyte, H3K9me3 CUT&Tag, ZNF189 depletion replicate 3


title: 13 weeks proximal intestine 2


title: 13 weeks distal intestine 4


title: dnmt1WT_pole1WT_1


title: 13 weeks proximal intestine 4


title: SCD +AID_POP2/CCR4_replicate2_t45

tag: time after_chase

value: 45 min


title: dnmt1WT_pole1MUT_3


title: human adipocyte, H3K9me3 CUT&Tag, control replicate 3

tag: genotype

value: control


title: CTCF-del iPSC 2


title: human adipocyte, H3K9me3 CUT&Tag, control replicate 1


title: SCD +AID_POP2/CCR4_replicate2_t40

value: 40 min


title: human adipocyte, H3K27ac CUT&Tag, control replicate 3


title: dnmt1WT_pole1MUT_2


title: human adipocyte, H3K9me3 CUT&Tag, control replicate 2


title: dnmt1WT_pole1MUT_4


title: human adipocyte, H3K27ac CUT&Tag, control replicate 2


title: SCD +AID_POP2/CCR4_replicate2_t50

value: 50 min


title: Mat2aWT_Pole1WT_3


title: SCD +AID_POP2/CCR4_replicate2_t35

value: 35 min


title: dnmt1MUT_pole1WT_4


title: human adipocyte, H3K27ac CUT&Tag, ZNF189 depletion replicate 2


title: human adipocyte, ATAC-seq, control replicate 1

data_processing:
To process the raw Bcl files obtained from Illumina sequencing, we used the bcl2fastq program to perform conversion and demultiplexing, resulting in fastq files
We used STAR to index to the human reference genome (hg38/GRCh38), which was obtained from UCSC, and then aligned the fastq files
Assembly: hg38
Supplementary files format and content: bedGraph

extract_protocol:
Nuclear isolation by hypotonic buffer and mechanical lysis followed by centrifugation in 0.3M sucrose buffer
PCR amplification, qPCR to determine additional cycles, and library purification were performed using reagents indicated in the Omni-ATAC protocol (Corces et al., https://doi.org/10.1038/nmeth.4396)

value: siRNA with nontargeting sequences


title: human adipocyte, ATAC-seq, ZNF189 depletion replicate 2

value: siRNA targeting ZNF189


title: human adipocyte, H3K27ac CUT&Tag, control replicate 1


title: SCD +AID_POP2/CCR4_replicate2_t25

value: 25 min


title: dnmt1WT_pole1MUT_1

value: 5dpf zebrafish embryos


title: human adipocyte, ATAC-seq, ZNF189 depletion replicate 1


title: SCD +AID_POP2/CCR4_replicate2_t30

value: Yeast cells

value: 30 min


title: Human adipocyte, IgG ChIP

data_processing:
The nf-core/chipseq pipeline (https://zenodo.org/record/7139814#.ZC3eMXtByUk (58)) was used to perform the Quality control, mapping and peak calling of the ChIP-seq analysis in conjunction with Docker
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Nuclear isolation by hypotonic buffer and mechanical lysis followed by centrifugation in 0.3M sucrose buffer. Isolated nuclei were crosslinked in 1% formaldehyde for 10 minutes, quenched with 137mM glycine for 5 minutes, lysed in denaturing buffer (50 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 150 mM NaCl and Protease Inhibitor Cocktail) and sonicated by 30x30 second cycles in the Bioruptor Pico (Diagenode B01060010).
NEBNext® UltraTM Library Prep Kit for Illumina with 12 cycles using dual index oligos for Illumina (New England Biolabs, E6440S)

tag: chip antibody

value: normal rabbit IgG polyclonal antibody - Millipore Sigma, 12-370


title: dnmt1MUT_pole1WT_3


title: Human adipocyte, ZNF189 ChIP

value: anti-ZNF189antibody - Sigma, HPA034814-100UL


title: dnmt1MUT_pole1WT_1


title: SCD +AID_POP2/CCR4_replicate2_t20

value: 20 min

value: replicate 2


title: dnmt1MUT_pole1WT_2


title: human adipocyte, ATAC-seq, control replicate 2

value: adipocyte


title: dnmt1MUT_pole1MUT_4


title: U049MAI 9h culture with CK21 [UR2_9h]

city: Chicago

first: Qiaomu

last: Tian

address: 5841 S. Maryland Ave

institute: University of Chicago

data_processing:
The reads were mapped to the Homosapien genome (GRCh38) using STAR software with ≥95% mapping rate.
Differential expression analysis was performed using DESeq2 package in R64
Molecular and cellular function analysis and pathway enrichment was analyzed using Ingenuine Pathway Analysis software (Qiagen).
Supplementary files format and content: GRCh38
Supplementary files format and content: read count, fpkm

extract_protocol:
Total RNA was extracted using a RNeasy® Plus Mini Kit (Qiagen), and total RNA quantified using the 2100 Bioanalyzer (Agilent).
Samples with a RIN >8 was outsourced to Novogene for library construction and sequencing (Illumina Platform (PE150)) with 20 M raw reads/sample.

treatment_protocol: Two organoids, U049MAI, U123M15-T, were cultured with CK21 at 50 nM for 3 hours, 6 hours, 9 hours and 12 hours.

value: Organoid

value: WT


title: U049MAI 12h culture No RX [UC2_12h]

value: No Rx


title: SCD +AID_POP2/CCR4_replicate2_t15

value: 15 min

value: plus Auxin and Estradiol


title: U049MAI 12h culture with CK21 [UR1_12h]


title: U049MAI 12h culture with CK21 [UR2_12h]


title: SCD +AID_POP2/CCR4_replicate2_t10

value: 10 min


title: SCD -AID_DCP2_replicate1_t55

value: 55 min

value: replicate 1

value: plus Ethanol


title: dnmt1MUT_pole1MUT_2

value: 5dpf zebrafish embryos


title: dnmt1MUT_pole1MUT_1


title: U049MAI 12h culture No RX [UC1_12h]


title: dnmt1MUT_pole1MUT_3


title: SCD +AID_POP2/CCR4_replicate2_t5

value: Yeast cells

value: 5 min


title: 13 weeks proximal intestine 1

value: normal


title: U049MAI 9h culture with CK21 [UR1_9h]


title: SCD +AID_POP2/CCR4_replicate2_t0

value: 0 min


title: U049MAI 9h culture No RX [UC2_9h]


title: U049MAI 9h culture No RX [UC1_9h]


title: U049MAI 6h culture No RX [UC2_6h]


title: U049MAI 3h culture with CK21 [UR1_3h]


title: Human adipocyte, Input

value: no antibody


title: U049MAI 3h culture with CK21 [UR2_3h]


title: U049MAI 6h culture with CK21 [UR2_6h]


title: SCD -AID_DCP2_replicate1_t50

value: 50 min


title: H2O2 treatment, bio rep2

city: Okazaki

first: Akira

last: Yamashita

state: Aichi

address: Nishigonaka 38, Myodaiji

country: Japan

institute: National Institute for Basic Biology

data_processing:
The reads were quality trimmed using sickle (v.1.33), aligned to the S. pombe reference genome (R64-1-1) using HISAT2 (v.2.2.1), and processed using Samtools (v. 1.13) and featureCouts (v.2.0.1).
Assembly: S. pombe reference genome (R64-1-1)
Supplementary files format and content: tab-delimited text files.
Supplementary files format and content: counts

organism: Schizosaccharomyces pombe

growth_protocol: Wild-type S. pombe cells were cultured in YE medium.

extract_protocol:
Total RNA was extracted with hot phenol.
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA.

treatment_protocol: Cells in the log phase or stationary phase were spotted onto a membrane filter on YE agar medium, and then irradiated.

tag: strain

value: wt

value: hydrogen peroxide


title: U049MAI 6h culture No RX [UC1_6h]

value: Organoid

value: WT


title: H2O2 treatment, bio rep3


title: SCD -AID_DCP2_replicate1_t45

value: 45 min

tag: biological replicate


title: U049MAI 3h culture No RX [UC2_3h]

tag: treatment

value: No Rx


title: H2O2 treatment, bio rep1


title: plasma, 30min, bio rep2

tag: time point

value: plasma


title: SCD -AID_DCP2_replicate1_t30

value: 30 min


title: SCD -AID_DCP2_replicate1_t35

value: 35 min

value: replicate 1


title: U123M15-T 12h culture with CK21 [mR1_12h]


title: U123M15-T 12h culture with CK21 [mR2_12h]


title: U123M15-T 12h culture No RX [mC1_12h]


title: SCD -AID_DCP2_replicate1_t25

value: 25 min

value: plus Ethanol


title: U049MAI 3h culture No RX [UC1_3h]


title: SCD -AID_DCP2_replicate1_t40

value: Yeast cells

value: 40 min


title: SCD -AID_DCP2_replicate1_t20

value: 20 min


title: U123M15-T 9h culture with CK21 [mR2_9h]


title: U123M15-T 9h culture with CK21 [mR1_9h]


title: U049MAI 6h culture with CK21 [UR1_6h]


title: plasma, 30min, bio rep1


title: U123M15-T 9h culture No RX [mC1_9h]


title: U123M15-T 9h culture No RX [mC2_9h]


title: plasma, 30min, bio rep3


title: SCD -AID_DCP2_replicate1_t15

value: 15 min


title: plasma, 15min, bio rep2


title: U123M15-T 6h culture with CK21 [mR1_6h]


title: U123M15-T 6h culture with CK21 [mR2_6h]


title: U123M15-T 12h culture No RX [mC2_12h]


title: plasma, 15min, bio rep1


title: U123M15-T 6h culture No RX [mC2_6h]


title: SCD -AID_DCP2_replicate1_t0

value: 0 min


title: U123M15-T 3h culture with CK21 [mR2_3h]


title: plasma, 10min, bio rep3

value: wt


title: SCD -AID_DCP2_replicate1_t5

value: 5 min


title: U123M15-T 3h culture with CK21 [mR1_3h]

value: Organoid


title: U123M15-T 3h culture No RX [mC2_3h]

value: WT


title: Hippocampus Het at P1 3

city: Gifu

first: Kazuya

last: Tokumura

address: 1-25-4 Daigakunishi

department: Bioactive Molecules

institute: Gifu Pharmaceutical University

data_processing:
Sequence reads were trimmed using Trimgalore version 0.6.6 to exclude low-quality bases.
Trimmed sequence reads were mapped to GRCm39/mm39 using STAR version 2.7.8a.
Gene expression levels were determined by measuring the number of reads mapped to each gene region using RSEM version 1.3.3.
Assembly: mm39
Supplementary files format and content: tab-delimited text file raw counts for each Sample

source_name: Hippocampus

growth_protocol: Mice with one day of life were sacrificed by decapitation and the tissues (testes or hippocampus) were dissecated and freeze immediately in liquid nitrogen for porterior RNA isolation

extract_protocol:
RNA was harvasted using the Rneasy mini kit plus (Qiagen)
RNA libraries for RNA-seq were generated using NEBNext Ultra™ RNA Library Prep Kit for Illumina

value: Hippocampus

value: Osteocalcin Heterozygous


title: Hippocampus Het at P1 2


title: no irradiation, bio rep3

value: control


title: plasma, 10min, bio rep2

value: plasma


title: SCD +AID_DCP2_replicate1_t45

value: 45 min

value: plus Auxin and Estradiol


title: plasma, 15min, bio rep3


title: plasma, 10min, bio rep1


title: no irradiation, bio rep2


title: no irradiation, bio rep1


title: Hippocampus Het at P1 1


title: Hippocampus KO at P1 3

value: Osteocalcin KO


title: SCD -AID_DCP2_replicate1_t10

value: 10 min

value: replicate 1

value: plus Ethanol


title: Hippocampus WT at P1 2


title: SCD +AID_DCP2_replicate1_t50

value: Yeast cells

value: 50 min


title: Hippocampus KO at P1 1