title: ElavGal4c155.UAS-AB-2x.6D.e07.Rep3 [experiment 07]

description: experiment 07

data_processing:
Paired-end FASTQs were trimmed using TrimGalore
Trimmed FASTQs were mapped using STAR-2.7.3a
Mapped BAM files were filtered for primary mapped reads in properly matching pairs using samtools
Count tables were produced for RNA-seq using an in-house R script utilizing the GenomicRanges summarizeOverlaps function
Differential expression tables were produced by DESeq2 from RNA-seq count tables
m6A-IP-seq was processed with RADAR for differential peak calling. FACS sorting expeirments, counts were processed using RUV-seq (RUVr) before differential expression analysis using Deseq2.
Assembly: dm6
Supplementary files format and content: bigWig files for each condition were produced using deepTools (bamCoverage to produce bw files from BAM files with --normalizeUsing CPM)


title: 20160817.B-C1_35

status: Public on Dec 28 2023

type: SRA

city: Lausanne

first: Yun-Tsan

last: Chang

address: Avenue de Beaumont 29

department: Dermatology

country: Switzerland

institute: CHUV

description:
fluidigm C1
MF028_BE.csv

library_source: transcriptomic single cell

data_processing:
The quality control was done using fastQC (v. 0.11.7) and the adaptors and low quality bases having phred quality score less than 20 were trimmed from the ends of the reads using Trim Galore (v. 0.4.4). The T-cell receptors (TCR) were identified using TraCeR and gene expressions were quantified with Kallisto (v. 0.45.0) for cells with an identified T cell receptor as part of the TraCeR workflow. TraCeR was also used to group the cells with identified TCR into groups of clones of different sizes, which all were required to have at least one TCR monomer in common with the other cells in the same clone. The remaining cells with TCR, sharing no identical TCR monomer with each other, were considered as heterogeneous cells. The gene expression data was normalised using Scater (v. 1.10.1) using CPM (counts per million).
Assembly: GRCh37
Supplementary files format and content: Matrix table with counts for every transcript and every cell

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
Capture and processing of single skin and blood T cells was performed using the Fluidigm C1 Autoprep system. Cells were loaded at a concentration of 2,000 cells/µL onto C1 integrated fluidic circuit chips for 5–10-µm cells. All C1 capture sites were microscopically inspected to identify the sites that contained only a single cell. Empty sites and those with multiple cells were excluded from further analysis. External RNA Controls Consortium spike-in RNAs served as a control. The SMARTer® Ultra® Low RNA Kit (Clontech) was used for reverse transcription and cDNA pre-amplification. The single-cell cDNA products from each cell were then used to prepare Illumina sequencing libraries and sequenced as paired-end 150-base reads on the Illumina HiSeq 4000 platform. Quality control was performed using FastQC v. 0.11.7 (Babraham Bioinformatics), and the adaptors and low-quality bases with a Phred quality score <20 were trimmed from the ends of the reads using Trim Galore v. 0.4.4 (Babraham Bioinformatics)
Cells were captured and performed using the Fluidigm C1 Autoprep system. The SMARTer® Ultra® Low RNA Kit (Clontech) was used for reverse transcription and cDNA pre-amplification. The single-cell cDNA products from each cell were then used to prepare Illumina sequencing libraries and sequenced as paired-end 150-base reads on the Illumina HiSeq 4000 platform.

tag: tissue

value: blood

tag: patient diagnosis

value: cutaneous T-cell lymphoma

tag: cell type

value: T cells


title: Human_Sample_939

type: genomic

city: Boston

first: Patrick

middle: T

last: Griffin

state: MA

address: 77 Avenue Louis Pasteur

department: Harvard Medical School, Dept. of Genetics

country: USA

institute: Patrick Griffin

hyb_protocol: standard protocols

scan_protocol: standard protocols

data_processing:
SeSAMe R package was used to obtain beta values and p values from raw data .idat files.
Average Beta

label: Cy3, Cy5

molecule: genomic DNA

source_name: whole blood

label_protocol: standard protocols

extract_protocol: see: https://doi.org/10.1101/2021.10.25.465725 for detailed extraction protocols

tag: Sex

value: male

tag: age


title: Human_Sample_921


title: ElavGal4c155.UAS-AB-2x.6D.e07.Rep2 [experiment 07]

city: Philadelphia

first: Alexandra

last: Perlegos

state: PA

address: 231 Lynch Laboratories

department: Biology

institute: University of Pennsylvania

description: experiment 07

library_source: transcriptomic

organism: Drosophila melanogaster

source_name: brain

growth_protocol: Drosophila crosses set up in 25 degree incubator. Male progeny collected 1-2 days post eclosion for aging to 34 D old and young 5D old and RNA extraction. For experiemnt 21 DaGal4> Control RNAi (BL35785) DaGal4> Mettl3 RNAi(BL80448). Experiment 08 and 07 ElavGal4-c155 x UAS-mcd8GFP and ElavGal4c155 x UAS-AB(2x) male flies 6D old. For experiment 25 FACS sorting ElavGal4>UAS-mcD8GFP x mCherry RNAi or ElavGal4>UAS-mcD8GFP x Ime4 RNAi for aging to 34 D old and young 5D old and FACS sorting GFP + cells. For experiment 27 FACS sorting RepoGal4>UAS-mcD8GFP x mCherry RNAi or RepoGal4>UAS-mcD8GFP x Ime4 RNAi for aging to 34 D old and young 5D old and FACS sorting GFP+ and GFP- cells. For exerpeiemnt 29 TRAP IP seq, ElavGAl4>UAS-RPL3-FLAG x mCherry RNAi, ElavGAl4>UAS-RPL3-FLAG x Ime4 RNAi, RepoGAl4>UAS-RPL3-FLAG x mCherry RNAi, RepoGAl4>UAS-RPL3-FLAG x Ime4 RNAi for aging to 34 D old and young 5D old and FLAG tag IP and RNA extraction.

extract_protocol:
For m6A-IP seq flies were flash frozen and head tissue was collected into cold RNAse free tubes. Total RNA was extracted from 200 Drosophila Heads per replicate using Trizol/ chloroform extraction. PolyA+ mRNA was obtained using NEBNext Poly(A) mRNA Magnetic Isolation Module. PolyA+ RNA was fragmented using the NEB Next Magnesium Fragmentation Module (NEB, E6150S) for 4 minutes at 95 °C for a 250 ng sample of polyA+ RNA, and RNA was repurified using the Zymo RNA clean & concentrator -5 kit (Zymo, R1013). 10% of the fragmented polyA+ RNA was saved as an input control for sequencing. M6A -immunoprecipitation was done using the EpiMark N6-Methyladenosine Enrichment kit protocol with some minor alteration. 30ul of protein G magnetic beads (NEB, #S1430) were washed and resuspended in IP buffer (150mM NaCl, 10mM Tris-HCL, 0.1% NP-40). 4ul of synaptic systems antibody (SYS, 202003) was conjugated to protein G-magnetic beads (NEB, S1430S) for 2 hours at 4°C. Beads/ antibody were washed twice in IP buffer. ~1μg PolyA+ RNA was incubated with beads/antibody in IP buffer supplemented with 0.1% SUPERase-In RNase Inhibitor (Thermo Fisher; AM2696) for 2 hours at 4°C. After incubation, RNA/beads/antibody are washed twice in IP buffer, twice in low salt IP buffer (50mM NaCl, 10mM Tris-HCL, 0.1% NP-40), and twice in high salt IP buffer (500mM NaCl, 10mM Tris-HCL, 0.1% NP-40). RNA is eluted from beads with 25μl of RLT buffer twice and elution was pooled and concentrated using Zymo RNA clean and concentrator kit-5 (R1015). Library preparation and sequencing was done by Admera Health. Total RNA was extracted from brains using trizol/chloroform and Zymo RNA clean and concentrator kit-5 (R1015). The RNA-seq libraries from brains were prepared using the Tru-seq stranded mRNA library prep. Library preparation and sequencing was done by Admera Health, and sequenced using illumina HiSeq with 40M paired end reads (2x150bp). Biological replicates were done for each experimental condition and genotype as indicated. For FACS sorting Brains (10–15 per replicate) from young (5days old) and old (34days old) males were dissected, collected into a tube with cold Schneider's medium (SM) containing 45μM actinomycin D, and washed twice in PBS. Next, we added 300μL of dissociating solution, which included Papain diluted in PBS (Worthington PAP2, LK003178) and liberase (2.5 mg/ml). Brains were dissociated at 25°C using a shaker at 1000rpm for 20 min and vigorous pipetting every 5min, and passing through 25G 5/8 needle 7x. Dissociated tissue was filtered through 40μm cell strainers and sorted on an BD FACS Aria II SORP with a 100μm nozzle into a 96 well plate at the sorting facility of the University of Pennsylvania. Dead cells were excluded by staining with 4,6-diamidino-2-phenylindole (DAPI). GFP+ cells gates were set according to the fluorescence profile of GFP- brain tissue, and nuclear stain Syto60. Desired glia or neuronal populations (~500 cells per replicate) were directly sorted into 10X lysis buffer (Takara 635013) plus RNAse inhibitor for library preparations using SMART-seq v4. For TRAP IP fly brains (30 brains/sample) were dissected and stored in buffer ( 10mM Hepes, 150 mM KCl, 5mM MgCl2, 100ug/ml Cyclohexamide, 1x protease inhibitor, Rnase inhibitor) in -80 until samples were ready to process. Protein G Magnetic beads were coated with 4 ug of anti-flag antibody, and resuspended in reaction buffer (10mM Hepes, 150 mM KCl, 5mM MgCl2, 100ug/ml Cyclohex, 1x protease inhibitor (Sigma, 11873580001), + 0.1% triton x-100, Rnase inhibitor (Thermo Fisher, AM2696). Samples with brain tissue were homogenized in lysis buffer (reaction buffer + 0.5% triton-x). 20% of sample was saved as input control and RNA extraction using zymo clean and concentrator kit -5. The rest of the sample was added to antibody plus beads, and incubated for 4 hr at 4°C. Beads + RNA was washed and RNA was extracted from beads using zymo clean and concentrator kit -5. Libraries were made using SMARTer Stranded Total RNA-Seq Kit V4 for IPed and input RNA, and sequenced with 40M paired end reads (2x150bp).
For experiment 21 and 08, m6A-IPseq libraries were made using SMARTer Stranded Total RNA-Seq Kit V3 without rRNA depletion (takarabio, 634486) for IPed and input RNA. Experiment 07 brain RNA-seq libraries were prepared using the Tru-seq stranded mRNA library prep. Experiment 25, 27, and 29 FACS sorting and TRAP-seq libraries were made using SMART-Seq V4 + NexteraXT Library Preparation. All libraries were sequenced using illumina Illumina NovaSeq 6000 with 40M paired end reads (2x150bp).

treatment_protocol: Drosophila progeny were collected and anesthetized. Tissue was collected in basal conditions, at young 5D or aged conditions 34D. For AB conditions, flies were collected after 6D of UAS-AB expression.

value: brain

tag: genotype

tag: treatment


title: Mouse_Sample_10

data_processing:
Raw methylation data were processed by the methylsuite series of packages. Packages used include: methylcheck (v.0.7.9), methylprep (v.1.6.0).
Average Beta

organism: Mus musculus


title: 20160817.B-C1_29

description:
fluidigm C1
MF028_BE.csv


title: Mouse_Sample_9


title: 20160817.B-C1_3

description:
fluidigm C1
MF028_BE.csv


title: Human_Sample_920


title: 20160817.B-C1_28

description:
fluidigm C1
MF028_BE.csv


title: ElavGal4c155.UAS-AB-2x.6D.e07.Rep1 [experiment 07]

description: experiment 07


title: Mouse_Sample_7


title: ElavGal4c155.UAS-mcd8GFP.6D.e07.Rep2 [experiment 07]

description: experiment 07


title: Human_Sample_912


title: Mouse_Sample_11


title: 20160817.B-C1_25

description:
fluidigm C1
MF028_BE.csv


title: Human_Sample_916


title: Mouse_Sample_6


title: ElavGal4c155.UAS-mcd8GFP.6D.e07.Rep1 [experiment 07]

description: experiment 07


title: ElavGal4c155.UAS-AB-2x.6D.M6A.e08.Rep2 [experiment 08]

description: experiment 08

source_name: Head

value: Head

tag: sample type


title: Mouse_Sample_5


title: 20160817.B-C1_26

description:
fluidigm C1
MF028_BE.csv


title: Mouse_Sample_4


title: ElavGal4c155.UAS-AB-2x.6D.M6A.e08.Rep1 [experiment 08]

description: experiment 08


title: Mouse_Sample_8


title: Human_Sample_905

value: female


title: 20160817.B-C1_18

description:
fluidigm C1
MF028_BE.csv


title: ElavGal4c155.UAS-mcd8GFP.6D.e07.Rep3 [experiment 07]

description: experiment 07


title: Mouse_Sample_2


title: 20160817.B-C1_21

description:
fluidigm C1
MF028_BE.csv


title: 20160817.B-C1_24

description:
fluidigm C1
MF028_BE.csv


title: ElavGal4c155.UAS-AB-2x.6D.Input.e08.Rep1 [experiment 08]

description: experiment 08

value: Input


title: Human_Sample_931


title: ElavGal4c155.UAS-AB-2x.6D.Input.e08.Rep2 [experiment 08]

description: experiment 08


title: Human_Sample_935


title: Mouse_Sample_1


title: 20160817.B-C1_17

description:
fluidigm C1
MF028_BE.csv


title: ElavGal4c155.UAS-mcd8GFP.6D.M6A.e08.Rep3 [experiment 08]

description: experiment 08


title: Human_Sample_910


title: Human_Sample_897


title: 20160817.B-C1_16

description:
fluidigm C1
MF028_BE.csv


title: Human_Sample_888


title: 20160817.B-C1_23

description:
fluidigm C1
MF028_BE.csv


title: ElavGal4c155.UAS-mcd8GFP.6D.M6A.e08.Rep2 [experiment 08]

description: experiment 08


title: T24 cells, siTRAIP, rep3

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

country: China

institute: Zhongnan Hospital of Wuhan University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The total reads are compared with the reference genome (clean data were mapped to the reference genome of Homo_sapiens.GRCh38 from NCBI using STRA software (version 2.5.3a) with default parameters) to obtain comprehensive transcript information.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor).
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: All_reads_counts.txt: Tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: All_reads_RPKM.txt: Tab-delimited text file includes RPKM values for each Sample.

molecule: total RNA

growth_protocol: T24 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026). 2 ug of total RNA was used for the construction of sequencing libraries.
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 the manufacturer’s instruction.

treatment_protocol: Transfection of siRNA followed LipofectamineTM 3000 Reagent’s (L3000015, Invitrogen) protocol.

tag: cell line

value: Bladder tumor cells

tag: sirna

value: siTRAIP


title: 20160817.B-C1_15

description:
fluidigm C1
MF028_BE.csv


title: T24 cells, siTRAIP, rep2


title: T24 cells, siTRAIP, rep1


title: ElavGal4c155.UAS-mcd8GFP.6D.M6A.e08.Rep1 [experiment 08]

description: experiment 08


title: 20160817.B-C1_13

description:
fluidigm C1
MF028_BE.csv


title: Human_Sample_885


title: Human_Sample_882


title: ElavGal4c155.UAS-mcd8GFP.6D.Input.e08.Rep3 [experiment 08]

description: experiment 08


title: 20160817.B-C1_11

description:
fluidigm C1
MF028_BE.csv


title: Human_Sample_899


title: Human_Sample_878


title: ElavGal4c155.UAS-mcd8GFP.6D.Input.e08.Rep2 [experiment 08]

description: experiment 08


title: Mouse_Sample_3


title: T24 cells, siNC, rep3

value: siNC


title: 20160817.B-C1_10

description:
fluidigm C1
MF028_BE.csv


title: T24 cells, siNC, rep2


title: ElavGal4c155.UAS-mcd8GFP.6D.Input.e08.Rep1 [experiment 08]

description: experiment 08


title: Human_Sample_874


title: T24 cells, siNC, rep1


title: SELEX of FXIII

city: Taoyuan

first: Kai Wen

last: Cheng

address: 259 Wen-Hwa 1st Road, Kwei-Shan

department: Physiology and Pharmacology

country: Taiwan

institute: Chang Gung University

library_source: genomic

data_processing:
adapter removed using Trimmomatic versoion 0.39
Supplementary_files_format_and_content: counts and percentage of each unique sequences

organism: synthetic construct

source_name: SELEX 10th library

extract_protocol:
ssDNA was amplified by PCR, and extract by MinElute PCR Purification Kit (#28004, Qiagen)
Library preparation was performed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB#E7645S) following the manufacturer’s instructions. Briefly, a total of 100 ng of PCR product was end repaired and A-tailed. The prepared DNA fragments were then ligated at their 5' ends with a sequencing specific adapter. After library amplification and size selection, the DNA library templates were analyzed with the Agilent Bioanalyzer 2100 to evaluate the library quality. Finally, the qualified libraries were sequenced using NextSeq 500 (Illumina) with high Output Kit V2 (2*75 paired end) according to the manufacturer’s protocol.       Briefly, the data processing principles were as follows. Bases after Ns in each read were considered low quality and subsequently removed. The 3’-fixed oligo and the 3’ Illumina adapter were identified and trimmed from each read. Reads with 40-nt after processing were considered usable and retained for further analysis. Unique reads in each sample were counted and the most frequent 1,000 unique sequences were identified.

tag: source

value: ssDNA library


title: DaGal4.ime4RNAi.34D.M6A.e21.Rep3 [experiment 21]

description: experiment 21

value: DaGal4>Ime4 RNAi


title: Human_Sample_873


title: Royal jelly vesicles sample 3

city: Daejeon

first: Islam

last: Saadeldin

address: Dehak ru

country: South Korea

institute: Chungnam National University

data_processing:
The reads were subjected to standard quality control (QC) criteria according to the following parameters: (1) trimming and cleaning reads that aligned to primers and/or adaptors, (2) reads with over 50% of low-quality bases (quality value ≤5) in one read, and (3) reads with over 10% unknown bases (N bases).
Clean reads were mapped to reference Apis melifera genome (NCBI Amel_HAv3.1), and small RNA sequences from miRBase (version 22.1) with bowtie1 software within miRDeep2.pl software.
Using miRDeep2.pl script, read number of each of known miRNAs and predicted novel small RNAs of each sample were counted.
Assembly: NCBI Amel_HAv3.1
Supplementary files format and content: tab-delimited text files include read counts for each sample

organism: Apis mellifera

source_name: royal jelly

extract_protocol:
Exosomal total RNA was isolated from exosomes of 3 honeybee samples (royal jelly) using Total Exosome RNA & Protein Isolation Kit (Invitrogen, Cat.No. 4478545) according to manufacturer's protocol.
small RNA UMI library; Small RNA sequencing libraries were prepared according to the manufacturer’s protocol (BGISEQ-500 Small RNA UMI Library Construction Protocol).

value: royal jelly

value: exosome

value: WT

tag: molecule type

value: small RNA


title: Sigleceko BMDM, XBB.1(S375)-RBD-NP, rep 3

city: Guangzhou

first: Xin

last: He

address: Zhongshan 2nd Road

institute: Sun Yat-Sen University

data_processing:
1. Raw sequence reads were quality controlled and trimmed for adapater using fastp with default parameters.
2. Trimmed reads were mapped to GRCm38 using STAR with parameter "--quantMode GeneCounts".
3. Read counts were extracted for unstranded columns from each STAR out "ReadsPerGene.out.tab" and referred as raw count matrix.
4. Raw count matrix was imported to DESeq2 to perferom differential expressed gene analysis (genes were filtered out if their total counts were less than 10.
Assembly: GRCm38
Supplementary files format and content: raw counts

source_name: BMDM

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Agilent 2200 and kept at −80°C. The RNA with RIN (RNA integrity number) > 7.0 is acceptable for cDNA library construction.
The cDNA libraries were constructed for each RNA sample using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (vazyme, Inc.) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: Poly-A containing mRNA was purified from 1ug total RNA using oligo(dT) magnetic beads and fragmented into 200-600 bp using divalent cations at 85℃ for 6 min. The cleaved RNA fragments were used for first- and second-strand complementary DNA (cDNA) synthesis . dUTP mix was used for second-strand cDNA synthesis, which allows for the removal of the second strand. The cDNA fragments were end repaired, A-tailed and ligated with indexed adapters. The ligated cDNA products were purified and treated with uracil DNA glycosylase to remove the second-strand cDNA. Purified first-strand cDNA was enriched by PCR to create the cDNA libraries. The libraries were quality controlled with Agilent 2200 and sequenced by DNBSEQ-T7 on a 150 bp paired-end run.

value: BMDM

value: Siglece-/-


title: Sigleceko BMDM, XBB.1(S375)-RBD-NP, rep 2


title: Human_Sample_870


title: DaGal4.ime4RNAi.34D.Input.e21.Rep3 [experiment 21]

description: experiment 21


title: Royal jelly vesicles sample 2


title: Human_Sample_866


title: Mouse testis rep2 F

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

data_processing:
Sequencing reads were trimmed by Trim_galore to remove low-quality nucleotides.
Clean reads were aligned to hg19 or mm9 reference genome by Bowtie2.
PCR duplicates were removed by Samtools.
Mutation calling was performed by VarScan.
Assembly: hg19/mm9
Supplementary files format and content: text files include 6mA modification levels

source_name: testis

extract_protocol:
Mitochondrial DNA of HepG2 cells, mouse brain and mouse liver were prepared using Mitochondrial DNA Purification Kit (Abcam, ab288088). NIH/3T3 and B104-1-1 cells were both purchased from ATCC (CRL-1658; CRL-1887), and cultured in DMEM (Gibco, 11965092) with 10% FBS (Gibco, 26140079). NIH/3T3 from ECACC were purchased from Sigma (93061524-1VL), but only used in sex determination. Genomic DNA of NIH/3T3 cells, B104-1-1 cells, 4-month-old male C57BL/6J mouse whole testis, 4-month-old male C57BL/6J mouse whole brain, and 2.5-month-old female C57BL/6J mouse whole brain were all prepared using Monarch Genomic DNA Purification Kit (NEB, T3010S). All the DNA samples were harshly treated with RNase A (NEB, T3018L) again prior to libraries construction to get rid of any RNA contaminants.
For mammalian gDNAs, antibody enrichment was performed prior to libraries construction: 50~100 μg RNA-free DNA was diluted by TE buffer (Invitrogen, AM9849) with 0.1 M NaOH and sonicated to 100~300 nt length. The fragmentated DNA was immunoprecipitated using 25 μg anti-6mA antibody (Sigma, ABE572 or Abcam, ab151230) by gently rotating at 4℃ overnight. Pierce Protein A Magnetic Beads (Thermo Scientific, 88845) were washed and used to pulldown antigen-antibody complex. Subsequentially, the beads were treated by proteinase K (NEB, P8111S) and the 6mA-enriched DNA were then purified with DNA Clean & Concentrator Kit-25 (Zymo research, D4033). The fragmented DNA was mixed with 15% (mass percentage) spike-in probes (Supplementary Table 1) and then spited into three in the proportion of 3:4:1, each for mutation group, demethylation control and high-fidelity control. For the demethylation control, DNA fragments was denatured and then incubated at 37 ℃ for 4 hours in a 300 μL reaction containing 50 mM HEPE 7.0, 60 mM KCl, 75 μM ammonium iron (II) sulfate hexahydrate, 2 mM L-asorbic acid, 300 μM α-ketoglutarate and 2.4 μM FTO purified protein. The demethylation reaction was then treated with proteinase K (NEB, P8111S) and cleaned up by Oligo Clean & Concentrator Kits (Zymo research, D4061).
OTHER: DRM-Seq

value: Mutation + demethylation group

value: testis


title: DaGal4.ime4RNAi.34D.M6A.e21.Rep2 [experiment 21]

description: experiment 21


title: Royal jelly vesicles sample 1


title: Sigleceko BMDM, XBB.1(S375)-RBD-NP, rep 1


title: DaGal4.ime4RNAi.34D.Input.e21.Rep2 [experiment 21]

description: experiment 21


title: DaGal4.ime4RNAi.34D.M6A.e21.Rep1 [experiment 21]

description: experiment 21


title: Sigleceko BMDM, XBB.1-RBD-NP, rep 1


title: E.coli rep3 F

data_processing:
Sequencing reads were trimmed by Trim_galore to remove low-quality nucleotides.
Clean reads were aligned to E.coli reference genome by Bowtie2.
PCR duplicates were removed by Samtools.
Mutation calling was performed by VarScan.
Assembly: ecoli_mutated
Supplementary files format and content: text files include 6mA modification levels
Library strategy: DRM-Seq

organism: Escherichia coli K-12

extract_protocol:
Genomic DNA from Escherichia coli strain K-12 was purchased from ATCC (10798D-5). All the DNA samples were harshly treated with RNase A (NEB, T3018L) again prior to libraries construction to get rid of any RNA contaminants.
For E.coli DNA and mtDNAs, 400 ng~1 μg RNA-free DNA was diluted by TE buffer (Invitrogen, AM9849) with 0.1 M NaOH and sonicated using Bioruptor Pico sonication device to 100~300 nt length. The fragmented DNA was mixed with 15% (mass percentage) spike-in probes (Supplementary Table 1) and then spited into three in the proportion of 3:4:1, each for mutation group, demethylation control and high-fidelity control. The three groups of DNAs was denatured and subjected to splint ligation following a previous protocol (Supplementary Table 1) [10.1093/nar/gkw1110]. The ligation products of mutation group and demethylation control underwent primer extension at 60℃ for 3 hours in the 50 μL reaction containing 6 μM biosample-primer-extension primer (Supplementary Table 1), 1200 units of Bst 2.0 DNA polymerase (NEB, M0537M), 1× EpiMark Hot Start Taq Reaction Buffer (NEB, M0490S), 8mM dATP (NEB, N0446S), 2mM dCTP (NEB, N0446S), 2mM dGTP (NEB, N0446S), 0.02 mM 2-thio-dTTP (Trilink, N-2035), 6 mM magnesium sulfate (NEB) and 8% PEG4000 (Rigaku, # 25322-68-3). The resulting libraries were purified by gel electrophoresis and recovery, and finally sequenced at 60~100M depth with single-ended 100 bp mode.

tag: strain


title: DaGal4.ime4RNAi.34D.Input.e21.Rep1 [experiment 21]

description: experiment 21


title: Crohn’s disease

city: Erlangen

first: Mark

last: Dedden

state: Bayern

address: Schwabachanlage 12

department: Department of Medicine 1

country: Germany

institute: Universitätsklinikum Erlangen

data_processing:
Raw reads were passed to the 10x CellRanger software v7.0.0.
Assembly: hg38
Supplementary files format and content: Comma-separated matrices

source_name: Peripheral blood

extract_protocol:
FACS was performed to isolate α4+ memory T cells for subsequent scRNA-seq, with α4+ memory T cells being defined as CD3+CD45RA-α4+ viable single lymphocytes.
Single cell suspensions obtained from FACS were loaded in the 10x Chromium Controller and cDNA single-cell library was constructed using the dual index Chromium Single Cell 3' v3.1 protocol of 10x Genomics, Inc.

value: Peripheral blood

value: T-cell

tag: disease state

value: Crohn’s disease

tag: facs


title: E.coli rep3 H

value: Control group


title: Healthy control

value: Healthy control


title: Sigleceko BMDM, XBB.1-RBD-NP, rep 2


title: E.coli rep3 B

value: Mutation group


title: DaGal4.mcherryRNAi.34D.M6A.e21.Rep3 [experiment 21]

description: experiment 21

value: Head

value: DaGal4>Mcherry RNAi


title: WT BMDM, XBB.1(S375)-RBD-NP, rep 3


title: E.coli rep2 H


title: DaGal4.mcherryRNAi.34D.Input.e21.Rep3 [experiment 21]

description: experiment 21

value: Input


title: WT BMDM, XBB.1(S375)-RBD-NP, rep 2


title: E.coli rep2 F


title: Cell,transfected with the oeCSGALNACT1 plasmids 1

city: shanghai

first: Ma

last: mingjun

address: Shanghai First Maternity and Infant Hospital一妇婴保健院

institute: Tongji University

data_processing:
CLC Genomics Workbenchv 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork(parameter-Quality limit:0.05)
Trmed sequence reads were mippedto GrC3/mmt0 usng cic genoric benchk panmeters mismath cost 2 insertion cot 3 dlen cost 3ledh facian 03 smianty tadior 08
Read count extractian and narnalization were performed using ClC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab delimited text fles include Rpky glues for each Sample

source_name: cell lines

growth_protocol: HEY cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM medium; Gibco, USA) with 10% fetal bovine serum (FBS, Gibco) and 1% penicillin–streptomycin, in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from cell lines by using TRIzol reagent (Takara, Japan) according to the instructions of the manufacturer.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer'protocols

treatment_protocol: HEY cells were transfected with the empty vector control or oeCSGALNACT2 plasmids.

value: cell lines

value: HEY

value: Ovarian Cancer Cell lines

value: Migration and Invasion

value: without


title: DaGal4.mcherryRNAi.34D.M6A.e21.Rep2 [experiment 21]

description: experiment 21


title: Cell,transfected with the oeCSGALNACT1 plasmids 2


title: Cell, transfected with the empty vector control 3


title: E.coli rep2 B

value: WT


title: WT BMDM, XBB.1-RBD-NP, rep 3

value: BMDM


title: E.coli rep1 H


title: Cell, transfected with the empty vector control 2


title: Sigleceko BMDM, XBB.1-RBD-NP, rep 3

value: Siglece-/-


title: Cell,transfected with the oeCSGALNACT1 plasmids 3


title: DaGal4.mcherryRNAi.34D.M6A.e21.Rep1 [experiment 21]

description: experiment 21


title: DaGal4.mcherryRNAi.34D.Input.e21.Rep1 [experiment 21]

description: experiment 21


title: Saliva of a patient affected by limited (ACA) sclerodermia [S_01_L]

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description: 16S V3-V4 sequencing of saliva from patient 1 affected by limited systemic sclerosis

data_processing:
demultiplexing: from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
pair merging: micca mergepairs -i pair1.fastq -r pair2.fastq -o out.joined.fastq -l 30 -d 5
primer check and trimming: micca trim -i out.joined.fastq -o out.trimmed.fastq -w CCTACGGGNBGCWSCAG -r GACTACHVGGGTATCTAATCC -W -R -c
quality check: micca filter -i out.trimmed.fastq -o out.hiqual.fastq -e 0.5 -m 350 -f fastq
read merging: micca merge -i *.hiqual.fastq -o merged.fastq -f fastq
OTU table creation by clustering: micca otu -m denovo_greedy -i merged.fasta -o otudata -d 0.97 -c -t 20
taxonomic assignment (RDP): micca classify -m rdp -i otudata/otus.fasta -o otudata/taxa.txt
further analyses: R phyloseq package (see https://github.com/matteoramazzotti/papers/tree/main/2022sclero)
Library strategy: paired-end amplicon sequencing

organism: human skin metagenome

source_name: saliva

growth_protocol: Stool, skin and saliva samples were collected and stored at -80°C

extract_protocol:
Genomic DNA extraction with DNeasy PowerLyzer PowerSoil Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

tag: sample

tag: disease type

value: limited

tag: patientid


title: WT BMDM, XBB.1-RBD-NP, rep 2

tag: tissue


title: Cell, transfected with the empty vector control 1

tag: cell type


title: DaGal4.mcherryRNAi.34D.Input.e21.Rep2 [experiment 21]

description: experiment 21


title: NSSCC-IgG-IP miR-34c Rep3 [miR_34c_IgG3]

city: Verona

first: Marzia

last: Rossato

address: Strada Le Grazie 15

department: Biotechnology

institute: University of Verona

data_processing:
Basecalls performed using bcl2fastq
Reads with more than 10% of undetermined bases or more than 50 bases with a quality score < 7 were discarded.Reads were then clipped from adapter sequences using  were trimmed with Sickle (https://github.com/vsbuffalo/sickle). Scythe software (https://github.com/vsbuffalo/scythe), and low quality ends (Q score < 20 on a 15 nt window)
Alignment of reads to reference human genome (hg38) was performed using STAR
Read counts were calculated by HTSeq-count. Normalized expression values expressed as Fragments per Kilobase per Million Mapped Reads (FPKM) for each transcript were calculated using the function fpkm in DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file (expression_table.txt) contains expression values normalized as Fragments per Kilobase per Million Mapped Reads (FPKM)

source_name: NSSCC-IgG-IP miR-34c

growth_protocol: Nasal septum squamous cell carcinoma cells (NSSCC) were grown  (typically 3 × 106 cells into a T75 flask) in RPMI-1640 with 10% FBS, 1% penicillin and 1% streptomycin in a humidified incubator at 37°C and in an atmosphere of 5% CO2.

extract_protocol:
The cell lysates were centrifuged at 16,000g for 10 minutes at 4°C and incubated for 180 minutes with Protein G Sepharose beads (Thermo Fisher Scientific) coupled with anti-Ago antibody (10 μg, Invitrogen) or rat IgG isotype control (10 µg, Millipore).
cDNA libraries were generated using the SMARTer Stranded Total RNA Sample Prep Kit (Takara Clontech)

treatment_protocol: NSSCCs (3.0 x 10^6) were transiently transfected with a miR-34c or miR-449a mimic or scrambled control (100 nM, MISSION microRNA Mimic, Sigma) using High Perfect Transfection reagent (Qiagen) according to the manufacturer's instructions.

value: Transfection mimic miR-34c

tag: immuno precipitation (ip)

value: rat IgG isotype


title: WT BMDM, XBB.1-RBD-NP, rep 1


title: DaGal4.ime4RNAi.5D.Input.e21.Rep3 [experiment 21]

description: experiment 21

value: DaGal4>Ime4 RNAi


title: Human_Sample_865

tag: Sex

value: male

tag: age


title: E.coli rep1 B

tag: genotype

tag: treatment

value: Mutation group


title: Skin of a patient affected by limited (ACA) sclerodermia [C_26_L]

description: 16S V3-V4 sequencing of skin from patient 26 affected by limited systemic sclerosis

source_name: skin


title: E.coli rep1 F

value: Mutation + demethylation group


title: DaGal4.ime4RNAi.5D.M6A.e21.Rep2 [experiment 21]

description: experiment 21

value: Head

tag: sample type


title: Skin of a patient affected by limited (ACA) sclerodermia [C_25_L]

description: 16S V3-V4 sequencing of skin from patient 25 affected by limited systemic sclerosis


title: NSSCC-IgG-IP miR-34c Rep1 [Ctrl_IgG_miR34c]

value: Nasal septum squamous cell carcinoma cells


title: WT BMDM, XBB.1(S375)-RBD-NP, rep 1


title: E.coli WGA rep3 B

data_processing:
Sequencing reads were trimmed by Trim_galore to remove low-quality nucleotides.
Clean reads were aligned to E.coli reference genome by Bowtie2.
Mutation calling was performed by VarScan.
Assembly: ecoli_mutated
Supplementary files format and content: reads count on mutational A sites.
Library strategy: DRM-Seq

organism: Escherichia coli

source_name: cells

extract_protocol:
Genomic DNA from Escherichia coli strain K-12 was purchased from ATCC (10798D-5). All the DNA samples were harshly treated with RNase A (NEB, T3018L) again prior to libraries construction to get rid of any RNA contaminants.
For E.coli DNA, 400 ng~1 μg RNA-free DNA was diluted by TE buffer (Invitrogen, AM9849) with 0.1 M NaOH and sonicated using Bioruptor Pico sonication device to 100~300 nt length. The fragmented DNA was mixed with 15% (mass percentage) spike-in probes (Supplementary Table 1) and then spited into three in the proportion of 3:4:1, each for mutation group, demethylation control and high-fidelity control. The three groups of DNAs was denatured and subjected to splint ligation following a previous protocol (Supplementary Table 1) [10.1093/nar/gkw1110]. The ligation products of mutation group and demethylation control underwent primer extension at 60℃ for 3 hours in the 50 μL reaction containing 6 μM biosample-primer-extension primer (Supplementary Table 1), 1200 units of Bst 2.0 DNA polymerase (NEB, M0537M), 1× EpiMark Hot Start Taq Reaction Buffer (NEB, M0490S), 8mM dATP (NEB, N0446S), 2mM dCTP (NEB, N0446S), 2mM dGTP (NEB, N0446S), 0.02 mM 2-thio-dTTP (Trilink, N-2035), 6 mM magnesium sulfate (NEB) and 8% PEG4000 (Rigaku, # 25322-68-3). The resulting libraries were purified by gel electrophoresis and recovery, and finally sequenced at 60~100M depth with single-ended 100 bp mode.
The 100-mer biotin-tagged NN-6mA-NN model DNA oligo and primer-extension primer was synthesized by IDT (Integrated DNA Technologies). At first, the primer-extension primer was denatured at 70 for 2 min and immediately chilled on ice. In a total volume of 50 L, 50 ng model DNA and 2.5 L 2 M oligo-primer-extension primer were mixed with different DNA polymerases, such as OneTaq DNA Polymerase, Vent DNA Polymerase, phi29 DNA Polymerase, Pwo SuperYield DNA Polymerase, EpiMark Hot Start Taq DNA Polymerase, Bst DNA Polymerase-full length, Bst 2.0 DNA Polymerase, Bst 2.0 WarmStart DNA Polymerase, Bst 3.0 DNA Polymerase, Recombinant HIV reverse transcriptase), and the supplied buffers, with the supplement of different concentration of magnesium sulfate, manganese chloride, polyethylene glycol (PEG8000, PEG4000, PEG1000, PEG600, PEG600, PEG200), dATP/dCTP/dGTP and modified dTTP/UTP (dUTP, UTP, 2-Thio-dTTP, 4-Thio-dTTP, 5-Aminoallyl -dUTP, Fluorescein-12-dUTP). Primer extension tests were further carried out under different temperatures. The newly synthesized strands by extension were subsequentially released from the biotinylated template strands immobilized on Streptavidin C1 beads (Thermo Fisher, 65001) by incubation in 150 mM NaOH. The released strands were neutralized, cleaned up by Oligo Clean & Concentrator Kit (Zymo Research, D4061), and incubated with Streptavidin C1 beads again for the complete removal of template strands. The supernatant was cleaned up with Oligo Clean & Concentrator Kit and amplified for 10 cycles by NEBNext Ultra II Q5 Master Mix (NEB, M0544S) and NEBNext Multiplex Oligos for Illumina (NEB, E7335S).
The resulting libraries were purified by gel electrophoresis and recovery (NEB, T1020S). All libraries were sequenced at 2M reads depth in single-ended 100 bp mode at NovaSeq 6000 sequencer (Illumina). The primer extension condition was finalized as: 1500 units of Bst 2.0 DNA polymerase (NEB, M0537M), 1× EpiMark Hot Start Taq Reaction Buffer (NEB, M0490S), 8mM dATP (NEB, N0446S), 2mM dCTP (NEB, N0446S), 2mM dGTP (NEB, N0446S), 0.02 mM 2-Thio-dTTP (Trilink, N-2035), 6 mM magnesium sulfate (NEB) and 8% PEG4000 (Rigaku, # 25322-68-3). All reactions were incubated at 60 for 1 h.

value: cells


title: NSSCC-AGO-IP miR-34c Rep3 [miR_34c_Ago3]

source_name: NSSCC-AGO-IP miR-34c

value: anti-Ago antibody


title: DaGal4.ime4RNAi.5D.M6A.e21.Rep3 [experiment 21]

description: experiment 21


title: NSSCC-AGO-IP miR-34c Rep2 [miR_34c_Ago2]


title: DaGal4.ime4RNAi.5D.M6A.e21.Rep1 [experiment 21]

description: experiment 21


title: E.coli WGA rep2 H

value: Control group


title: E.coli WGA rep3 H


title: NSSCC-AGO-IP miR-34c Rep1 [Ago2_miR34c]


title: Skin of a patient affected by limited (ACA) sclerodermia [C_22_L]

description: 16S V3-V4 sequencing of skin from patient 22 affected by limited systemic sclerosis


title: Skin of a patient affected by limited (ACA) sclerodermia [C_23_L]

description: 16S V3-V4 sequencing of skin from patient 23 affected by limited systemic sclerosis


title: DaGal4.ime4RNAi.5D.Input.e21.Rep1 [experiment 21]

description: experiment 21

value: Input


title: E.coli WGA rep2 F


title: E.coli WGA rep2 B


title: NSSCC-IgG-IP miR-34c Rep2 [miR_34c_IgG2]


title: E.coli WGA rep1 H


title: Skin of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [C_21_D]

description: 16S V3-V4 sequencing of skin from patient 21 affected by diffuse systemic sclerosis

value: diffuse


title: NSSCC-input miR-34c Rep3 [miR_34c_Input3]

source_name: NSSCC-input miR-34c


title: E.coli WGA rep3 F

value: WT


title: NSSCC-input miR-34c Rep2 [miR_34c_Input2]


title: E.coli WGA rep1 F


title: E.coli WGA rep1 B


title: Skin of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [C_19_D]

description: 16S V3-V4 sequencing of skin from patient 19 affected by diffuse systemic sclerosis


title: DaGal4.ime4RNAi.5D.Input.e21.Rep2 [experiment 21]

description: experiment 21


title: DaGal4.mcherryRNAi.5D.M6A.e21.Rep2 [experiment 21]

description: experiment 21

value: DaGal4>Mcherry RNAi


title: DaGal4.mcherryRNAi.5D.Input.e21.Rep2 [experiment 21]

description: experiment 21


title: Skin of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [C_24_D]

description: 16S V3-V4 sequencing of skin from patient 24 affected by diffuse systemic sclerosis


title: NSSCC-IgG-IP miR-449 Rep3 [miR_449_IgG3]

source_name: NSSCC-IgG-IP miR-449

value: Transfection mimic miR-449a


title: DaGal4.mcherryRNAi.5D.M6A.e21.Rep3 [experiment 21]

description: experiment 21


title: Skin of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [C_18_D]

description: 16S V3-V4 sequencing of skin from patient 18 affected by diffuse systemic sclerosis


title: Neonatal Mice Cardiac Fibroblasts, si-TEAD1_3

city: Shanghai

first: shuai

last: song

address: No. 1609 Xietu Road, Xuhui District, Shanghai

department: Department of Cardiology

institute: Zhongshan  Hospital, Fudan University

data_processing:
fastp software was used to process raw reads in fastq format. clean reads were obtained after low-quality reads were removed for subsequent data analysis.
Clean reads were compared with mm39 reference genome using HISAT2 software, and gene expression volume (FPKM) was calculated. The reads of each gene were obtained by HTSeq-count.
Assembly: mm39
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

source_name: Neonatal Mice Cardiac Fibroblasts

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit(Ambion) followingthe manufacturer's protocol. 4 μg of total RNA was used to construct sequencing libraries.
RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number(RIN)≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (llumina, San Diego, CA, USA) according to the manufacturer's instructions. Then these libraries were sequenced on the llumina sequencing platform.

value: Neonatal Mice Cardiac Fibroblasts


title: NSSCC-IgG-IP miR-449 Rep2 [miR_449_IgG2]


title: Skin of a patient affected by limited (ACA) sclerodermia [C_17_L]

description: 16S V3-V4 sequencing of skin from patient 17 affected by limited systemic sclerosis

value: limited


title: DaGal4.mcherryRNAi.5D.Input.e21.Rep3 [experiment 21]

description: experiment 21


title: NSSCC-IgG-IP miR-449 Rep1 [Ctrl_IgG_miR449]

value: rat IgG isotype


title: Skin of a patient affected by limited (ACA) sclerodermia [C_16_L]

description: 16S V3-V4 sequencing of skin from patient 16 affected by limited systemic sclerosis


title: Neonatal Mice Cardiac Fibroblasts, si-TEAD1_2


title: Skin of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [C_20_D]

description: 16S V3-V4 sequencing of skin from patient 20 affected by diffuse systemic sclerosis


title: Neonatal Mice Cardiac Fibroblasts, si-TEAD1_1


title: Neonatal Mice Cardiac Fibroblasts, si-NC_3

value: si-NC


title: NSSCC-input miR-34c Rep1 [Input_miR34c]

value: Transfection mimic miR-34c


title: Skin of a patient affected by limited (ACA) sclerodermia [C_14_L]

description: 16S V3-V4 sequencing of skin from patient 14 affected by limited systemic sclerosis


title: DaGal4.mcherryRNAi.5D.Input.e21.Rep1 [experiment 21]

description: experiment 21


title: cNK control, 6

city: Wuerzburg

first: Georg

last: Gasteiger

address: Versbacher Strasse 9

department: Institute of Systems Immunology

institute: University Wuerzburg

data_processing:
The obtained FASTQ files were controlled for quality with FastQC, trimmed for adaptor sequences with Skewer and all files were aligned using STAR to the GRCm38.98 reference genome using standard settings.
The aligned data were counted using the featureCounts function of the Rsubread.
Differential expression analysis based on the raw count-matrix was performed using DESeq2

source_name: spleen

extract_protocol:
Skin:Liberase (0,245mg/ml) +DNAse (20ng/ml) in DMEM for 90' @37C
FGT: three rounds of digestion (20' each) with Collagenase D (0,33mg/m) + DNAse (40ng/ml) + Dispase (0,5U/ml) in 2% HBSS  150rpm@37C
Spleen: Red blood cell lysis buffer 2'@RT

value: spleen

value: Lymphocytes

value: wild type

value: VACV ear infection

tag: time

value: Day 35


title: Neonatal Mice Cardiac Fibroblasts, si-NC_2


title: cNK control, 5


title: NSSCC-AGO-IP miR-449 Rep2 [miR_449_Ago2]

source_name: NSSCC-AGO-IP miR-449

value: Nasal septum squamous cell carcinoma cells

value: anti-Ago antibody


title: NSSCC-AGO-IP miR-449 Rep3 [miR_449_Ago3]


title: Neonatal Mice Cardiac Fibroblasts, si-NC_1


title: Skin of a patient affected by limited (ACA) sclerodermia [C_13_L]

description: 16S V3-V4 sequencing of skin from patient 13 affected by limited systemic sclerosis


title: cNK control, 4


title: Skin of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [C_12_D]

description: 16S V3-V4 sequencing of skin from patient 12 affected by diffuse systemic sclerosis


title: NSSCC-input miR-449 Rep3 [miR_449_Input3]

source_name: NSSCC-input miR-449


title: NSSCC-AGO-IP miR-449 Rep1 [Ago2_miR449]


title: cNK control, 3


title: DaGal4.mcherryRNAi.5D.M6A.e21.Rep1 [experiment 21]

description: experiment 21

data_processing:
Paired-end FASTQs were trimmed using TrimGalore
Trimmed FASTQs were mapped using STAR-2.7.3a
Mapped BAM files were filtered for primary mapped reads in properly matching pairs using samtools
Count tables were produced for RNA-seq using an in-house R script utilizing the GenomicRanges summarizeOverlaps function
Differential expression tables were produced by DESeq2 from RNA-seq count tables
m6A-IP-seq was processed with RADAR for differential peak calling. FACS sorting expeirments, counts were processed using RUV-seq (RUVr) before differential expression analysis using Deseq2.
Assembly: dm6
Supplementary files format and content: bigWig files for each condition were produced using deepTools (bamCoverage to produce bw files from BAM files with --normalizeUsing CPM)

source_name: Head

value: Head


title: NSSCC-input miR-449 Rep2 [miR_449_Input2]


title: Neonatal Mice Cardiac Fibroblasts, OE-TEAD1_3


title: cNK control, 2


title: Skin of a patient affected by limited (ACA) sclerodermia [C_11_L]

description: 16S V3-V4 sequencing of skin from patient 11 affected by limited systemic sclerosis


title: Skin of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [C_15_D]

description: 16S V3-V4 sequencing of skin from patient 15 affected by diffuse systemic sclerosis

value: diffuse


title: Neonatal Mice Cardiac Fibroblasts, OE-TEAD1_2


title: Neonatal Mice Cardiac Fibroblasts, OE-NC_3

value: OE-NC


title: VACV induced TrNK,5

value: skin


title: Neonatal Mice Cardiac Fibroblasts, OE-NC_1


title: NSSCC-input miR-449 Rep1 [Input_miR449]

value: Transfection mimic miR-449a


title: Neonatal Mice Cardiac Fibroblasts, si-TEAD1+Ang-II_3

value: Neonatal Mice Cardiac Fibroblasts


title: NSSCC-AGO-IP Rep3 [Scr3_Ago]

source_name: NSSCC-AGO-IP

value: Transfection mimic scramble


title: Skin of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [C_10_D]

description: 16S V3-V4 sequencing of skin from patient 10 affected by diffuse systemic sclerosis


title: Skin of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [C_06_D]

description: 16S V3-V4 sequencing of skin from patient 6 affected by diffuse systemic sclerosis


title: VACV induced TrNK,6


title: Skin of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [C_09_D]

description: 16S V3-V4 sequencing of skin from patient 9 affected by diffuse systemic sclerosis


title: Skin of a patient affected by limited (ACA) sclerodermia [C_07_L]

description: 16S V3-V4 sequencing of skin from patient 7 affected by limited systemic sclerosis

value: limited


title: NSSCC-IgG-IP Rep3 [Scr3_IgG]

source_name: NSSCC-IgG-IP

value: rat IgG isotype


title: Neonatal Mice Cardiac Fibroblasts, OE-TEAD1_1


title: Skin of a patient affected by limited (ACA) sclerodermia [C_05_L]

description: 16S V3-V4 sequencing of skin from patient 5 affected by limited systemic sclerosis


title: cNK control, 1


title: NSSCC-IgG-IP Rep1 [Scr1_IgG]


title: VACV induced TrNK,2


title: Neonatal Mice Cardiac Fibroblasts, si-TEAD1+Ang-II_2


title: NSSCC-AGO-IP Rep1 [Scr1_Ago]


title: VACV induced TrNK,1


title: NSSCC-AGO-IP Rep2 [Scr2_Ago2]


title: NSSCC-IgG-IP Rep2 [Scr2_IgG]


title: Skin of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [C_04_D]

description: 16S V3-V4 sequencing of skin from patient 4 affected by diffuse systemic sclerosis


title: VACV induced TrNK,3


title: Neonatal Mice Cardiac Fibroblasts, si-TEAD1+Ang-II_1


title: Skin of a patient affected by limited (ACA) sclerodermia [C_08_L]

description: 16S V3-V4 sequencing of skin from patient 8 affected by limited systemic sclerosis


title: VACV induced TrNK,4


title: Neonatal Mice Cardiac Fibroblasts, OE-NC_2


title: Ontegenic TrNK control 3

source_name: Lymphocytes

value: Untreated


title: Neonatal Mice Cardiac Fibroblasts, Ang-II_3

value: Ang-II


title: NSSCC-input Rep3 [Scr3_Input]

source_name: NSSCC-input


title: Skin of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [C_02_D]

description: 16S V3-V4 sequencing of skin from patient 2 affected by diffuse systemic sclerosis


title: Neonatal Mice Cardiac Fibroblasts, Ang-II_2


title: Skin of a patient affected by diffuse (anti Scl70/RNA Pol III) sclerodermia [C_03_D]

description: 16S V3-V4 sequencing of skin from patient 3 affected by diffuse systemic sclerosis


title: Ontegenic TrNK control 2

value: Lymphocytes


title: NSSCC-input Rep2 [Scr2_Input]


title: Ontegenic TrNK control 1

value: wild type


title: NSSCC-input Rep1 [Scr1_Input]


title: Skin of a patient affected by limited (ACA) sclerodermia [C_01_L]

description: 16S V3-V4 sequencing of skin from patient 1 affected by limited systemic sclerosis


title: Neonatal Mice Cardiac Fibroblasts, Ang-II_1


title: ID18024_muscle_2yr

status: Public on Dec 27 2023

first: Wenhe

last: Lin

state: Illinois

address: 920 E 58th St

institute: University of Chicago

data_processing:
RNA-seq data were aligned to the baboon reference genome Panubis1.0 with STAR v2.7.7a. FASTQC was used to confirm that the reads were of high quality. Gene-level expression quantification was performed using featureCounts. Quality controls were performed on two levels using a similar pipeline for GTEx. On the sample level, we first identified and removed sample swaps and contaminations where a sample was not matched to its genotype or contained a mixture of two or more samples using verifyBamID. We removed outlier samples based on expression profile using PCA. We checked sex correctness by examining gene expression for genes on the Y chromosome for each sample. On the gene level, gene expression values for all samples from a given tissue were normalized using the following procedure: 1) read counts were normalized between samples using trimmed mean of M-values (TMM); 2) genes were selected based on expression thresholds of ≥0.1 TPM in ≥10% of samples, and > 3 reads (unnormalized) in ≥10% of samples for both diet conditions; 3) expression values for each gene were inverse normal transformed across samples. After the quality controls, we obtained 570 high-quality RNA samples and 20,224 genes for downstream analyses.
Assembly: Panubis1.0
Supplementary files format and content: raw count matrix of all samples (n=588)
Supplementary files format and content: raw count matrix of post-QC samples (n=570)

organism: Papio anubis

source_name: muscle

extract_protocol:
Approximately 10 mg of each frozen tissue sample was homogenized in 1ml QIAzol Lysis Reagent (79306, QIAGEN) using BeadBug 6 Microtube Homogenizer (D1036, Benchmark Scientific) with 1.5mm Zirconium beads (D1032-15, Benchmark Scientific). RNA was immediately extracted from the homogenate using QIAGEN RNeasy Universal Kit (73404, QIAGEN). RNA concentration and quality was measured using Agilent RNA 6000 Nano Kit and RNA 6000 Pico Kit (5067-1511 & 5067-1513, Agilent) on Agilent 2100 Bioanalyzer.
TruSeq RNA Library Preparation Kit v2 (RS-122-2001, RS-122-2002, Illumina); TruSeq stranded mRNA Library Preparation Kit (20020595, Illumina)
96 libraries from 16 animals in batch 1 were performed using TruSeq RNA Library Preparation Kit v2 (RS-122-2001, RS-122-2002, Illumina) and were sequenced 50 base pairs, single-end using the Illumina HiSeq4000 according to manufacturer instructions with the goal of achieving at least 15 million reads per sample. Each sequencing lane contained 24 multiplexed samples from different RNA extraction batches. 498 libraries from 83 animals in batch 2 were performed using TruSeq stranded mRNA Library Preparation Kit (20020595, Illumina) and were sequenced 50 base pairs, paired-end using the Illumina NovaSeq6000 according to manufacturer instructions with the goal of achieving at least 30 million reads per sample. Each sequencing lane contained 84 multiplexed samples from different RNA extraction batches. Samples from the same animal were always in the same RNA extraction, library preparation, and sequencing batches. Samples from different animals were randomized in every processing step to avoid potential batch effects.

treatment_protocol: The animals were feeding a high cholesterol, high fat diet for two years, switching from a low cholesterol, low fat diet.

value: muscle

tag: animal id

value: HCHF


title: ID16761_muscle_2yr


title: ID17776_muscle_0yr

value: LCLF


title: ID17981_muscle_2yr


title: ID17829_muscle_0yr


title: ID16880_muscle_0yr


title: ID16363_muscle_0yr


title: ID16880_muscle_2yr


title: ID17776_muscle_2yr


title: ID16363_muscle_2yr


title: ID18024_muscle_0yr


title: ID17829_muscle_2yr


title: ID17981_muscle_0yr


title: ID16761_muscle_0yr


title: ID16741_muscle_0yr


title: ID16246_muscle_2yr


title: ID16741_muscle_2yr


title: ID16246_muscle_0yr


title: ID16000_muscle_0yr


title: ID16000_muscle_2yr


title: ID15571_muscle_2yr


title: ID15475_muscle_2yr


title: ID15475_muscle_0yr


title: ID15163_muscle_2yr


title: ID15232_muscle_0yr


title: ID15232_muscle_2yr


title: ID14642_muscle_2yr


title: ID15163_muscle_0yr


title: ID14642_muscle_0yr


title: ID12152_muscle_2yr


title: ID16363_liver_2yr

source_name: liver

value: liver


title: ID12152_muscle_0yr


title: ID16363_liver_0yr


title: ID17829_liver_0yr


title: ID17776_liver_2yr


title: ID17981_liver_2yr


title: ID18024_liver_0yr


title: ID17981_liver_0yr


title: ID17776_liver_0yr


title: ID16761_liver_2yr


title: ID16761_liver_0yr


title: ID16880_liver_2yr


title: ID16880_liver_0yr


title: ID15571_muscle_0yr


title: ID17829_liver_2yr


title: ID16741_liver_2yr


title: ID16246_liver_2yr


title: ID16246_liver_0yr


title: ID15571_liver_2yr


title: ID16000_liver_2yr


title: ID16000_liver_0yr


title: ID16741_liver_0yr


title: ID18024_liver_2yr


title: ID15232_liver_2yr


title: ID15475_liver_2yr


title: ID15232_liver_0yr


title: ID15163_liver_2yr


title: ID12152_liver_2yr


title: ID14642_liver_2yr


title: ID12152_liver_0yr


title: ID15163_liver_0yr


title: ID14642_liver_0yr


title: ID17981_adipose_0yr

source_name: adipose

value: adipose


title: ID16363_adipose_2yr


title: ID17829_adipose_2yr


title: ID18024_adipose_0yr


title: ID17829_adipose_0yr


title: ID16363_adipose_0yr


title: ID17981_adipose_2yr


title: ID17776_adipose_0yr


title: ID16880_adipose_2yr


title: ID17776_adipose_2yr


title: ID15571_liver_0yr


title: ID16880_adipose_0yr


title: ID16761_adipose_0yr


title: ID16741_adipose_2yr


title: ID16246_adipose_2yr


title: ID16246_adipose_0yr


title: ID15571_adipose_2yr


title: ID16000_adipose_2yr


title: ID16000_adipose_0yr


title: ID18024_adipose_2yr


title: ID15571_adipose_0yr


title: ID15232_adipose_2yr


title: ID15232_adipose_0yr


title: ID15475_adipose_0yr


title: ID15163_adipose_2yr


title: ID15475_adipose_2yr


title: ID15163_adipose_0yr


title: ID14642_adipose_2yr


title: ID14642_adipose_0yr


title: ID12152_adipose_0yr


title: ID18938_liver_2yr


title: ID12152_adipose_2yr


title: ID18938_muscle_2yr


title: ID18938_adipose_2yr


title: ID16761_adipose_2yr


title: ID16741_adipose_0yr


title: ID18938_muscle_0yr


title: ID18938_liver_0yr


title: ID18938_adipose_0yr


title: ID18395_muscle_2yr


title: ID18395_adipose_2yr


title: ID16708_liver_0yr


title: ID18395_liver_2yr


title: ID16708_muscle_0yr


title: ID16708_adipose_0yr


title: ID18141_muscle_2yr


title: ID18141_adipose_2yr


title: ID18141_liver_2yr


title: ID18141_liver_0yr


title: ID18015_muscle_2yr


title: ID18141_muscle_0yr


title: ID18015_adipose_2yr


title: ID18015_liver_2yr


title: ID18015_adipose_0yr


title: ID17971_muscle_2yr


title: ID17971_muscle_0yr


title: ID18015_muscle_0yr


title: ID17971_liver_0yr


title: ID17971_adipose_0yr


title: ID17971_adipose_2yr


title: ID17916_liver_2yr


title: ID17916_adipose_2yr


title: ID17916_adipose_0yr


title: ID17903_adipose_0yr


title: ID17903_liver_2yr


title: ID17898_liver_2yr


title: ID17903_muscle_2yr


title: ID17903_muscle_0yr


title: ID17903_adipose_2yr


title: ID17916_muscle_0yr


title: ID17903_liver_0yr


title: ID17165_adipose_2yr


title: ID17165_muscle_2yr


title: ID18141_adipose_0yr


title: ID18015_liver_0yr


title: ID17898_adipose_0yr


title: ID17898_liver_0yr


title: ID17916_muscle_2yr


title: ID17873_muscle_2yr


title: ID17873_adipose_2yr


title: ID17871_muscle_2yr


title: ID17873_muscle_0yr


title: ID17873_adipose_0yr


title: ID17873_liver_0yr


title: ID17916_liver_0yr


title: ID17871_liver_2yr


title: ID17871_muscle_0yr


title: ID17871_adipose_2yr


title: ID17871_liver_0yr


title: ID17826_adipose_2yr


title: ID17826_adipose_0yr


title: ID17340_muscle_2yr


title: ID17871_adipose_0yr


title: ID17340_liver_0yr


title: ID17826_muscle_2yr


title: ID17340_liver_2yr


title: ID17826_muscle_0yr


title: ID17826_liver_0yr


title: ID17340_adipose_0yr


title: ID17340_muscle_0yr


title: ID17325_muscle_2yr


title: ID17898_muscle_0yr


title: ID17325_adipose_2yr


title: ID17325_muscle_0yr


title: ID17873_liver_2yr


title: ID17325_adipose_0yr


title: ID17325_liver_0yr


title: ID17268_muscle_2yr


title: ID17268_muscle_0yr


title: ID17268_liver_0yr


title: ID17268_adipose_0yr


title: ID17268_adipose_2yr


title: ID17233_muscle_2yr


title: ID17233_liver_2yr


title: ID17233_adipose_2yr


title: ID17199_muscle_2yr


title: ID17233_liver_0yr


title: ID17199_adipose_0yr


title: ID17199_liver_0yr


title: ID17199_adipose_2yr


title: ID17199_liver_2yr


title: ID17199_muscle_0yr


title: ID17190_liver_0yr


title: ID17190_muscle_0yr


title: ID17190_liver_2yr


title: ID17190_muscle_2yr


title: ID17898_muscle_2yr


title: ID17268_liver_2yr


title: ID17190_adipose_0yr


title: ID17190_adipose_2yr


title: ID17233_muscle_0yr


title: RepoGal4.ime4RNAi.34D.GFP-.e27.Rep2 [experiment 27]

description: experiment 27

data_processing:
library strategy: TRAP-seq
Paired-end FASTQs were trimmed using TrimGalore
Trimmed FASTQs were mapped using STAR-2.7.3a
Mapped BAM files were filtered for primary mapped reads in properly matching pairs using samtools
Count tables were produced for RNA-seq using an in-house R script utilizing the GenomicRanges summarizeOverlaps function
Differential expression tables were produced by DESeq2 from RNA-seq count tables
m6A-IP-seq was processed with RADAR for differential peak calling. FACS sorting expeirments, counts were processed using RUV-seq (RUVr) before differential expression analysis using Deseq2.
Assembly: dm6
Supplementary files format and content: bigWig files for each condition were produced using deepTools (bamCoverage to produce bw files from BAM files with --normalizeUsing CPM)

source_name: brain

value: brain

value: Repo GFP- cells (500)


title: ID17233_adipose_0yr


title: ID17898_adipose_2yr


title: ID17165_muscle_0yr


title: ID17165_adipose_0yr


title: ID17165_liver_0yr


title: ID17141_liver_2yr


title: ID17165_liver_2yr


title: ID17141_muscle_0yr


title: ID17141_muscle_2yr


title: ID17141_adipose_2yr


title: ID17141_liver_0yr


title: ID17139_liver_2yr


title: ID17141_adipose_0yr


title: ID17139_muscle_0yr


title: ID16879_muscle_2yr


title: ID17139_adipose_0yr


title: ID16879_muscle_0yr


title: ID16879_liver_2yr


title: ID16879_adipose_2yr


title: ID16879_adipose_0yr


title: ID16827_muscle_2yr


title: ID17325_liver_2yr


title: ID16827_liver_2yr


title: ID17139_muscle_2yr


title: ID17139_liver_0yr


title: ID16827_muscle_0yr


title: ID16787_muscle_2yr


title: ID16827_adipose_2yr


title: ID17139_adipose_2yr


title: ID16879_liver_0yr


title: ID16787_liver_2yr


title: ID16827_liver_0yr


title: ID16787_muscle_0yr


title: ID16748_muscle_2yr


title: ID16787_liver_0yr


title: ID16748_adipose_2yr


title: ID16748_muscle_0yr


title: ID16748_liver_2yr


title: ID16708_liver_2yr


title: ID18395_muscle_0yr


title: ID16708_adipose_2yr


title: ID18395_liver_0yr


title: ID18395_adipose_0yr


title: ID16548_liver_2yr


title: ID16548_adipose_2yr


title: ID16548_muscle_2yr


title: ID16548_muscle_0yr


title: ID17340_adipose_2yr


title: ID16827_adipose_0yr


title: ID16548_liver_0yr


title: ID16538_adipose_2yr


title: ID16538_liver_2yr


title: ID16538_muscle_0yr


title: ID16748_liver_0yr


title: ID16538_muscle_2yr


title: ID16538_adipose_0yr


title: ID16548_adipose_0yr


title: ID16787_adipose_2yr


title: ID16748_adipose_0yr


title: ID16538_liver_0yr


title: ID16708_muscle_2yr


title: ID16527_adipose_2yr


title: ID16527_muscle_0yr


title: ID16527_liver_0yr


title: ID16517_muscle_2yr


title: ID16527_adipose_0yr


title: ID16517_adipose_2yr


title: ID16517_liver_2yr


title: ID16787_adipose_0yr


title: ID16517_liver_0yr


title: ID16517_muscle_0yr


title: ID16499_liver_2yr


title: ID16517_adipose_0yr


title: ID16527_liver_2yr


title: ID16499_adipose_2yr


title: ID16436_muscle_2yr


title: ID16527_muscle_2yr


title: ID16499_adipose_0yr


title: ID16499_muscle_0yr


title: ID16499_muscle_2yr


title: ID16436_muscle_0yr


title: ID16436_adipose_2yr


title: ID16499_liver_0yr


title: ID16413_muscle_2yr


title: ID16413_liver_2yr


title: ID16413_adipose_2yr


title: ID16436_liver_2yr


title: ID16436_adipose_0yr


title: ID16413_liver_0yr


title: ID16408_muscle_2yr


title: ID16413_muscle_0yr


title: ID16408_adipose_2yr


title: ID16408_muscle_0yr


title: ID16408_liver_2yr


title: ID16408_adipose_0yr


title: ID16436_liver_0yr


title: ID16400_muscle_2yr


title: ID16408_liver_0yr


title: ID16400_liver_2yr


title: ID16400_adipose_0yr


title: ID16400_liver_0yr


title: ID16400_adipose_2yr


title: ID16383_liver_2yr


title: ID16383_muscle_0yr


title: ID16383_adipose_2yr


title: ID16413_adipose_0yr


title: ID16383_muscle_2yr


title: ID16383_liver_0yr


title: ID16371_liver_2yr


title: ID16383_adipose_0yr


title: ID16371_liver_0yr


title: ID16371_muscle_0yr


title: ID16371_adipose_0yr


title: ID16338_muscle_2yr


title: ID16371_adipose_2yr


title: ID16338_adipose_2yr


title: ID16338_liver_0yr


title: ID16338_muscle_0yr


title: ID16329_muscle_2yr


title: ID16329_adipose_2yr


title: ID16338_liver_2yr


title: ID16338_adipose_0yr


title: ID16329_liver_2yr


title: ID16321_muscle_2yr


title: ID16329_muscle_0yr


title: ID16329_liver_0yr


title: ID16371_muscle_2yr


title: ID16329_adipose_0yr


title: ID16321_liver_0yr


title: ID16321_adipose_2yr


title: ID16321_adipose_0yr


title: ID16321_muscle_0yr


title: ID16321_liver_2yr


title: ID16289_liver_2yr


title: ID16289_adipose_2yr


title: ID16289_muscle_2yr


title: ID16101_liver_2yr


title: ID16289_adipose_0yr


title: ID16101_muscle_2yr


title: ID16289_muscle_0yr


title: ID16400_muscle_0yr


title: ID16101_adipose_2yr


title: ID16289_liver_0yr


title: ID16101_muscle_0yr


title: LTT 2 (PA 8698

first: Donald

last: Lavelle

address: 2030 W. Taylor St., Room 6215

department: Medicine

institute: University of Illinois at Chicago

data_processing:
Raw reads were aligned to reference genome Panu_2.0 using BWA MEM.39 Gene expression was quantified using FeatureCounts.40 Differential expression statistics (fold-change and p-value) were computed using edgeR,41,42 including both multi-group comparisons using generalized linear models as well as pair-wise tests between experimental groups using the exactTest function. In all cases we adjusted p-values for multiple testing using the false discovery rate (FDR) correction of Benjamini and Hochberg.43
For STT vs CTRL, baboon1 (PA 8697) and baboon2 (PA 8548) are involved. In this case, we can
used ANOVA to compare the treatment effect as well as the baboon effect.
For LTT vs CTRL, all four baboons are involved in the analysis. We
simply compared LTT (PA8695 and PA 8698) vs CTRL (Pa 8697 and PA 8548) without considering baboon effect (which can't
Assembly: be identified by this experiment design).
Supplementary files format and content: Table submitted (STT vs CTRL DEG Pathway.xlsx).  This table contains data showing comparison of pooled CTRL1 and CTRL2 with STT1 and STT2)
Supplementary files format and content: Table submitted (LTT vs CTRL DEG Pathway.xlsx).  This table contains data showing comparison of pooled CTRL1 and CTRL2 with LTT1 and LTT2)

source_name: CD34-CD105+CD117+bRBC+ FACS-purified bone marrow cells

extract_protocol:
RNA was isolated using the RNeasy minikit (Qiagen #74104)) and treated with Rnase-free Dnase (Ambion #AM1906) according to the manufacturer's insructions.
Sequencing libraries were prepared using strand-specific QuantSeq 3’ RNAseq kit (Lexogen, FWD, Cat. No. 015). The QuantSeq protocol generates only one fragment per transcript, resulting in accurate gene expression values, and the sequences obtained are close to the 3’ end of the transcripts. Total RNA in the amount of 50 nanograms per sample was used as an input. Library construction was performed according to the manufacturer’s protocol. In brief, during the first strand cDNA synthesis, an oligo dT primer containing an Illumina-compatible sequence at its 5’ end was hybridized to mRNA, and reverse transcription was performed. After that, the RNA template was degraded, and during second strand synthesis, the library was converted to dsDNA. Second-strand synthesis was initiated by a random primer containing an Illumina-compatible linker sequence at its 5’ end. The double-stranded libraries were purified by using magnetic beads to remove all reaction components. Next, the libraries were amplified to add the complete adapter sequences required for cluster generation and to generate sufficient material for quality control and sequencing. A number of PCR amplification cycles was 18, as determined by test qPCR using a small pre-amplification library aliquot for each individual sample.  Final amplified libraries were purified, quantified, and fragment sizes were confirmed to be within 275-300 bp by gel electrophoresis using Agilent 4200 TapeStation (D5000 Screen Tape). Concentration of the final library pool was confirmed by qPCR.

treatment_protocol: CD34-CD105+CD117+bRBC+ bone marrow cells were FACS-purified from 2 untreated contrOl baboons (CTRL1 and CTRL2,  PA 8697 and PA8548, two baboons (STT1 and STT2; PA 8697 and 8548) treated for three days with RN-1 (0.25mg/kg/d) and two baboons (Ltt1 and Ltt2, PA 8695 and PA 8698) treated with RN-1 (0.25mg/kg/d; 5d/wk) for >265 days.

value: Long-term (>265d) RN-1 treatment (PA 8698)


title: LTT 1 (PA 8695)

value: CD34-CD105+CD117+bRBC+ FACS-purified bone marrow cells

value: Long-term (>265d) RN-1 treatment (PA 8695)


title: ID16101_liver_0yr


title: STT 2 (PA 8548)

value: Short-term (3d) RN-1 treatment (PA 8548)


title: ID16101_adipose_0yr


title: AEBP2_2

city: Baltimore

first: Seth

last: Blackshaw

state: MD

address: 733 N Broadway

department: Neuroscience

institute: Johns Hopkins University

description:
Biosample B
AEBP2_peaks.narrowPeak

data_processing:
library strategy: CUT&RUN-seq
Raw reads were quality and adapter trimmed using Trim Galore! (v0.6.4_dev) with parameters –phred33 –paired –length 36 -e 0.1 -q 5 –stringency 1
Trimmed reads were aligned against chicken genome GRCg7b with Bowtie 2 (v2.4.1) using parameters -X 2000 --local --no-mixed --no-discordant --no-dovetail
Peaks were called using MACS2 (v2.2.7.1) and parameters -f BAMPE -g 1070887886 --keep-dup all -q 0.05, providing IgG alignment files as background
Assembly: GRCg7b
Supplementary files format and content: Processed files contain narrow peak files generated using MACS2

organism: Gallus gallus

source_name: Lens

growth_protocol: Chicken embryos were obtained from Michigan State University and lenses were dissected from embryonic day 4.5 chicken embryos. Dissected lenses were collected on ice and pooled into 3 biological replicates consisting of approximately 44 lenses each.

extract_protocol:
In brief, nuclei extraction was carried out via an optimized variation of the demonstrated protocols described in 10X Genomics Protocol CG000124 Rev E and 10X Genomics Protocol CG000366 Rev D. Cell lysis was performed by triturating sample and incubating in a cold buffer comprised of lysis was performed via trituration and 30 second incubation in a buffer containing 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.005% Tween-20, 0.001% Surfact-Amps NP-40, 0.0005% digitonin (Thermo Fisher Scientific, BN2006), 1% fraction V bovine serum albumin, 1X proteinase inhibitor (MilliporeSigma, 11873580001), and 1.5 mM spermidine. Nuclei were washed twice by resuspending in cold buffer containing 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 1% fraction V bovine serum albumin, 0.1% Tween-20, 1X proteinase inhibitor (MilliporeSigma, 11873580001), and 1.5 mM spermidine. Nuclei were passed twice through 20 µm cell strainers (pluriSelect, 43-10020-40) during isolation to filter debris and cell aggregates.
Nuclei across all samples were diluted to 1000 nuclei / µl and loaded at 100000 nuclei per reaction for CUT&RUN-seq using the CUTANA ChIC / CUT&RUN Kit Version 3 (EpiCypher, 14-1048) and CUTANA CUT&RUN Library Prep Kit (EpiCypher, 14-1002). The protocol was carried out according to manufacturer protocol, with slight modification. . Antibodies were delivered at the following concentrations: EZH2 (Cell Signaling, 5246) 1:100; SUZ12 (Cell Signaling, 3737) 1:100; H3K27me3 (Cell Signaling, 9733S) 1:50; H3K4me3 (EpiCypher, 13-0041k) 1:50; IgG (EpiCypher, 13-0042k) 1:50; JARID2 (Cell Signaling, 13594) 1:50; AEBP2 (Cell Signaling, 14129) 1:25.

value: Lens

tag: antibody

value: Embryonic day 4.5


title: ID16019_adipose_2yr


title: ID16019_liver_2yr


title: Control 2 (PA 8548)

value: untreated control (PA 8548)


title: AEBP2_1

description:
Biosample A
AEBP2_peaks.narrowPeak


title: JARID2_2

description:
Biosample B
JARID2_peaks.narrowPeak


title: JARID2_1

description:
Biosample A
JARID2_peaks.narrowPeak


title: JARID2_3

description:
Biosample C
JARID2_peaks.narrowPeak


title: AEBP2_3

description:
Biosample C
AEBP2_peaks.narrowPeak


title: Control 1 (PA 8697)

value: untreated control (PA 8697)


title: SUZ12_3

description:
Biosample C
SUZ12_peaks.narrowPeak


title: ID16017_liver_0yr


title: ID16017_muscle_2yr


title: ID16019_muscle_0yr


title: ID16017_muscle_0yr


title: ID16017_adipose_2yr


title: ID16017_liver_2yr


title: ID16019_liver_0yr


title: STT 1 (PA 8697)

value: Short-term (3d) RN-1 treatment (PA 8697)


title: ID15889_muscle_2yr


title: ID16017_adipose_0yr


title: ID16019_muscle_2yr


title: ID15889_liver_2yr


title: G10-B

city: Montreal

first: Lorenzo

last: Ferri

state: Quebec

address: 1650 Cedar Avenue

department: Surgery & Oncology

country: Canada

institute: McGill University

description:
CRUK_storming_cancer_gastric_all_cells_2022_v2.h5ad
CRUK_storming_cancer_gastric_epithelial_2022_v2.h5ad
CRUK_storming_cancer_gastric_fibroblasts_2022_v2.h5ad

data_processing:
fastqs generated with bcl2fastq (2.20.0.422) for illumina or by fgbio (1.3.0) for MGI G400
After polyA-trimming via cutadapt (v3.2), reads were pseudoaligned to the GRCh38 reference transcriptome (ENSEMBL release 96) with kallisto (v0.46.2) using the default kmer size of 31. The pseudoaligned reads were processed into a cell-bygene count matrix using bustools (0.40.0). Cell barcodes were filtered using the whitelist (v3) provided by 10xGenomics. All further processing was done in scanpy (v1.9.1).
Cell barcodes with less than 1000 counts or less than 500 genes expressed were removed. Cell barcodes with more than 20% mitochondrial gene expression were removed. Doublet cells were identified using scrublet, removing any cell barcode with a scrublet score > 0.2. Only coding genes were retained in the final count matrix. Expression profiles were normalized by total counts, the 4000 most highly variable genes identified, renormalized, log-transformed and z-scored. The data was projected onto the first 50 principal components.
Detailed bioinformatics methods found in the supplementary materials: https://www.sciencedirect.com/science/article/pii/S001650852300731X#appsec1
Assembly: GRCh38/ENSEMBL release 96
Supplementary files format and content: hdf5 file with anndata objects

source_name: Diffuse-type adenocarcinoma

extract_protocol:
single cell capture using 10x genomics 3' mRNA library contruction from cells (v3)
After the dissociation protocol, using the single cell 3’ v3 protocol (10x Genomics), the cells were captured with the maximum target of 6000 cells.  During the capture the transcripts are first converted to cDNA and amplified.  The cell barcode and unique molecular identifier are added during the first strand synthesis of the double stranded cDNA.  The full length cDNA is then further processed to fragment the library to size for short read sequencing and amplified further to add the sequencing adapters and capture library index.

treatment_protocol: Tissue specimens were dissected and dissociated into single cell suspentions

value: Diffuse-type adenocarcinoma

tag: tumor stage

value: Male

value: NS


title: SUZ12_2

description:
Biosample B
SUZ12_peaks.narrowPeak


title: EZH2_3

description:
Biosample C
EZH2_peaks.narrowPeak


title: ID15889_adipose_2yr

value: HCHF


title: ID16019_adipose_0yr

value: LCLF


title: G10-D

tag: disease state

value: T


title: G10-A


title: G10-E

value: M


title: G10-C


title: ID15889_muscle_0yr

value: muscle


title: EZH2_2

description:
Biosample B
EZH2_peaks.narrowPeak


title: ID15889_adipose_0yr

value: adipose


title: G09-F


title: ID15874_muscle_2yr


title: EZH2_1

description:
Biosample A
EZH2_peaks.narrowPeak


title: ID15874_liver_2yr

value: liver


title: ID15874_adipose_2yr


title: G09-E


title: G09-D


title: H3K27me3_3

description:
Biosample C
H3K27me3_peaks.narrowPeak


title: ID15874_liver_0yr


title: ID15874_muscle_0yr


title: H3K27me3_2

description:
Biosample B
H3K27me3_peaks.narrowPeak


title: G09-C


title: H3K27me3_1

description:
Biosample A
H3K27me3_peaks.narrowPeak


title: ID15870_muscle_2yr


title: G09-B


title: ID15874_adipose_0yr


title: ID15870_liver_2yr


title: ID15870_adipose_2yr


title: H3K4me3_3

description:
Biosample C
H3K4me3_peaks.narrowPeak


title: ID15889_liver_0yr


title: ID15870_liver_0yr


title: H3K4me3_2

description:
Biosample B
H3K4me3_peaks.narrowPeak


title: G06-D

source_name: Gastric adenocarcinoma

value: Gastric adenocarcinoma

value: dM


title: G09-A


title: ID15820_liver_2yr


title: ID15870_adipose_0yr


title: H3K4me3_1

description:
Biosample A
H3K4me3_peaks.narrowPeak

value: Lens


title: ID15820_muscle_2yr


title: ID15820_adipose_2yr


title: IgG_2

description: Biosample B

value: IgG

value: Embryonic day 4.5


title: G06-C

value: cM


title: ID15820_muscle_0yr


title: G06-A

value: aMD


title: ID15581_muscle_2yr


title: ID15820_liver_0yr


title: IgG_1

description: Biosample A


title: ID15820_adipose_0yr


title: Sublibrary_3_3

data_processing:
Reads were aligned to chicken genome GRCg7b and analyzed using the chicken annotation from Ensembl Release 109 using the Parse Biosciences alignment suite (v1.0.3)
Assembly: GRCg7b
Supplementary files format and content: all_genes.csv contains the list of genes output from the Parse Biosciences alignment suite
Supplementary files format and content: cell_metadata.csv contains the list of cell barcodes and gene counts output from the Parse Biosciences alignment suite
Supplementary files format and content: DGE.mtx contains the digital gene expression matrix output from the Parse Biosciences alignment suite

source_name: Eye

growth_protocol: Fertile Specific Pathogen Free eggs (Charles River Laboratories, 10100329) were incubated in a rotating, humidified incubator at 37° C.

extract_protocol:
Whole chicken eyes were enucleated at E4 or E5 in PBS containing 0.2 U / µl RNasin Plus RNase Inhibitor (Promega, N2615). Eyes from 3 embryos were pooled for each condition. Nuclei were immediately extracted and fixed for snRNA-seq. In brief, nuclei extraction was carried out via an optimized variation of the demonstrated protocols described in 10X Genomics Protocol CG000124 Rev E and 10X Genomics Protocol CG000366 Rev D. For snRNA-seq, cell lysis was performed by triturating sample and incubating in a cold buffer comprised of 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.01% Surfact-Amps NP-40 (Thermo Fisher Scientific, 28324), and 0.2 U / µl RNase Inhibitor. Nuclei were washed 3 times by resuspending in cold PBS containing 2% fraction V bovine serum albumin and 0.2 U / µl RNase inhibitor (Promega, N2615). Nuclei were passed twice through 20 µm cell strainers (pluriSelect, 43-10020-40) during isolation to filter debris and cell aggregates.
snRNA-seq libraries were generated via the split-pool barcoding method using the Parse Biosciences Single Cell Whole Transcriptome Kit Chemistry Version 1 (Parse Biosciences, SB2001). Nuclei were fixed according to the Nuclei Fixation Kit Protocol (Parse Biosciences, SB1003) and stored at -80°C. During library preparation, nuclei were loaded for library prep as follows: embryonic day 4 (wells A1-A6), embryonic day 5 (wells A7-B1), embryonic day 4 6 hours post-retinectomy (wells B2-B8), and embryonic day 4 6 hours post-retnectomy + FGF2 (wells B9-C3). cDNA was amplified with 13 total PCR cycles. Final libraries were assessed with the Agilent Bioanalyzer and Qubit 4. Libraries were sequenced across two lanes of HiSeq X Ten and a lane of NovaSeq 6000 at the Novogene Sequencing Core (Sacramento, CA).

treatment_protocol: Retinectomies and FGF2 delivery were performed by creating an incision around the anterior eye chamber with surgical scissors and the neural retina was dislodged with a wire probe. For FGF2-delivery, approximately 20 acrylic beads with immobilized surface heparin (MilliporeSigma, H5263) were incubated overnight in 4 µl of 250 ng/µl of bovine basic FGF2 (R&D Biosystems, 133-FB-025). At the time of surgery, FGF2 beads were deposited into the posterior chamber of the eye cup and the eye was closed. Embryos were incubated for 6 hours before enucleating the eyes for use with the Parse Biosciences snRNA-seq workflow.

value: Eye

value: Embryonic day 4, Embryonic day 5, Embryonic day 4 6 hours post-retinectomy, Embryonic day 4 6 hours post-retinectomy + FGF2


title: G06-B

value: Male

value: bT


title: ID15581_liver_2yr

value: HCHF


title: ID15870_muscle_0yr

value: LCLF


title: oeESRP1_3

first: Chengguo

last: Li

state: Hubei

address: Union Hospital, No. 1277 Jiefang Avenue

institute: Wuhan Union Hospital

data_processing:
DNBSEQ, PE150
The raw data contains reads of low quality, reads with adaptor sequences and reads with high levels of N base. Those reads need to be filtered before the data analysis for reliability analysis results.
We used HISAT to align the clean reads to the reference genome.
We used Bowtie2 to align the clean reads to the reference genes.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: xls files includes raw counts for each Sample
Supplementary files format and content: xls files includes FPKM values for each Sample
Supplementary files format and content: xls files includes tpm values for each Sample

source_name: gastric cancer

extract_protocol:
RNA was harvested using RNAiso Plus* (#9109, Takara).  1.3 ug of total RNA was used for the construction of seduencing library.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocol.

value: gastric cancer

tag: cell line

value: gastric cancer cells

value: ESRP1 overexpression


title: ID15581_muscle_0yr

value: muscle


title: ID15581_adipose_2yr

value: adipose


title: ID15581_liver_0yr

value: liver


title: oeESRP1_2


title: ID15581_adipose_0yr


title: Sublibrary_2_3


title: oeESRP1_1


title: Sublibrary_1_3


title: ID15575_muscle_2yr


title: oeVector_3

value: WT


title: ID15575_liver_0yr


title: Sublibrary_2_2


title: ID15575_adipose_2yr


title: ID15575_liver_2yr


title: Sublibrary_1_2


title: Sublibrary_3_2


title: ID15575_muscle_0yr


title: oeVector_2


title: ID15575_adipose_0yr


title: ID15566_muscle_2yr


title: oeVector_1


title: HY-3 (RNA-Seq)

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Oncorhynchus mykiss Omyk_1.1
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each Sample

organism: Oncorhynchus mykiss

source_name: dorsal skin

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: dorsal skin

value: yellow mutant


title: HY-2 (RNA-Seq)


title: HY-1 (RNA-Seq)


title: WT_2

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

data_processing:
All sequencing reads were quality controlled using FastQC v0.11.2. Illumina adapters were trimmed using TrimGalore! V.0.6.6, replicates were aligned to the reference genome (UCSC mouse genome build mm10) using STAR v.2.7.9a.
The BAM files from alignment were processed using STAR v.2.7.9a  to obtain the counts per gene in all samples. Mus_musculus.GRCm38.100.gtf gene definition file was used.
The differential expression analysis was performed using edgeR v3.18.1. Genes having counts per million less than 2 in all samples were excluded. Differentially expressed genes were defined using p-value <0.01 and FDR-corrected p-value <0.1 cutoffs.
All bioinformatics analyses were conducted in R/Bioconductor computing environment v4.0.1
Assembly: mm10
Supplementary files format and content: STAR-processed gene count files in text format

source_name: wild type

growth_protocol: Alb/MDA-9 transgenic mouse in B6CBAF1 background was generated by directing the expression of C-terminal HA-tagged human MDA-9/SDCBP under an upstream enhancer region (–10400 to –8500) fused to the 335-bp core region of mouse albumin promoter. WT and Alb/MDA-9 heterozygote mice were bred to generate WT and Alb/MDA-9 littermates. Mice were fed regular chow.

extract_protocol:
Total RNA was extracted using the QIAGEN miRNAeasy Mini Kit (QIAGEN, Valencia, CA). cDNA preparation was done using ABI cDNA synthesis kit (Applied Biosystems, Foster City, CA). Real-time polymerase chain reaction (RT-PCR) was performed using an ABI ViiA7 fast real-time PCR system and Taqman gene expression assays according to the manufacturer’s protocol (Applied Biosystems, Foster City, CA)
RNA-Seq library was prepared using Illumina TruSeq RNA sample preparation kit and subject to two rounds of sequencing on Illumina HiSeq3000 platform.
RNA-Seq libraries were pooled together to aim about 25-40M read passed filtered reads per sample.

treatment_protocol: Primary mouse hepatocytes were isolated and cultured. No treatment was done.

value: wild type

value: hepatocytes


title: ID15566_liver_0yr


title: ID15560_muscle_2yr


title: HW-3 (RNA-Seq)

value: wild-type


title: WT_1


title: ID15566_adipose_0yr


title: HW-2 (RNA-Seq)


title: Alb_Mda_9_3

source_name: liver-specific overexpression of human MDA-9/SDCBP


title: ID15560_adipose_2yr


title: ID15560_muscle_0yr


title: ID15560_liver_0yr


title: HW-1 (RNA-Seq)


title: ID15566_liver_2yr


title: ID15560_adipose_0yr


title: ID15566_adipose_2yr


title: Alb_Mda_9_1

value: liver-specific overexpression of human MDA-9/SDCBP


title: ID15545_muscle_2yr


title: ID15545_liver_2yr


title: ID15566_muscle_0yr


title: ID15545_adipose_2yr


title: Alb_Mda_9_2


title: 0_minutes_control_2

city: New Delhi

first: Agam

middle: Prasad

last: Singh

state: Delhi

address: Aruna Asaf Ali Marg

department: IDL

country: India

institute: NII

description: 0 minutes overnight growth in YPD at 150 RPM

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were trimmed off adaptor sequences and YPD grown sample sequence reads wer trimmed to make it 36 base pairs to maintain uniformity across the samples. Sequence reads were independently aligned using QIAGEN CLC Genomics Workbench 21.0.3 with default setting against Candida albicans genome (Assembly 22).
Differential expression, p-value and fold changes for each gene were determined using QIAGEN CLC Genomics Workbench 21.0.3 with default parameters.
Genome_build: Candida albicans SC5314 genome assembly 22
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each mRNA of respective samples.

organism: Candida albicans

source_name: whole organism total RNA

growth_protocol: Candida albicans NCCPF 400034 was grown at 37 °C overnight in YPD medium. The cells were then washed with PBS and counted using the hemocytometer.

extract_protocol:
RNA was extracted using the Ribopure Yeast Kit (Ambion).  The total RNA extraction was performed as per the mannual described in the Kit protocol. Briefly, Candida albicans grown in serum for different time points were washed with the PBS and then the total RNA was extracted using the Ribopure yeast kit. RNA purity was confirmed by the nandrop and RNA integrity were confirmed by analysis on an Agilent 2100 bioanalyzer, using the RNA 6000 nano kit (Agilent) to conform RINs above 8.0. The YPD grown samples was also extracted with the above kit and the RNA purity was checked by Nanodrop.
RNA library was prepared as recommended by the IlluminaTruseq RNA sample preparation kit V2 for serum grown samples and sequencing was performed using Genome Analyzer IIX for 36 cycles. For the YPD grown sample RNA library was prepared using Ribo-zero gold kit and sequencing was performed on Illumina Hiseq for 150 cycles.

treatment_protocol: The overnight grown Candida albicans NCCPF 400034 was then placed in complete human serum (O+ve) with 5 % CO2 and incubated at 37 °C. The cells were then harvested at different time points to extract the total mRNA. The YPD grown Candida was treated as control and the extracted RNA was sequenced using the next generation sequencing techniques.

tag: strain

tag: protocol

value: overnight growth in YPD at 150 RPM0 minutes

tag: time point

value: 0 minutes


title: HLE-WT34 [UT_TH8]

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: replicate 2

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Assembly: GRCh38.p13
Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.

source_name: HLE cells (human HCC)

growth_protocol: All cells were cultured in DMEM medium at 37 °C and 5% CO2

extract_protocol:
RNA was extracted using the Qiagen RNAeasy kit.
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

treatment_protocol: Cells were left untreated


title: ID15545_muscle_0yr

tag: tissue


title: SUZ12_1

description:
Biosample A
SUZ12_peaks.narrowPeak

value: Lens

value: Embryonic day 4.5


title: ID15545_liver_0yr

value: LCLF


title: ID15545_adipose_0yr


title: HLE-WT34 [UT_TH9]

description: replicate 3


title: ID15494_muscle_2yr

value: HCHF


title: HCC68-LOH3.230 [UT_TH6]

description: replicate 3

source_name: HCC68 cells (human HCC)


title: ID15560_liver_2yr


title: HLE-WT34 [UT_TH7]

description: replicate 1


title: MH63_rep2

city: Beijing

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

institute: Peiking University

description: PolyA RNA isolated

data_processing:
C92 and MH63 RNA-seq reads were mapped to the corresponding assembled genomes, respectively, using HISAT2 (version 2.0.5) software with default parameters (Kim et al. 2015). Reads that can map to multiple position were discarded before subsequent analyses. For F1 hybrid, we aligned RNA-seq reads to both of the parental genomes. We then split F1 RNA-seq reads into reads that can mapped to both of the parental genomes (common reads) or only to one of the genome (allele reads) based upon the highest quality alignment. Both of the common reads and allele reads were used to calculation mRNA expression levels in F1 hybrid.
Genome_build: MSU 7.0 (http://rice.plantbiology.msu.edu)
Supplementary_files_format_and_content: FPKM.txt: Tab-delimited text files include FPKM values for each Sample.

organism: Oryza sativa Indica Group

source_name: 14-day-old seedling

growth_protocol: Rice cultivar C92, MH63 and their hybrid were used for all experiments in this study. Seeds were grown in water under long-day conditions (16-h light at 28°C and 8-h dark at 28°C) in a growth chamber (100 μmol·m-2·s-1) for 2 weeks.

extract_protocol:
Total RNA was extracted using an RNeasy Plant Mini Kit (Qiagen) and treated with RNase-free DNase I (Promega) to remove any contaminating genomic DNA.
First- and second-strand cDNAs were generated using SuperScript II reverse transcriptase (Invitrogen) and random hexamer primers. Double-stranded cDNAs were fragmented by nebulization and used for RNA-seq library construction following the standard Illumina protocol.

tag: cultivar

value: Shoot

value: 14 days


title: ID15494_liver_2yr


title: HCC68-LOH3.230 [UT_TH5]

description: replicate 2


title: 0_minutes_control_1


title: MH63_rep3

description: PolyA RNA isolated


title: MH63_rep1

description: PolyA RNA isolated


title: ID15494_liver_0yr


title: myocardium, I/R3, 30 min and 6 h, rep3

city: Daqing

first: Long

middle: Pi

last: Shi

state: Heilongjiang

address: No.39, Xinyang Road, Longfeng District, Daqing City

department: Department of Pharmacology

institute: Harbin Medical University

data_processing:
Paired-end sequencing was performed on cDNA library using HiSeq 2500 instrument (Illumina).
The qualified reads were mapped to Rat6 using STAR split mapping algorithm.
The expression level of genes was determined based on the value of FPKM which was calculated by htseq-count.
Assembly: Rat6
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Rattus norvegicus

source_name: Myocardial tissue

growth_protocol: The rats were placed in a colony room with controlled temperature and humidity, where food and water were freely available in a 12-h light/dark cycle.

extract_protocol:
Total RNA was harvested from the cells using Trizol reagent. TruSeq Stranded Total RNA Library Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Male rats were anesthetized, placed supine, and surgically assisted breathing with animal ventilator, and left thoracotomy was performed through a horizontal incision in the fourth intercostal space.
Ischemia was observed when the left anterior descending (LAD) coronary artery was ligated around the PE-10 tube with moving nodule with 6-0 sutures, and occlusion of the left anterior descending coronary artery was confirmed by elevation of the ST segment of the electrocardiogram.
Ischemia is released after 30 min for reperfusion. 6 h after reperfusion, the heart was harvested.

value: Myocardial tissue

value: I/R


title: ID15292_liver_2yr

source_name: liver

value: liver


title: ID15494_adipose_0yr

source_name: adipose

value: adipose


title: myocardium, I/R2, 30 min and 6 h, rep2

value: WT


title: ID15292_muscle_2yr

source_name: muscle

value: muscle


title: HCC68-WT3 [UT_TH3]

description: replicate 3


title: HCC68-LOH3.230 [UT_TH4]

description: replicate 1


title: ID15292_adipose_2yr


title: HCC68-WT3 [UT_TH2]

description: replicate 2


title: ID15292_muscle_0yr


title: myocardium, I/R1, 30 min and 6 h, rep1


title: ID15292_adipose_0yr


title: myocardium, sham3, 30 min and 6 h, rep3

value: Sham


title: ID15494_adipose_2yr


title: ID15279_muscle_2yr


title: HLF-WT45 [UT_TH159_2]

description: replicate 2

source_name: HLF cells (human HCC)


title: myocardium, sham2, 30 min and 6 h, rep2


title: ID15494_muscle_0yr


title: ID15279_liver_2yr


title: ID15279_liver_0yr


title: ID15279_muscle_0yr


title: ID15279_adipose_2yr


title: myocardium, sham1, 30 min and 6 h, rep1


title: ID15178_muscle_2yr


title: ID15178_adipose_2yr


title: HLE-LOH34.31 [UT_TH11]

description: replicate 2


title: HLF-WT41 [UT_TH106_6]

description: replicate 3


title: ID15178_liver_2yr


title: ID15292_liver_0yr


title: ISW2_2

city: Munich

first: Stephan

last: Hamperl

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz-Zentrum Munich

data_processing:
Base- and modified basecalling were performed with megalodon (v2.3.3) and guppy (v5.0.11) using the res_dna_r941_min_modbases-all-context_v001 model and default parameters.
ARS sequences derived from genome build/assembly Saccharomyces_cerevisisae.R64-1-1 targeted for affinity purification, an in vitro assembled nucleosomal array of 12x601 sequences and a spike-in naked plasmid DNA added in the experiments served as spike-in controls to normalize for methylation efficiencies.
Assembly: Saccharomyces_cerevisiae.R64-1-1
Supplementary files format and content: comma separated files that contain binary information about methylation

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Logarithmic yeast cells were grown in YPR medium and arrested with alpha-factor together with addition of 2% galactose to induce site-specific recombination of native replication origin chromatin domains. Cells were harvested and frozed for subsequent affinity purification.

extract_protocol:
Cell pellets were lysed with dry ice in a commercial coffee grinder and chromatin domains affinity-purified as described in the manuscript. The purified chromatin circles were then treated with the M.CviPI/M.SssI (GpC/CpG-5-methyl-Cytosine-specific) and EcoGII (methyl-6-Adenine-specific) DNA methyltransferases. Methylated DNA was then isolated using Phenol-chloroform extraction.  EcoGII (methyl-6-Adenine-specific) DNA methyltransferases,
MinIONTM Seqencing Library Preparation (Oxford Nanopore Sequencing)
Nanopore long-read sequencing for direct detection of methylated bases

tag: cell lines

tag: cell type

value: yeast cells

value: Y0105:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;  RS_LEXA_NS-  3_ARS305_NS+3_RS; Chr I 212kb::LEU2 pTEF2-LEXATAP  pGAL1-10  RecR ;isw2delta::ura3

value: Y0106:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;  RS_LEXA_NS-  3_ARS316_NS+3_RS; Chr I  212kb::LEU2 pTEF2-LEXATAP  pGAL1-10  RecR;isw2delta::ura3

value: Y0102:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;RS_LEXA_NS-  3_ARS315_NS+3_RS; Chr I  212kb::LEU2 pTEF2-LEXATAP  pGAL1-10 RecR ;  isw2delta::ura3

value: Y0107:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;RS_LEXA_NS-  3_ARS313_NS+3_RS; Chr I  212kb::LEU2 pTEF2-LEXATAP  pGAL1-10  RecR;isw2delta::ura3


title: WT_3

value: wild type

value: hepatocytes


title: HLF-WT45 [UT_TH159_3]

description: replicate 3


title: ID15178_muscle_0yr

value: LCLF


title: ID15178_liver_0yr


title: Control_2

value: Y0065:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;  RS_LEXA_NS-  3_ARS305_NS+3_RS; Chr I  212kb::LEU2 pTEF2-LEXATAP  pGAL1-10 RecR

value: Y0069:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;  RS_LEXA_NS-  3_ARS316_NS+3_RS; Chr I  212kb::LEU2 pTEF2-LEXATAP  pGAL1-10 RecR

value: Y0091:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;RS_LEXA_NS-  3_ARS315_NS+3_RS; Chr I  212kb::LEU2 pTEF2-LEXATAP  pGAL1-10 RecR

value: Y0094:MATa; ura3delta0; leu2delta0;  his3delta1; met15delta0;  bar1::kanMX4;RS_LEXA_NS-  3_ARS313_NS+3_RS; Chr I  212kb::LEU2 pTEF2-LEXATAP  pGAL1-10 RecR


title: ID15178_adipose_0yr


title: HLF-WT41 [UT_TH106_5]

description: replicate 2


title: ID14944_muscle_2yr

value: HCHF