title: F94513

description:
39309-OCT-1_Per-Site-Unphased-Methylation, 39309-OCT-1_Per-Read-Unphased-Methylation, 39309-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 39309-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 39309-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 39309-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F94511

status: Public on Oct 15 2024

type: SRA

city: Vancouver

first: Marco

last: Marra

state: BC

address: 570 W 7th Ave

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

description:
37080-OCT-1_Per-Site-Unphased-Methylation, 37080-OCT-1_Per-Read-Unphased-Methylation, 37080-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 37080-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 37080-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 37080-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2

library_source: genomic

data_processing:
Per-site and per-read unphased methylation data detected from nanopore sequencing raw signals using nanopolish. Phased methylation data were obtained using NanoMethPhase.
Assembly: GRCh38
Supplementary files format and content: Phased and Unphased CpG methylation data in tsv.gz format.
Library strategy: NanoMethPhase

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Frozen tissue sections were immersed in 420 μL of RLT Plus buffer (QIAGEN) containing tris(2-carboxyethyl)phosphine (a reducing agent; TCEP) and a unique sample tracking DNA plasmid, and gently agitated overnight at room temperature. Lysates were transferred from 2 mL tubes to wells of a 1.2 mL plate (Thermo Scientific, AB1127) to which was added 400 mL of 5x bind buffer (80 mL beads in 320 mL isopropyl alcohol). Following a 5 minute incubation at room temperature lysates were cleared on a Magnum FLX magnet place (Alpaqua Inc) for 6 minutes and the protein-containing supernatant removed. The beads, with bound nucleic acids, were washed by pipetting 10 times in wash buffer and returned to the magnet. Beads were washed three times in 70% ethanol then dried for 10 minutes. 40 mL nuclease-free water was added to the dried beads and returned to the magnet. The eluted total nucleic acids were transferred to a 96-well storage plate and aliquots taken for quantification using Invitrogen Qubit 4 Fluorometer (Thermo Fisher Q33226)  For samples with concentrations below 166 ng/µL or in volumes greater than 30 µL, 5000 ng of Total Nucleic Acid (TNA) was transferred to a 1.5 mL DNase/RNase free tube and concentrated without heat on the Savant SpeedVac Plus (SC210A) to a maximum volume of 30 µL. This 5000 ng sample in 30 µL was topped up with 10 µL of Qiagen Buffer EB (Cat.19086). The samples were then run on the SAGE Science Blue Pippin instrument using the High Pass Plus Cassette (BPPLUS 10) with a maximum of 4 samples per run. The start range was selected at 15,000 base pairs and the end range was selected at 150,000 base pairs yielding a targeted size of 82,500 base pairs. Following the run completion, each sample was eluted in 80 µL and each sample elution well was then washed with 80 µL of 10 mM Tris, 1mM EDTA containing 0.1% Tween to maximize sample recovery. The total volume of 160µL was then concentrated without heat to 50 µL using the SpeedVac Plus. Each sample was then quantified using the Invitrogen Qubit 4 Fluorometer (Q33226) and normalized to 2000 ng in 47.5 µL for PromethION genome sequencing.
Library construction and sequencing followed the Oxford Nanopore Technologies Genomic DNA by Ligation (SQK-LSK110) protocol. DNA libraries starting with 2 µg of sample per library. No shearing was performed. The NEBUltra-II kit, (New England Biolabs, Ipswich, MA, USA, cat. no. E7646A) was used for end-repair and A-tailing. NEBNext quick ligase (E6056S) was used to ligate the Oxford Nanopore sequencing adapter. A final size selection of 0.4:1 ratio beads:library (PCRClean – DX Aline Biosciences L/N 06180316) was done to select against smaller molecules. These library preparation steps were performed on Hamilton Nimbus96 liquid handlers. An example deck layout, in this case for the bead purification step, is shown in Extended Data Figure 1c. DNA libraries were loaded in R9.4.1 pore flow cells on PromethION 24 instrument running software version 19.06.9 (MinKNOW GUI v4.0.23). Sequencing was carried out for 72 hours. DNase I (Invitrogen cat no. AM2222) nuclease flush was performed after 24-48 hours by reloading the flow cell with the same library mix.

tag: tissue


title: GMP, Pristane, Replicate 3 [Lup_GMP_3]

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

country: USA

institute: University of Colorado Anschutz Medical Campus

library_source: transcriptomic

data_processing:
Illumina adapters were removed and reads <50bp after trimming were discarded
Reads were aligned and quantified using STAR (2.6.0a) to the Ensembl mouse transcriptome (GRCm38.p6, release 96)
Lowly abundant genes were removed as those <1 mean raw count or <1 mean count per million (CPM) across the dataset
Differential gene expression was calculated using the voom function in limma
Assembly: GRCm38
Supplementary files format and content: Text file containing STAR gene count values

molecule: total RNA

organism: Mus musculus

source_name: Bone Marrow

extract_protocol:
Sorted cells were pelleted and then lysed in mild lysis buffer (10mM Nacl, 10mM Tris-HSC, 0.5% NP-40, Rnase inhibitor) for 30 minutes. Cells were vortexed for 1 minute and centrifuged at 2000 g for 5 minutes at 4oC. The lysis supernatant, containing the RNA fraction was removed and immediately placed into RLT buffer from the Qiagen RNeasy micro kit and processed following manufacturer's instructions
Ribo-depleted RNA isolation

treatment_protocol: N/A cells were processed immediately after sorting

value: Bone Marrow

tag: cell type

value: GMP

tag: treatment

value: Pristane


title: Kidney_1457_post (R9732-6_S44)

city: Los Angeles

first: Fei-Man

last: Hsu

state: California

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

data_processing:
Reads were aligned to reference genome GRCh38 using STAR using default parameters (Dobin et al, 2013).   A gene count table was generated using featurecount (Liao et al, 2013).  Gene count matrix was first normalized and DEGs were identified using R package DEseq2 (Love et al, 2014).  Genes with adjusted p value < 0.05 and at least 2-fold difference between CMV serostatus were considered differentially expressed.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

molecule: polyA RNA

source_name: Blood

extract_protocol:
8ml of blood was drawn into the ACD tube.  After Ficol density gradient centrifugation, PBMCs were separated isolated  and cryopreserved in FCS/DMSO.
mRNA libraries were constructed using KAPA RNA HyperPrep Kit following the manufacture’s instruction (Cat# KK8540).  RNA was sheared and primed with oligos for cDNA synthesis.  After adapter ligation and PCR amplified, the final library was quantified and accessed quality with TapeStation.

value: Blood

value: PBMC

tag: patient id

tag: age

tag: Sex

value: F

tag: time

value: PostTx

value: POS

tag: atg

value: Y

tag: simulect

value: N


title: GMP, Pristane, Replicate 2 [Lup_GMP_2]


title: F94518

description:
43019-FF-1_Per-Site-Unphased-Methylation, 43019-FF-1_Per-Read-Unphased-Methylation, 43019-FF-1_Per-Read-Phased-Methylation-Haplotype1, 43019-FF-1_Per-Site-Phased-Methylation-Haplotype1, 43019-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 43019-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Kidney_1494_post (R9696-6_S4)

value: NEG


title: F94510

description:
35290-OCT-1_Per-Site-Unphased-Methylation, 35290-OCT-1_Per-Read-Unphased-Methylation, 35290-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 35290-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 35290-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 35290-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GSCs, shMDH2_03_in02

city: Pittsburgh

first: Jeremy

last: Rich

state: PA

address: 5115 Centre Ave

department: Hillman Cancer Center

institute: University of Pittsburgh Medical Center

data_processing:
MeRIP-seq reads were aligned to human genome hg38 by using the Hisat2 with reference annotation from NCBI. To minimize the rate of false positives, only uniquely mapped and without-duplication reads were selected by samtools. Then, the reads were extended to a length of 200 nt in the 5’-to-3’ direction, accounting for the length of RNA fragments, to calculate the reads coverage along the genome by MACS2.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: 738 GSC

growth_protocol: Cells were cultured as spheres in Neurobasal medium supplemented with B27, L-glutamine, sodium pyruvate, 1% penicillin/streptomycin, 10 ng/ml basic fibroblast growth factor (bFGF), and 10 ng/ml epidermal growth factor (EGF).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) and treated with RNase-free DNase I (Roche) to deplete DNA contamination.
PolyA RNA was purified using a GenElute mRNA Miniprep Kit (Sigma-Aldrich) as per the manufacturer's instructions and fragmented using an RNA fragmentation kit (Ambion). Note that 200 μg of fragmented RNA was incubated with 3 μg anti-m6A (Synaptic Systems, Cat# 202 003) in RIP buffer (150 mmol/L NaCl, 10 mmol/L Tris, and 0.1% NP-40) for 2 hours at 4°C, followed by addition of washed protein A/G magnetic beads (Millipore) and incubation at 4°C for a further 2 hours. Beads were washed 6 times in RIP buffer and incubated with 50 μL immunoprecipitation buffer containing 0.5 mg/mL m6AMP (Sigma-Aldrich) to elute RNA. Immunoprecipitated RNA was extracted with phenol/chloroform, and RNA samples were sent for next-generation sequencing.

tag: cell line

value: 738 GSC

value: Glioblastoma stem cells


title: GMP, Pristane, Replicate 1 [Lup_GMP_1]


title: GMP, Control, Replicate 3 [Con_GMP_3]

value: Control


title: GSCs, shCONT_IP01

value: shCONT


title: Kidney_1489_post (R9690-6_S14)

value: M


title: F94508

description:
34491-OCT-1_Per-Site-Unphased-Methylation, 34491-OCT-1_Per-Read-Unphased-Methylation, 34491-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 34491-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 34491-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 34491-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F94509

description:
36749-OCT-1_Per-Site-Unphased-Methylation, 36749-OCT-1_Per-Read-Unphased-Methylation, 36749-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 36749-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 36749-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 36749-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GSCs, shCONT_IP02


title: GSCs, shMDH2_03_in01


title: F94507

description:
35258-OCT-1_Per-Site-Unphased-Methylation, 35258-OCT-1_Per-Read-Unphased-Methylation, 35258-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 35258-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 35258-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 35258-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Kidney_1476_post (R9597-6_S62)


title: Kidney_1484_post (R9653-6_S46)


title: GMP, Control, Replicate 2 [Con_GMP_2]


title: F94515

description:
39982-FF-1_Per-Site-Unphased-Methylation, 39982-FF-1_Per-Read-Unphased-Methylation, 39982-FF-1_Per-Read-Phased-Methylation-Haplotype1, 39982-FF-1_Per-Site-Phased-Methylation-Haplotype1, 39982-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 39982-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GSCs, shCONT_in02


title: GSCs, shMDH2_03_IP01


title: Kidney_U1111R_pre (PRETX31-6_S23)

value: PreTx


title: F94506

description:
35337-OCT-1_Per-Site-Unphased-Methylation, 35337-OCT-1_Per-Read-Unphased-Methylation, 35337-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 35337-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 35337-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 35337-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Kidney_1476_pre (PRETX26-6_S61)


title: GMP, Control, Replicate 1 [Con_GMP_1]

value: Bone Marrow


title: F94505

description:
33480-OCT-1_Per-Site-Unphased-Methylation, 33480-OCT-1_Per-Read-Unphased-Methylation, 33480-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 33480-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 33480-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 33480-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GMP, Pristane, replicate 2

data_processing:
The quality of the fastq files was accessed using FastQC.
Illumina adapters and low-quality reads were filtered out using BBDuk.
Bowtie2 (v.2.3.4.3) was used to align the sequencing reads to the mm10 reference murine genome.
Samtools (v.1.11) was used to select the mapped reads (samtools view -b -q 30) and sort the bam files.
PCR duplicates were removed usign Picard MarkDuplicates tool.
The normalization ratio for each sample was calculated by dividing the  number of uniquely mapped murine reads of the sample with the lowest number of reads by the number of uniquely mapped murine reads of each sample. These normalizations ratios were used to randomly sub-sample reads to obtain the same number of reads for each sample using using samtools view -s.
Bedtools genomecov was used to create bedgraph files from the bam files
Bigwig files were created using deepTools bamCoverage
Peaks were called using MACS2 (v2.1.2) with  ENCODE recommended parameters.
Bigwig files were created using deepTools bamCoverage
IDR was used to identify the reproducible peaks between the replicates.
Further processing of the peak data was performed in R. Average profiles and heatmaps were generated using ngs.plot.
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak

source_name: Bone marrow

extract_protocol:
Sorted cells were pelleted and then lysed in mild lysis buffer (10mM Nacl, 10mM Tris-HSC, 0.5% NP-40, Rnase inhibitor) for 30 minutes. Cells were vortexed for 1 minute and centrifuged at 2000 g for 5 minutes at 4oC. The lysis supernatant was removed, then the transposase reaction mix (Transposase enzyme, buffer, and digitonin) was added to the pelleted nuclei and incubated for 30 minutes at 37oC. DNA was then purified and cleaned.
ATAC-seq libraries were prepared by amplifying the DNA fragments using barcoded primers and the NEBNext HF PCR kit. The samples were amplified on a thermocycler for 10-11 cycles depending on amplification efficiency determined using qRT-PCR. Libraries were validated using the Agilent D1000 ScreenTape system.

treatment_protocol: Cells were processed immediately after sorting

value: Bone marrow

value: GMP

value: Granulocyte-monocyte progenitor


title: R341_duct

city: bethesda

first: Efsun

last: Arda

state: Maryland

address: 41 medlars drive

institute: National Institutes of Health

data_processing:
Raw reads Mapping: HiC pro
Loop calling: hichipper and FitHiChIP
Assembly: hg38
Supplementary files format and content: tab-delimited text file include consensus loops with pair-ended tags (PETs) for each cell type
Library strategy: HiChIP

source_name: duct

extract_protocol:
Sorted cells are fixed with 1% formaldehyde for 10 minutes at room temperature, after quenching, cell lysis, in situ chromatin digestion and proximity ligation, the ligated chromatin was extracted from nuclei following the protocol described in Mumbach et al (PMID: 27643841)
custom DNA libraries were prepared following the protocol described in Mumbach et al (PMID: 27643841)

value: duct

tag: sample origin

value: Pancreas

tag: disease status

value: normal

value: Male

tag: bmi


title: Kidney_U1112R_pre (PRETX12-6_S25)

value: Blood

value: PBMC

value: F

value: Y


title: F94504

description:
33532-OCT-1_Per-Site-Unphased-Methylation, 33532-OCT-1_Per-Read-Unphased-Methylation, 33532-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 33532-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 33532-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 33532-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GMP, Pristane, replicate 1

value: Pristane


title: SAMN13283508_acinar.

source_name: acinar

value: acinar


title: Kidney_1534_pre (768490_S5)

value: NEG

value: N


title: GMP, Control, replicate 2

value: Control


title: R325_beta

source_name: beta

value: beta


title: F94502

description:
31184-OCT-1_Per-Site-Unphased-Methylation, 31184-OCT-1_Per-Read-Unphased-Methylation, 31184-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 31184-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 31184-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 31184-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Kidney_1551_pre (767837_S27)

value: M

value: PreTx

value: POS


title: Kidney_1547_pre (768075_S55)


title: Kidney_1546_pre (767804_S53)


title: SAMN12572087_duct

value: duct


title: F94499

description:
26465-OCT-1_Per-Site-Unphased-Methylation, 26465-OCT-1_Per-Read-Unphased-Methylation, 26465-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 26465-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 26465-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 26465-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F94498

description:
26125-FF-1_Per-Site-Unphased-Methylation, 26125-FF-1_Per-Read-Unphased-Methylation, 26125-FF-1_Per-Read-Phased-Methylation-Haplotype1, 26125-FF-1_Per-Site-Phased-Methylation-Haplotype1, 26125-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 26125-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: T.chuii_3

city: Gangneung-si, Gangwon-do

first: Sung-Chul

last: Hong

address: Saimdang-ro 679

department: Smart Farm Research Center

country: South Korea

institute: Korea Institute of Science and Technology

data_processing:
QC/adapter sequence trimming for raw FASTQ sequences Raw read quality evaluation by FastQC v0.11.7 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc) with default options.
Remove the adapter sequence through Trimmomatic 0.38, and remove bases with base quality less than 3 from the ends of the reads and bases that do not satisfy window size=4, mean quality=15 by sliding window trim method. Then, we generate trimmed data by removing reads shorter than min length = 36 bp.
We used genomic DNA reference (mm10) for mapping and mapped to HISAT2 (v.2.1.0) which can be spliced read mapping process via Bowtie2 aligner (2.3.4.1).
Assemble the known gene/transcript using the reference gene model via StringTie (v.2.1.3b) and calculate the amount of transcript abundance to the FPKM (Fragments Per Kilobase of transcripts per Million mapped reads) values of read count and within sample normalized value.
In order to proceed with DEG (Differentially Expressed Genes) analysis, we filtered genes with low quality from the read count value of genes obtained by the StringTie-e option, and then proceeded with RLE normalization.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files with FPKM and read counts

source_name: Eyeball

growth_protocol: Fifteen female BALB/C mice (six-week-old, female) were obtained from the Orientbio (Gyunggi-do, Republic of Korea). All mice were housed in an air-conditioned animal room and maintained at 22°C ± 2°C, 50% ± 10% humidity, and a 12-h light/12-h dark circadian cycle for 1 week after arrival

extract_protocol:
Eye balls were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA LT Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At 6 weeks of age, they were randomly divided into 3 groups and 2 groups (DES, T.chuii) injected scopolamine via intraperuitoneal injection and fed a water (CON, DES), 300 mg/kg T. chuii (T.chuii) for 2 weeks

tag: strain

value: BALB/C

value: Eyeball

value: post nature day 56

tag: genotype

value: WT

value: Scoplamine induced and T. chuii treated


title: GMP, Control, replicate 1

value: Bone marrow

value: GMP

value: Granulocyte-monocyte progenitor


title: SAMN11788169_duct

value: Pancreas

value: normal

value: Female


title: T.chuii_2


title: Kidney_1535_pre (767726_S73)

value: Blood

value: PBMC

value: N


title: F94494

description:
36067-OCT-1_Per-Site-Unphased-Methylation, 36067-OCT-1_Per-Read-Unphased-Methylation, 36067-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 36067-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 36067-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 36067-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GSCs, shCONT_in01

value: 738 GSC

value: Glioblastoma stem cells

value: shCONT


title: T.chuii_1

value: BALB/C


title: SAMN11788169_acinar

value: acinar


title: F94492

description:
23187-OCT-1_Per-Site-Unphased-Methylation, 23187-OCT-1_Per-Read-Unphased-Methylation, 23187-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 23187-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 23187-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 23187-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F94503

description:
33129-OCT-1_Per-Site-Unphased-Methylation, 33129-OCT-1_Per-Read-Unphased-Methylation, 33129-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 33129-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 33129-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 33129-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Kidney_1528_pre (767370_S59)

value: F

value: PreTx

value: POS

value: Y


title: SAMN11773852_duct

value: duct

value: Male


title: DES_3

value: Eyeball

value: post nature day 56

value: WT

value: Scoplamine induced


title: Kidney_1536_pre (767438_S35)

value: Blood

value: PBMC

value: M


title: SAMN11773852_acinar

value: Pancreas

value: normal


title: DES_2

value: BALB/C


title: Kidney_1527_pre (767196_S57)

value: N


title: R325_alpha

source_name: alpha

value: alpha


title: SAMN14132340_alpha

data_processing:
Raw reads were processed using PEPATAC package (PMID: 34859208)
Homer Suite was used to generate counts table
Assembly: hg38
Supplementary files format and content: tab-delimited file containing consensus peaks with normalized counts in each donor and cell type

extract_protocol:
sorted cells were transposed following steps described in Corces et al (PMID: 28846090), then transcposed DNA fragments were purified using a Zymo DNA Clean and Concentrator-5 Kit
custom DNA libraries were prepared following the protocol described in Corces et al (PMID: 28846090).

value: male

tag: dsease status


title: F94485

description:
23808-FF-1_Per-Site-Unphased-Methylation, 23808-FF-1_Per-Read-Unphased-Methylation, 23808-FF-1_Per-Read-Phased-Methylation-Haplotype1, 23808-FF-1_Per-Site-Phased-Methylation-Haplotype1, 23808-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 23808-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: DES_1


title: Kidney_1522_pre (767020_S11)

value: F

value: PreTx

value: NEG


title: CON_3


title: Kidney_1543_pre (766944_S9)


title: F94484

description:
23189-FF-1_Per-Site-Unphased-Methylation, 23189-FF-1_Per-Read-Unphased-Methylation, 23189-FF-1_Per-Read-Phased-Methylation-Haplotype1, 23189-FF-1_Per-Site-Phased-Methylation-Haplotype1, 23189-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 23189-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: CON_2


title: Kidney_1523_pre (766943_S72)

value: POS

value: Y


title: SAMN14124567_duct

value: duct


title: F94483

description:
18843-OCT-1_Per-Site-Unphased-Methylation, 18843-OCT-1_Per-Read-Unphased-Methylation, 18843-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 18843-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 18843-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 18843-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: R361_delta

source_name: delta

value: delta

value: female


title: CON_1

value: Eyeball

value: post nature day 56

value: WT


title: F94489

description:
31189-OCT-1_Per-Site-Unphased-Methylation, 31189-OCT-1_Per-Read-Unphased-Methylation, 31189-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 31189-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 31189-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 31189-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F94481

description:
32971-OCT-1_Per-Site-Unphased-Methylation, 32971-OCT-1_Per-Read-Unphased-Methylation, 32971-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 32971-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 32971-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 32971-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Kidney_1553_pre (766767_S63)

value: Blood

value: PBMC

value: M


title: F94480

description:
31981-OCT-1_Per-Site-Unphased-Methylation, 31981-OCT-1_Per-Read-Unphased-Methylation, 31981-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 31981-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 31981-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 31981-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: R361_alpha

value: Pancreas

value: normal


title: Kidney_1558_pre (766672_S1)

value: N


title: R360_delta


title: Root sample from control plants under salt stress, replicate 3

city: Valencia

first: Javier

last: Forment

address: Ingeniero Fausto Elio, s/n

country: Spain

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (Universitat Politècnica de València-CSIC)

data_processing:
Sequencing data were filtered using SOAPnuke. Clean reads were mapped to the reference genome using HISAT2. After that, Ericscript (0.5.5-5) and rMATS (v4.1.1) were used to detect fusion genes and differential splicing genes (DSG), respectively.
Assembly: Reference Genome Version: GCF_002870075.4_Lsat_Salinas_v11
Supplementary files format and content: Tab-separated read counts per gene (gene_expression_read_counts.tsv) and transcript (rna_expression_read_counts.tsv) per sample

organism: Lactuca sativa

source_name: Root

growth_protocol: Lettuce plants were grown in a greenhouse under normal and salt stress conditions.

extract_protocol:
NucleoSpin® RNA Plant kit (Macherey–Nagel GmbH & Co. KG, Düren, Germany) according to the manufacturer's instructions
Eukaryotes stranded transcriptome library
RNA-seq was performed on the DNBseq™ platform by sequencing 150 bp read lengths.

treatment_protocol: control (without product), Calbio (BS), Bacteria (PGPB), mycorrhizal fungus (AMF), Calbio with bacteria (BS+PGPB) and Valbio with mycorrhizal fungus (BS+AMF)

value: Root

value: Control

tag: condition

value: Salt stress


title: R360_beta

value: beta


title: F94488

description:
30221-OCT-2_Per-Site-Unphased-Methylation, 30221-OCT-2_Per-Read-Unphased-Methylation, 30221-OCT-2_Per-Read-Phased-Methylation-Haplotype1, 30221-OCT-2_Per-Site-Phased-Methylation-Haplotype1, 30221-OCT-2_Per-Read-Phased-Methylation-Haplotype2 and 30221-OCT-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2

tag: tissue


title: Root sample from plants treated with the combination of calbio and bacteria under salt stress, replicate 3

value: Combination of calbio and bacteria (BS+PGPB)


title: Kidney_1517_pre (764694_S51)

tag: cell type

value: PreTx

value: POS

value: Y


title: SAMN14124567_acinar

value: acinar

value: male


title: Kidney_1515_pre (765367_S49)


title: Root sample from plants treated with the combination of calbio and mycorrhiza under salt stress, replicate 3

tag: treatment

value: Combination of calbio and mycorrhiza (BS+AMF)


title: R360_alpha

value: alpha

value: female


title: Kidney_1511_pre (763946_S31)

value: Blood

value: PBMC

tag: patient id

value: F


title: F94476

description:
28126-OCT-1_Per-Site-Unphased-Methylation, 28126-OCT-1_Per-Read-Unphased-Methylation, 28126-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 28126-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 28126-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 28126-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Root sample from plants treated with bacteria under salt stress, replicate 3

value: Bacteria (PGPB)


title: Root sample from plants treated with Calbio under salt stress, replicate 3

value: Root

value: Calbio(BS)


title: F94475

description:
27504-OCT-1_Per-Site-Unphased-Methylation, 27504-OCT-1_Per-Read-Unphased-Methylation, 27504-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 27504-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 27504-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 27504-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Kidney_1512_pre (763915_S67)

tag: age

value: N


title: R357_alpha

tag: Sex

value: Pancreas

value: normal


title: R357_delta

value: delta


title: F94474

description:
27329-OCT-1_Per-Site-Unphased-Methylation, 27329-OCT-1_Per-Read-Unphased-Methylation, 27329-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 27329-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 27329-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 27329-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F94479

description:
31042-OCT-1_Per-Site-Unphased-Methylation, 31042-OCT-1_Per-Read-Unphased-Methylation, 31042-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 31042-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 31042-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 31042-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: R357_beta

value: beta


title: Kidney_1521_pre (763866_S15)

value: M

tag: time

value: PreTx

value: NEG

value: Y


title: F94473

description:
30811-OCT-1_Per-Site-Unphased-Methylation, 30811-OCT-1_Per-Read-Unphased-Methylation, 30811-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 30811-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 30811-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 30811-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Root sample from control plants under normal conditions, replicate 3

value: Control

value: Normal conditions


title: Kidney_1541_pre (763205_S19)

value: Blood

tag: atg


title: Root sample from plants treated with bacteria under normal conditions, replicate 3


title: F94478

description:
30519-OCT-1_Per-Site-Unphased-Methylation, 30519-OCT-1_Per-Read-Unphased-Methylation, 30519-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 30519-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 30519-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 30519-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: R356_alpha

value: alpha

value: female


title: R356_delta


title: Kidney_1508_pre (762191_S37)

value: PBMC

value: F

value: POS

tag: simulect


title: Root sample from plants treated with the combination of calbio and bacteria under normal conditions, replicate 3

value: Root

value: Combination of calbio and bacteria (BS+PGPB)


title: Root sample from plants treated with mycorrhizae under salt stress, replicate 3

value: Mycorrhizal fungus (AMF)

value: Salt stress


title: F94472

description:
26051-OCT-1_Per-Site-Unphased-Methylation, 26051-OCT-1_Per-Read-Unphased-Methylation, 26051-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 26051-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 26051-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 26051-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Kidney_U1146R_pre (761101_S65)

value: N


title: F94470

description:
25426-FF-1_Per-Site-Unphased-Methylation, 25426-FF-1_Per-Read-Unphased-Methylation, 25426-FF-1_Per-Read-Phased-Methylation-Haplotype1, 25426-FF-1_Per-Site-Phased-Methylation-Haplotype1, 25426-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 25426-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: R356_beta

value: beta

value: Pancreas

value: normal


title: Root sample from plants treated with the combination of calbio and mycorrhiza under normal conditions, replicate 3

value: Combination of calbio and mycorrhiza (BS+AMF)


title: F94469

description:
23737-OCT-1_Per-Site-Unphased-Methylation, 23737-OCT-1_Per-Read-Unphased-Methylation, 23737-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 23737-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 23737-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 23737-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Root sample from plants treated with Calbio under normal conditions, replicate 3

value: Calbio(BS)


title: Kidney_U1143R_pre (760863_S17)

value: PreTx

value: NEG

value: Y


title: Root sample from plants treated with mycorrhizae under normal conditions, replicate 3

value: Normal conditions


title: HP20010_duct

value: duct

value: male


title: Kidney_U1148R_pre (758557_S29)

value: Blood

value: PBMC

value: M

value: POS


title: Kidney_1457_pre (757911_S43)

value: F


title: F94464

description:
32973-OCT-1_Per-Site-Unphased-Methylation, 32973-OCT-1_Per-Read-Unphased-Methylation, 32973-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 32973-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 32973-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 32973-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: SAMN14327036_delta

value: delta


title: Leaf sample from plants treated with bacteria under salt stress, replicate 3

source_name: Leaf

value: Leaf

value: Bacteria (PGPB)

value: Salt stress


title: Kidney_1501_pre (756760_S47)

value: N


title: Leaf sample from control plants under salt stress, replicate 3

value: Control


title: SAMN14327036_alpha

value: alpha

value: Pancreas

value: normal


title: F94463

description:
32034-FF-1_Per-Site-Unphased-Methylation, 32034-FF-1_Per-Read-Unphased-Methylation, 32034-FF-1_Per-Read-Phased-Methylation-Haplotype1, 32034-FF-1_Per-Site-Phased-Methylation-Haplotype1, 32034-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 32034-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F94462

description:
30784-OCT-1_Per-Site-Unphased-Methylation, 30784-OCT-1_Per-Read-Unphased-Methylation, 30784-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 30784-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 30784-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 30784-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: R364_delta


title: F94461

description:
25902-OCT-1_Per-Site-Unphased-Methylation, 25902-OCT-1_Per-Read-Unphased-Methylation, 25902-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 25902-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 25902-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 25902-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Kidney_1505_pre (756689_S33)

value: PreTx

value: Y


title: R364_beta

value: beta

value: male


title: Leaf sample from plants treated with the combination of calbio and mycorrhiza under salt stress, replicate 3

value: Combination of calbio and mycorrhiza (BS+AMF)


title: Kidney_1468_pre (761070_S7)

value: Blood

value: PBMC

value: M

value: NEG


title: Kidney_U1136R_pre (755385_S21)

value: F


title: Leaf sample from plants treated with the combination of calbio and bacteria under salt stress, replicate 3

value: Leaf

value: Combination of calbio and bacteria (BS+PGPB)


title: Kidney_U1132R_pre (754643_S69)

value: POS

value: N


title: F94460

description:
25980-OCT-1_Per-Site-Unphased-Methylation, 25980-OCT-1_Per-Read-Unphased-Methylation, 25980-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 25980-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 25980-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 25980-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: R362_delta

value: delta


title: F94459

description:
20794-OCT-1_Per-Site-Unphased-Methylation, 20794-OCT-1_Per-Read-Unphased-Methylation, 20794-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 20794-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 20794-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 20794-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F94466

description:
37076-OCT-1_Per-Site-Unphased-Methylation, 37076-OCT-1_Per-Read-Unphased-Methylation, 37076-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 37076-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 37076-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 37076-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: HP20010_acinar

value: acinar

value: Pancreas


title: Leaf sample from plants treated with Calbio under salt stress, replicate 3

value: Calbio(BS)

value: Salt stress


title: R362_alpha

value: alpha

value: normal


title: Kidney_1489_pre (753984_S13)

value: PreTx

value: Y


title: Leaf sample from plants treated with bacteria under normal conditions, replicate 3

value: Bacteria (PGPB)

value: Normal conditions


title: Kidney_1494_pre (753559_S3)

value: Blood

value: PBMC

value: NEG


title: HP19244_duct

value: duct

value: female


title: Leaf sample from control plants under normal conditions, replicate 3

value: Leaf

value: Control


title: F94430

description:
37097-OCT-1_Per-Site-Unphased-Methylation, 37097-OCT-1_Per-Read-Unphased-Methylation, 37097-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 37097-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 37097-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 37097-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Kidney_U1124R_pre (753145_S39)

value: M

value: POS

value: N


title: F94428

description:
36684-OCT-2_Per-Site-Unphased-Methylation, 36684-OCT-2_Per-Read-Unphased-Methylation, 36684-OCT-2_Per-Read-Phased-Methylation-Haplotype1, 36684-OCT-2_Per-Site-Phased-Methylation-Haplotype1, 36684-OCT-2_Per-Read-Phased-Methylation-Haplotype2 and 36684-OCT-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: SAMN12736601_acinar

value: acinar

value: male

value: Pancreas


title: Leaf sample from plants treated with mycorrhizae under salt stress, replicate 3

value: Mycorrhizal fungus (AMF)

value: Salt stress


title: F94426

description:
33740-OCT-1_Per-Site-Unphased-Methylation, 33740-OCT-1_Per-Read-Unphased-Methylation, 33740-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 33740-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 33740-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 33740-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Kidney_1484_pre (751946_S45)

value: PreTx


title: SAMN13047843_duct

value: normal


title: SAMN12736601_duct


title: Kidney_U1123R_pre (751799_S41)

value: Blood

value: Y


title: F94427

description:
34120-OCT-1_Per-Site-Unphased-Methylation, 34120-OCT-1_Per-Read-Unphased-Methylation, 34120-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 34120-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 34120-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 34120-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F94425

description:
33546-OCT-1_Per-Site-Unphased-Methylation, 33546-OCT-1_Per-Read-Unphased-Methylation, 33546-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 33546-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 33546-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 33546-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Leaf sample from plants treated with Calbio under normal conditions, replicate 3

value: Calbio(BS)

value: Normal conditions


title: Leaf sample from plants treated with the combination of calbio and mycorrhiza under normal conditions, replicate 3

value: Combination of calbio and mycorrhiza (BS+AMF)


title: Root sample from plants treated with bacteria under salt stress, replicate 2

value: Root

value: Bacteria (PGPB)


title: F94431

description:
37620-OCT-1_Per-Site-Unphased-Methylation, 37620-OCT-1_Per-Read-Unphased-Methylation, 37620-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 37620-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 37620-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 37620-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: SAMN13086797_acinar


title: Leaf sample from plants treated with the combination of calbio and bacteria under normal conditions, replicate 3

value: Leaf

value: Combination of calbio and bacteria (BS+PGPB)


title: SAMN13283508_duct

value: duct


title: hESC_derived_mesodermal_cells_CRISPRi_SPTAN1_rep1

city: 嘉兴市

first: Jin

last: Jiang

state: 浙江省

address: 硖石街道

country: China

institute: 浙江大学爱丁堡大学联合学院

data_processing:
quality control by FastQC v0.11.9
sequence reads were cut by cutadapt v4.1 according to the results of FastQC(usually 15 bp in the head and the tail of the sequence reads)
sequence reads were trimmed by trim_galore v0.6.7 for adapter sequence/low quality sequence
sequence reads were mapped to hg38 using STAR v2.7.10a
read counts were counted using featureCounts v2.0.1
Assembly: hg38
Supplementary files format and content: Raw_Counts_mRNA.csv, csv type, store the raw counts of mRNA for samples
Supplementary files format and content: Raw_Counts_lncRNA.csv, csv type, store the raw counts of lncRNA for samples
Supplementary files format and content: Raw_Counts_Repeatsequence.csv, csv type, store the raw counts of Repeatsequence for samples

source_name: hESC H1

extract_protocol:
RNA was harvested using TRIzol (Invitrogen), for P-bodies samples, ~10-30ng RNA were used for the construction of sequencing libraries, for cytoplasm or whole cells samples, 2μg RNA  were used for the construction of sequencing libraries.
RNA libraries for RNAseq were prepared using Universal V8 RNA-seq Library Prep Kit for Illumina (VAHTS) following manufacturer's protocols

tag: cell line

value: hESC H1

value: hESC derived mesodermal cells

value: mesoderm induction


title: hESC_derived_mesodermal_cells_CRISPRi_SPTAN1_rep2

institute: 浙江大学爱丁堡大学联合学院


title: F94424

description:
33127-OCT-1_Per-Site-Unphased-Methylation, 33127-OCT-1_Per-Read-Unphased-Methylation, 33127-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 33127-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 33127-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 33127-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: hESC_derived_mesodermal_cells_CRISPRi_control_rep2

institute: 浙江大学爱丁堡大学联合学院


title: SAMN13898077_acinar

value: acinar

value: male

tag: sample origin

value: Pancreas


title: Root sample from control plants under salt stress, replicate 2

value: Control

value: Salt stress


title: hESC_derived_mesodermal_cells_CRISPRi_control_rep1

institute: 浙江大学爱丁堡大学联合学院


title: hESC_CRISPRi_SPTAN1_rep2

institute: 浙江大学爱丁堡大学联合学院

value: human embryonic stem cells


title: F94423

description:
32972-OCT-1_Per-Site-Unphased-Methylation, 32972-OCT-1_Per-Read-Unphased-Methylation, 32972-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 32972-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 32972-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 32972-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: SAMN13898077_duct

value: normal


title: F94422

description:
33373-OCT-1_Per-Site-Unphased-Methylation, 33373-OCT-1_Per-Read-Unphased-Methylation, 33373-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 33373-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 33373-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 33373-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: SAMN13283508_acinar


title: F94421

description:
31095-FF-1_Per-Site-Unphased-Methylation, 31095-FF-1_Per-Read-Unphased-Methylation, 31095-FF-1_Per-Read-Phased-Methylation-Haplotype1, 31095-FF-1_Per-Site-Phased-Methylation-Haplotype1, 31095-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 31095-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Root sample from plants treated with the combination of calbio and mycorrhiza under salt stress, replicate 2


title: Root sample from plants treated with the combination of calbio and bacteria under salt stress, replicate 2


title: hESC_CRISPRi_control_rep2

institute: 浙江大学爱丁堡大学联合学院


title: Leaf sample from plants treated with mycorrhizae under normal conditions, replicate 3

value: Mycorrhizal fungus (AMF)

value: Normal conditions


title: F94418

description:
30616-OCT-1_Per-Site-Unphased-Methylation, 30616-OCT-1_Per-Read-Unphased-Methylation, 30616-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 30616-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 30616-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 30616-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: hESC_CRISPRi_control_rep1

institute: 浙江大学爱丁堡大学联合学院


title: PJ1-2 cells

city: Seoul

first: Eun-Ji

last: Kwon

address: 1, Gwanak-ro

institute: Seoul National University

data_processing:
Read quality was assessed using FastQC (v) and poor-quality bases (Phred score < 20) were eliminated using TrimGalore (v0.6.6)
Trimmed reads were aligned to the mouse reference genome (GRCm38) using the STAR aligner (v2.7.9a) with default parameters
Gene-level expression values such as transcripts per million (TPM) and read counts were calculated using RSEM (v1.3.3.) with human gene annotation (GRCh38.84)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

growth_protocol: J1 were cultured on 0.5% porcine gelatin-coated dish in Naïve mESC culture media -DMEM high glucose (Gibco) supplemented with 15% FBS (Gibco), 1% Glutamax (Gibco), 1% MEM-nonessential amino acids (Gibco), 0.1% Gentamycin (Gibco), 0.1mM β-mercaptoethanol (Gibco), 1,000 U/ml mouse leukemia inhibitory factor (mLIF) (Millipore, Merck), 1 μM PD0325901 (Peprotech) and 3 μM CHIR99021- at 37 °C and 5% CO2 incubating condition. PJ1 were cultured on Matrigel (Corning# 354277)-coated dish in EpiSC culture media -DMEM/F12 (Gibco) supplemented with 20% KnockOut Serum Replacement (Gibco), 1% GlutaMAX (Gibco), 1% MEM-nonessential amino acids (Gibco), 0.1% Gentamycin (Gibco), 10 ng/ml murine bFgf (Peprotech), 20 ng/ml murine Activin (Peprotech)- at 37 °C and 5% CO2 condition.

extract_protocol:
RNA was harvested using Easy-BLUETM RNA isolation kit (iNtRON Biotechnology) . 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA)
Briefly, the strand-specific protocol included the following steps: (1) strand cDNA synthesis, (2) strand synthesis using dUTPs instead of dTTPs, (3) end repair, A-tailing, and adaptor ligation, and (4) PCR amplification. Each library was then diluted to 8 pM for 76 cycles of paired-read sequencing (2 × 75 bp) on an Illumina NextSeq 500 following the manufacturer’s recommended protocol.

value: embryonic stem cell

value: WT


title: PJ1-1 cells


title: Root sample from plants treated with mycorrhizae under salt stress, replicate 2

value: Root


title: F94416

description:
30504-FF-1_Per-Site-Unphased-Methylation, 30504-FF-1_Per-Read-Unphased-Methylation, 30504-FF-1_Per-Read-Phased-Methylation-Haplotype1, 30504-FF-1_Per-Site-Phased-Methylation-Haplotype1, 30504-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 30504-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Root sample from plants treated with bacteria under normal conditions, replicate 2

value: Bacteria (PGPB)


title: Root sample from control plants under normal conditions, replicate 2


title: F94415

description:
30009-FF-1_Per-Site-Unphased-Methylation, 30009-FF-1_Per-Read-Unphased-Methylation, 30009-FF-1_Per-Read-Phased-Methylation-Haplotype1, 30009-FF-1_Per-Site-Phased-Methylation-Haplotype1, 30009-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 30009-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: J1-GKO-1 cells

value: GYS1 KO


title: J1-GKO-2 cells


title: hESC_derived_mesodermal_cells_LSM14A_OE_rep1

institute: 浙江大学爱丁堡大学联合学院

source_name: hESC H9

value: hESC H9

value: Dox treat for 5 days, mesoderm induction


title: Root sample from plants treated with Calbio under salt stress, replicate 2

value: Calbio(BS)


title: J1-DKO-2 cells

value: AMPK, GYS1 KO


title: hESC_derived_mesodermal_cells_rep2

institute: 浙江大学爱丁堡大学联合学院

value: hESC derived mesodermal cells

value: mesoderm induction


title: SAMN14132340_beta

value: beta

value: male

value: Pancreas


title: Root sample from plants treated with the combination of calbio and mycorrhiza under normal conditions, replicate 2

value: Combination of calbio and mycorrhiza (BS+AMF)


title: J1-DKO-1 cells


title: F94414

description:
30000-FF-1_Per-Site-Unphased-Methylation, 30000-FF-1_Per-Read-Unphased-Methylation, 30000-FF-1_Per-Read-Phased-Methylation-Haplotype1, 30000-FF-1_Per-Site-Phased-Methylation-Haplotype1, 30000-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 30000-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: hESC_derived_mesodermal_cells_LSM14A_OE_rep2

institute: 浙江大学爱丁堡大学联合学院


title: hESC_CRISPRi_SPTAN1_rep1

institute: 浙江大学爱丁堡大学联合学院

value: hESC H1

value: human embryonic stem cells


title: Root sample from plants treated with the combination of calbio and bacteria under normal conditions, replicate 2

value: Combination of calbio and bacteria (BS+PGPB)

value: Normal conditions


title: hESC_derived_mesodermal_cells_rep1

institute: 浙江大学爱丁堡大学联合学院


title: F94417

description:
30809-OCT-1_Per-Site-Unphased-Methylation, 30809-OCT-1_Per-Read-Unphased-Methylation, 30809-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 30809-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 30809-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 30809-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F94412

description:
27981-FF-2_Per-Site-Unphased-Methylation, 27981-FF-2_Per-Read-Unphased-Methylation, 27981-FF-2_Per-Read-Phased-Methylation-Haplotype1, 27981-FF-2_Per-Site-Phased-Methylation-Haplotype1, 27981-FF-2_Per-Read-Phased-Methylation-Haplotype2 and 27981-FF-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: J1-AKO-2 cells

value: embryonic stem cell

value: AMPK KO


title: hESC_LSM14A_OE_rep2

institute: 浙江大学爱丁堡大学联合学院

value: Dox treat for 5 days


title: F94411

description:
27981-FF-1_Per-Site-Unphased-Methylation, 27981-FF-1_Per-Read-Unphased-Methylation, 27981-FF-1_Per-Read-Phased-Methylation-Haplotype1, 27981-FF-1_Per-Site-Phased-Methylation-Haplotype1, 27981-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 27981-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Root sample from plants treated with mycorrhizae under normal conditions, replicate 2

value: Root

value: Mycorrhizal fungus (AMF)


title: J1-AKO-1 cells


title: F94409

description:
27545-OCT-1_Per-Site-Unphased-Methylation, 27545-OCT-1_Per-Read-Unphased-Methylation, 27545-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 27545-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 27545-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 27545-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: hESC_LSM14A_OE_rep1

institute: 浙江大学爱丁堡大学联合学院

value: hESC H9


title: Leaf sample from plants treated with bacteria under salt stress, replicate 2

value: Leaf

value: Bacteria (PGPB)

value: Salt stress


title: hESC_rep2

institute: 浙江大学爱丁堡大学联合学院


title: F94408

description:
27026-OCT-1_Per-Site-Unphased-Methylation, 27026-OCT-1_Per-Read-Unphased-Methylation, 27026-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 27026-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 27026-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 27026-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Leaf sample from control plants under salt stress, replicate 2

value: Control


title: J1-WT-1 cells

value: WT


title: F94413

description:
29766-OCT-2_Per-Site-Unphased-Methylation, 29766-OCT-2_Per-Read-Unphased-Methylation, 29766-OCT-2_Per-Read-Phased-Methylation-Haplotype1, 29766-OCT-2_Per-Site-Phased-Methylation-Haplotype1, 29766-OCT-2_Per-Read-Phased-Methylation-Haplotype2 and 29766-OCT-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: GF4

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

country: Germany

institute: Philipps University Marburg

data_processing:
de-multiplexed fastq files were tested with FastQC. Over-represented sequences and adapters were trimmed with the Qiagen CLC Workbench Software v. 10.0.1.
Reads were mapped with the Qiagen CLC Workbench Software v. 10.0.1., using the GRCm39 mouse reference genome using default mapping parameters
Mapped total reads were analysed with the R package DeSeq2 v. 1.22.2 in R version 3.5.1, and the contrasts Lactate vs. Control and IPA vs. Control were calculated
The DeSeq2 output, namely the contrasts SPF vs. GF, SPF vs. CS and GF vs. CS , is provided as excel file processed_results.xlsx
Assembly: GRCm39
Supplementary files format and content: processed_results.xlsx, DeSeq2 contrast of  SPF vs. GF, SPF vs. CS and GF vs. CS

source_name: colon tissue

extract_protocol:
Colon tissue was homogenized with a blender and RNA was extracted via Trizol/Chloroform extraction, and silica based purification column (EXTRACTME TOTAL RNA KIT (Blirt))
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Colon tissue from DSS-treated (2.5%, 5 days) GF, CS, and SPF mice was isolated on day 7, and RNA was extracted and sequenced.

value: colon tissue

value: colon

value: wild type

value: no microbiom


title: Leaf sample from plants treated with the combination of calbio and bacteria under salt stress, replicate 2

value: Combination of calbio and bacteria (BS+PGPB)


title: hESC_rep1

institute: 浙江大学爱丁堡大学联合学院

value: human embryonic stem cells


title: hESC_TGFβi_rep3

institute: 浙江大学爱丁堡大学联合学院

value: hESC H1

value: TGFbi treat for 2 days


title: hESC_TGFβi_rep2

institute: 浙江大学爱丁堡大学联合学院


title: F94406

description:
25901-OCT-1_Per-Site-Unphased-Methylation, 25901-OCT-1_Per-Read-Unphased-Methylation, 25901-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 25901-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 25901-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 25901-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Root sample from plants treated with Calbio under normal conditions, replicate 2

value: Calbio(BS)

value: Normal conditions


title: Leaf sample from plants treated with Calbio under salt stress, replicate 2


title: F94405

description:
25589-FF-1_Per-Site-Unphased-Methylation, 25589-FF-1_Per-Read-Unphased-Methylation, 25589-FF-1_Per-Read-Phased-Methylation-Haplotype1, 25589-FF-1_Per-Site-Phased-Methylation-Haplotype1, 25589-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 25589-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Leaf sample from plants treated with the combination of calbio and mycorrhiza under salt stress, replicate 2

value: Combination of calbio and mycorrhiza (BS+AMF)


title: GF1


title: GF2


title: F94403

description:
23401-OCT-1_Per-Site-Unphased-Methylation, 23401-OCT-1_Per-Read-Unphased-Methylation, 23401-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 23401-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 23401-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 23401-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: hESC_TGFβi_rep1

institute: 浙江大学爱丁堡大学联合学院


title: Leaf sample from plants treated with mycorrhizae under salt stress, replicate 2

value: Mycorrhizal fungus (AMF)


title: hESC_control_rep3

institute: 浙江大学爱丁堡大学联合学院


title: J1-WT-2 cells

value: embryonic stem cell


title: hESC_control_rep2

institute: 浙江大学爱丁堡大学联合学院


title: CS4

value: C. sporogenes microbiom


title: CS1


title: hESC_control_rep1

institute: 浙江大学爱丁堡大学联合学院


title: CS2


title: F94407

description:
25990-OCT-1_Per-Site-Unphased-Methylation, 25990-OCT-1_Per-Read-Unphased-Methylation, 25990-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 25990-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 25990-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 25990-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Leaf sample from control plants under normal conditions, replicate 2

value: Leaf


title: F94400

description:
18153-FF-1_Per-Site-Unphased-Methylation, 18153-FF-1_Per-Read-Unphased-Methylation, 18153-FF-1_Per-Read-Phased-Methylation-Haplotype1, 18153-FF-1_Per-Site-Phased-Methylation-Haplotype1, 18153-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 18153-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Leaf sample from plants treated with the combination of calbio and bacteria under normal conditions, replicate 2


title: F94401

description:
23315-OCT-2_Per-Site-Unphased-Methylation, 23315-OCT-2_Per-Read-Unphased-Methylation, 23315-OCT-2_Per-Read-Phased-Methylation-Haplotype1, 23315-OCT-2_Per-Site-Phased-Methylation-Haplotype1, 23315-OCT-2_Per-Read-Phased-Methylation-Haplotype2 and 23315-OCT-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F94399

description:
17827-OCT-1_Per-Site-Unphased-Methylation, 17827-OCT-1_Per-Read-Unphased-Methylation, 17827-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 17827-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 17827-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 17827-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Leaf sample from plants treated with the combination of calbio and mycorrhiza under normal conditions, replicate 2


title: 293T_P_body_rep2

institute: 浙江大学爱丁堡大学联合学院

library_source: other

molecule: other

value: Dox treat for 5 days


title: SPF2

value: SPF microbiom


title: LMR3_control_4

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

data_processing:
The FASTQ read files were first trimmed and cleaned using fastp/0.23.2 and assessed for quality using FastQC/0.11.8.
The reads were then aligned using HISAT2/2.2.1.0 with an index created using the GRCm38.p6 genome.
The trimmed reads were aligned with default settings of HISAT2/2.2.1.0 and quantified using featureCounts (subread/2.0) with mouse GENCODE vm24.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include TPM (Transcripts Per Million) for each sample

source_name: Liver

extract_protocol:
The RNAs that have been extracted by Trizol were purified using the MagMAX RNA extraction kit (Thermo Fisher Scientific, Cat.AM1830).
RNA libraries were prepared for sequencing using standard Illumina kit and protocols; strand-specific

value: Liver


title: F81633

description:
34115-OCT-1_Per-Site-Unphased-Methylation, 34115-OCT-1_Per-Read-Unphased-Methylation, 34115-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 34115-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 34115-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 34115-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Leaf sample from plants treated with Calbio under normal conditions, replicate 2


title: SPF4

value: colon tissue

value: colon


title: 293T_P_body_rep1

institute: 浙江大学爱丁堡大学联合学院


title: F94402

description:
23315-FF-1_Per-Site-Unphased-Methylation, 23315-FF-1_Per-Read-Unphased-Methylation, 23315-FF-1_Per-Read-Phased-Methylation-Haplotype1, 23315-FF-1_Per-Site-Phased-Methylation-Haplotype1, 23315-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 23315-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F48645

description:
42120-OCT-2_Per-Site-Unphased-Methylation, 42120-OCT-2_Per-Read-Unphased-Methylation, 42120-OCT-2_Per-Read-Phased-Methylation-Haplotype1, 42120-OCT-2_Per-Site-Phased-Methylation-Haplotype1, 42120-OCT-2_Per-Read-Phased-Methylation-Haplotype2 and 42120-OCT-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: SPF1

value: wild type


title: 293T_cytoplasm_rep2

institute: 浙江大学爱丁堡大学联合学院

molecule: cytoplasmic RNA


title: 293T_cytoplasm_rep1

institute: 浙江大学爱丁堡大学联合学院


title: F47396

description:
20800-FF-1_Per-Site-Unphased-Methylation, 20800-FF-1_Per-Read-Unphased-Methylation, 20800-FF-1_Per-Read-Phased-Methylation-Haplotype1, 20800-FF-1_Per-Site-Phased-Methylation-Haplotype1, 20800-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 20800-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Root sample from plants treated with bacteria under salt stress, replicate 1

value: Root

value: Bacteria (PGPB)

value: Salt stress


title: AntiCD40_4h_DZ_4

city: Rehovot

first: Sharon

last: Kagan Ben Tikva

state: Israel

address: 234 Herzl street

country: Israel

institute: Weizmann Institute

data_processing:
Reads were trimmed using Cutadapt
Reads were aligned to the genome using STAR
Quantification was done using htseq-count as previously described in R. Kohen, BMC Bioinformatics, 2019.
Assembly: mm10
Supplementary files format and content: Excel file with Deseq2 output

source_name: Lymph node

extract_protocol:
mRNA was extracted from sorted cells using mRNA direct kit (Invitrogen) and mRNA from each sample was barcoded during reverse transcription and pooled.
Libraries were prepared using a bulk adaptation of the previously described protocol (Keren-Shaul et al. Nat. Protoc, 2019 and Jaitin et al. Science, 2014).Following Agencourt Ampure XP bead cleanup (Beckman Coulter), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR.  Libraries were quantified by Qubit and TapeStation as well as by qPCR for the ACTB gene as previously described. Sequencing was done using a Nextseq 75 cycle high output kit (Illumina; paired end sequencing).

value: Lymph node

value: Germinal center dark zone B cells

value: WT

tag: group

value: Anti CD40


title: F118228

description:
231878-OCT-1_Per-Site-Unphased-Methylation, 231878-OCT-1_Per-Read-Unphased-Methylation, 231878-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 231878-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 231878-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 231878-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: AntiCD40_4h_DZ_3


title: Leaf sample from plants treated with bacteria under normal conditions, replicate 2

value: Normal conditions


title: Root sample from control plants under salt stress, replicate 1

value: Control


title: hESC_derived_mesodermal_cells_P_body_rep2

institute: 浙江大学爱丁堡大学联合学院

value: hESC H9

value: hESC derived mesodermal cells

value: Dox treat for 5 days, mesoderm induction


title: hESC_derived_mesodermal_cells_cytoplasm_rep2

institute: 浙江大学爱丁堡大学联合学院


title: Root sample from plants treated with the combination of calbio and bacteria under salt stress, replicate 1

value: Combination of calbio and bacteria (BS+PGPB)


title: AntiCD40_4h_DZ_1


title: F117325

description:
27504-PB_Per-Site-Unphased-Methylation, 27504-PB_Per-Read-Unphased-Methylation, 27504-PB_Per-Read-Phased-Methylation-Haplotype1, 27504-PB_Per-Site-Phased-Methylation-Haplotype1, 27504-PB_Per-Read-Phased-Methylation-Haplotype2 and 27504-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F116452

description:
25603-OCT-1_Per-Site-Unphased-Methylation, 25603-OCT-1_Per-Read-Unphased-Methylation, 25603-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 25603-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 25603-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 25603-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: hESC_derived_mesodermal_cells_P_body_rep1

institute: 浙江大学爱丁堡大学联合学院


title: hESC_derived_mesodermal_cells_cytoplasm_rep1

institute: 浙江大学爱丁堡大学联合学院


title: IsoCtrl_4h_DZ_4

value: Isotype control


title: hESC_P_body_rep2

institute: 浙江大学爱丁堡大学联合学院

value: human embryonic stem cells

value: Dox treat for 5 days


title: IsoCtrl_4h_DZ_3


title: Root sample from plants treated with mycorrhizae under salt stress, replicate 1

value: Mycorrhizal fungus (AMF)


title: F116451

description:
65474-OCT-1_Per-Site-Unphased-Methylation, 65474-OCT-1_Per-Read-Unphased-Methylation, 65474-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 65474-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 65474-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 65474-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F116450

description:
30811-PB_Per-Site-Unphased-Methylation, 30811-PB_Per-Read-Unphased-Methylation, 30811-PB_Per-Read-Phased-Methylation-Haplotype1, 30811-PB_Per-Site-Phased-Methylation-Haplotype1, 30811-PB_Per-Read-Phased-Methylation-Haplotype2 and 30811-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Leaf sample from plants treated with mycorrhizae under normal conditions, replicate 2

value: Leaf


title: IsoCtrl_4h_DZ_2


title: hESC_cytoplasm_rep2

institute: 浙江大学爱丁堡大学联合学院


title: IsoCtrl_4h_DZ_1


title: AntiCD40_4h_DZ_2


title: Root sample from control plants under normal conditions, replicate 1

value: Root


title: Root sample from plants treated with bacteria under normal conditions, replicate 1

value: Bacteria (PGPB)


title: Root sample from plants treated with Calbio under salt stress, replicate 1

value: Calbio(BS)

value: Salt stress


title: F116448

description:
23189-PB_Per-Site-Unphased-Methylation, 23189-PB_Per-Read-Unphased-Methylation, 23189-PB_Per-Read-Phased-Methylation-Haplotype1, 23189-PB_Per-Site-Phased-Methylation-Haplotype1, 23189-PB_Per-Read-Phased-Methylation-Haplotype2 and 23189-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: AntiCD40_4h_LZ_4

value: Lymph node

value: Germinal center light zone B cells

value: WT


title: Root sample from plants treated with the combination of calbio and bacteria under normal conditions, replicate 1

value: Normal conditions


title: F116445

description:
25719-OCT-1_Per-Site-Unphased-Methylation, 25719-OCT-1_Per-Read-Unphased-Methylation, 25719-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 25719-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 25719-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 25719-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: AntiCD40_4h_LZ_3

value: Anti CD40


title: hESC_cytoplasm_rep1

institute: 浙江大学爱丁堡大学联合学院

value: hESC H9


title: F116444

description:
39883-OCT-1_Per-Site-Unphased-Methylation, 39883-OCT-1_Per-Read-Unphased-Methylation, 39883-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 39883-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 39883-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 39883-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F116449

description:
37013-PB_Per-Site-Unphased-Methylation, 37013-PB_Per-Read-Unphased-Methylation, 37013-PB_Per-Read-Phased-Methylation-Haplotype1, 37013-PB_Per-Site-Phased-Methylation-Haplotype1, 37013-PB_Per-Read-Phased-Methylation-Haplotype2 and 37013-PB_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: PML-RARA-2

city: Beijing

first: Feng

last: Wang

address: 1 Tian Tan Xi Li

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data).
Bowtie v1.0.1  was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 V2.1.0.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq V0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq2 V1.20.0  was used for differential gene expression analysis between two samples with  biological replicates.
Assembly: Homo_sapiens.GRCh38.94.chr
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: mobilized peripheral blood

growth_protocol: The hCD34+ cells were cultured with StemSpanTM SFEM IImedium supplemented with 2mM Glutamine, 100 units/ml Penicillin/Streptomycin, 100 ng/mL for human SCF, 100 ng/mL human TPO, 20 ng/mL human GM-CSF, 100 ng/mL human Flt3L, 50 ng/mL human IL-6, and 50 ng/mL human IL-3.

extract_protocol:
cells were collected , flash frozen on dry ice, and the total RNA was extracted from hCD34+ cells with or without RARG fusions overexpression by using RNA-QuickTM MicroPrep Kit (ZYMO RESEARCH, R1055).
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA).

treatment_protocol: Human CD34+ cells infected with control, RARG fusions or PML-RARA retrovirus for 48 hours and then GFP positive cells were sorted and cultured for RNA-seq.

value: mobilized peripheral blood

value: primary hCD34+ cells

value: human hemopoietic stemcells

value: PML-RARA


title: PML-RARA-1


title: AntiCD40_4h_LZ_2


title: Root sample from plants treated with the combination of calbio and mycorrhiza under normal conditions, replicate 1

value: Combination of calbio and mycorrhiza (BS+AMF)


title: Root sample from plants treated with the combination of calbio and mycorrhiza under salt stress, replicate 1


title: F112965

description:
25535-OCT-1_Per-Site-Unphased-Methylation, 25535-OCT-1_Per-Read-Unphased-Methylation, 25535-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 25535-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 25535-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 25535-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Root sample from plants treated with Calbio under normal conditions, replicate 1


title: AntiCD40_4h_LZ_1


title: hESC_P_body_rep1

institute: 浙江大学爱丁堡大学联合学院

value: human embryonic stem cells

value: Dox treat for 5 days


title: F112964

description:
25535-FF-1_Per-Site-Unphased-Methylation, 25535-FF-1_Per-Read-Unphased-Methylation, 25535-FF-1_Per-Read-Phased-Methylation-Haplotype1, 25535-FF-1_Per-Site-Phased-Methylation-Haplotype1, 25535-FF-1_Per-Read-Phased-Methylation-Haplotype2 and 25535-FF-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: IsoCtrl_4h_LZ_4

value: Isotype control


title: Leaf sample from plants treated with bacteria under salt stress, replicate 1

value: Leaf

value: Bacteria (PGPB)


title: Root sample from plants treated with mycorrhizae under normal conditions, replicate 1

value: Root

value: Mycorrhizal fungus (AMF)


title: F112963

description:
38505-OCT-2_Per-Site-Unphased-Methylation, 38505-OCT-2_Per-Read-Unphased-Methylation, 38505-OCT-2_Per-Read-Phased-Methylation-Haplotype1, 38505-OCT-2_Per-Site-Phased-Methylation-Haplotype1, 38505-OCT-2_Per-Read-Phased-Methylation-Haplotype2 and 38505-OCT-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: IsoCtrl_4h_LZ_3

value: Lymph node

value: Germinal center light zone B cells


title: Leaf sample from control plants under salt stress, replicate 1

value: Control

value: Salt stress


title: NUP98-RARG-1


title: F112962

description:
38505-OCT-1_Per-Site-Unphased-Methylation, 38505-OCT-1_Per-Read-Unphased-Methylation, 38505-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 38505-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 38505-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 38505-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: IsoCtrl_4h_LZ_2

value: WT


title: F112961

description:
34252-OCT-2_Per-Site-Unphased-Methylation, 34252-OCT-2_Per-Read-Unphased-Methylation, 34252-OCT-2_Per-Read-Phased-Methylation-Haplotype1, 34252-OCT-2_Per-Site-Phased-Methylation-Haplotype1, 34252-OCT-2_Per-Read-Phased-Methylation-Haplotype2 and 34252-OCT-2_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: Leaf sample from plants treated with the combination of calbio and mycorrhiza under salt stress, replicate 1


title: PML-RARG-2

value: mobilized peripheral blood

value: PML-RARG


title: IsoCtrl_4h_LZ_1


title: F112959

description:
43133-OCT-1_Per-Site-Unphased-Methylation, 43133-OCT-1_Per-Read-Unphased-Methylation, 43133-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 43133-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 43133-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 43133-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: F112958

description:
18650-OCT-1_Per-Site-Unphased-Methylation, 18650-OCT-1_Per-Read-Unphased-Methylation, 18650-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 18650-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 18650-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 18650-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: NUP98-RARG-2

value: primary hCD34+ cells

value: human hemopoietic stemcells


title: WI-38-hTERT, 40°C, RNA-seq, rep2

city: Kyoto-shi

first: Yoshikazu

last: Nagagaki

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

country: Japan

institute: Kyoto University

description:
40C_RNA-seq_rep2
2019_005A_40C_RNA-seq_rep2

data_processing:
mapping: STAR v2.7.0d
Expression estimation: RSEM v1.3.1
DEG analysis: edgeR
Assembly: UCSC hg19
Supplementary files format and content: excel file includes CPM values for each sample

growth_protocol: Cells were grown at 37°C and 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) (Nissui) supplemented with 10% FBS (GIBCO), L-glutamine, and antibiotics.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy kit following the manufacture’s protocol.1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat following manufacture's protocol.

treatment_protocol: Cells were seeded at a density of 1.1 × 104 or 1.7 × 104 cells/cm2 in 35 mm dishes for immortalized cells and primary cells, respectively, and incubated for 24 hr at 37°C before heat shock treatment. For priming stress treatment, culture media was replaced with fresh media pre-heated at 40°C, and cells were cultured in an incubator at 40°C (± 0.5°C) and 5% CO2 for 2 hr.

value: immortalized human fibroblast cells

value: heat stress treatment (40°C, 2 hours)


title: PML-RARG-1


title: HNRNPC-RARG-2

value: HNRNPC-RARG


title: Leaf sample from plants treated with the combination of calbio and bacteria under salt stress, replicate 1

value: Combination of calbio and bacteria (BS+PGPB)


title: F112957

description:
30498-OCT-1_Per-Site-Unphased-Methylation, 30498-OCT-1_Per-Read-Unphased-Methylation, 30498-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 30498-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 30498-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 30498-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: WI-38-hTERT, 40°C, RNA-seq, rep1

description:
40C_RNA-seq_rep1
2019_005A_40C_RNA-seq_rep1


title: NPM1-RARG-2

value: NPM-RARG


title: HNRNPC-RARG-1


title: Leaf sample from plants treated with mycorrhizae under salt stress, replicate 1

value: Leaf


title: Leaf sample from plants treated with Calbio under salt stress, replicate 1

value: Calbio(BS)


title: NPM1-RARG-1


title: Leaf sample from plants treated with bacteria under normal conditions, replicate 1

value: Bacteria (PGPB)

value: Normal conditions


title: F112956

description:
19843-OCT-1_Per-Site-Unphased-Methylation, 19843-OCT-1_Per-Read-Unphased-Methylation, 19843-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 19843-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 19843-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 19843-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: CPSF6-RARG-2


title: Leaf sample from control plants under normal conditions, replicate 1


title: WI-38-hTERT, 37°C, RNA-seq, rep1

description:
37C_RNA-seq_rep1
2019_005A_37C_RNA-seq_rep1

value: control


title: F112955

description:
18568-OCT-1_Per-Site-Unphased-Methylation, 18568-OCT-1_Per-Read-Unphased-Methylation, 18568-OCT-1_Per-Read-Phased-Methylation-Haplotype1, 18568-OCT-1_Per-Site-Phased-Methylation-Haplotype1, 18568-OCT-1_Per-Read-Phased-Methylation-Haplotype2 and 18568-OCT-1_Per-Site-Phased-Methylation-Haplotype2
Per-Site-Unphased-Methylation, Per-Read-Unphased-Methylation, Per-Read-Phased-Methylation-Haplotype1, Per-Site-Phased-Methylation-Haplotype1, Per-Read-Phased-Methylation-Haplotype2 and Per-Site-Phased-Methylation-Haplotype2


title: WI-38-hTERT, 40°C, input

data_processing:
The overall read quality was checked using FastQC v0.11.3.
DROMPA2 v2.6.4 software with its default settings (p < 0.001 and FDR < 0.01 for ChIP/Input enrichment for each 100-bp bin) was used to call peaks representing enriched binding sites.
A total of approximately 45 million sequenced reads were mapped to the human genome (UCSC, hg19) using Bowtie v1.1.1 alignment software, allowing only unique reads mapped to a single location with no more than two mismatches.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: lung

extract_protocol:
Cells were fixed with 1% formaldehyde for 8 min at room temperature and quenched with 125 mM glycine for 3 min. After cell lysis, chromatin was sonicated using a Branson Sonifier 250 at 4°C to generate DNA fragments of 100 – 500 bp.
ChIP-seq libraries were prepared from ChIP-DNA or input DNA using a NEBNext ChIP-seq Library kit (New England Biolabs) according to the manufacturer’s instructions.

treatment_protocol: For heat stress treatment, cells were cultured in an incubator at 40°C (± 0.5°C) and 5% CO2 for 2 hours. Control cells were cultured in an incubator at 37°C (± 0.5°C) and 5% CO2 for 2 hours.

value: lung