title: Periferal blood mother [PL2738_Mother]


title: Periferal blood father [PL281_Father]

status: Public on Oct 05 2023

type: genomic

city: Maastricht

first: Rick

last: Essers

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Centre (MUMC+)

hyb_protocol: According to the manual of Infinium II Assay (Illumina, USA).

scan_protocol: The scanning of the bead-chips was performed on an iScan, using the iScan Control software (Illumina, USA)

data_processing:
The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. We subsequently fed these data into haplarithmisis (Zamani Esteki et al. 2019, Nature medicine).
Image data was analyzed using Genomestudio with genotyping module (Illumina). Subsequently, genotype calls (AA,AB,BB,or NC (no call), SNP B-allele frequency values, LogR.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Periferal blood

label_protocol: The samples were not labelled before the hybridization. The staining is based on post-hybridization Cy5/Cy3 labelling by extension, according to the manual of Infinium II Assay (Illumina, USA).

growth_protocol: The tissues were chopped with scissors to small fragments, and long-term cultures were set up in 25 cm2 flasks with 5 mL of DMEM/F12 (1:1) medium (Gibco) supplemented with 20% fetal bovine serum (HyClone), 1% MEM NEAA solution (Gibco), 1% Pen-Strep (Gibco). Tissues were incubated at 37°C with once-weekly medium renewal.

extract_protocol: Genomic DNA was extracted using a standard phenol-chloroform extraction method that allows for the isolation of up to 900 ng DNA from the tissues. Likewise, genomic DNA was extracted from peripheral blood of parents using the standard phenol-chloroform method.

treatment_protocol: The two tissues were mechanically separated and the yield of chorionic cytotrophoblast cells was increased by maceration of chorionic villi under an Axiovert 200 inverted microscope (Carl Zeiss, Germany) and treatment with 70% acetic acid for 3-5 min followed by three washes of the obtained cell suspension with PBS according to a modified protocol (Simoni, G. et al. Efficient direct chromosome analyses and enzyme determinations from chorionic villi samples in the first trimester of pregnancy. Human Genetics 63, 349-357 (1983)).

tag: gender

value: Male

tag: family member

value: Father

tag: tissue

value: Periferal blood


title: Extraembryonic mesoderm fetal biopsy [PL2738_EM3718]

source_name: Extraembryonic mesoderm

value: Product of conception

value: Extraembryonic mesoderm


title: Extraembryonic mesoderm fetal biopsy [PL445_EM1431]


title: Periferal blood father [PL383_Father]


title: Periferal blood father [PL2734_Father]


title: Extraembryonic mesoderm fetal biopsy [PL383_EM1316]

value: Female


title: Chorionic villi fetal biopsy [PL379_CV1311]

source_name: Chorionic villi

value: ND

value: Chorionic villi


title: Chorionic villi fetal biopsy [PL384_CV1332]


title: Periferal blood mother [PL290_Mother]

value: Mother


title: Extraembryonic mesoderm fetal biopsy [PL2734_EM3714]


title: Periferal blood father [PL290_Father]


title: Periferal blood mother [PL2733_Mother]


title: Chorionic villi fetal biopsy [PL2734_CV3714]


title: Extraembryonic mesoderm fetal biopsy [PL290_EM1136]


title: Chorionic villi fetal biopsy [PL281_CV1216]


title: Chorionic villi fetal biopsy [PL2733_CV3711]


title: Periferal blood father [PL2730_Father]


title: Periferal blood father [PL2728_Father]


title: Chorionic villi fetal biopsy [PL2728_CV3666]


title: Periferal blood father [PL2738_Father]


title: Periferal blood mother [PL278_Mother]


title: Chorionic villi fetal biopsy [PL2738_CV3718]


title: Extraembryonic mesoderm fetal biopsy [PL2728_EM3666]


title: Periferal blood father [PL2727_Father]


title: Extraembryonic mesoderm fetal biopsy [PL2727_EM3708]


title: Periferal blood mother [PL2734_Mother]


title: Chorionic villi fetal biopsy [PL2727_CV3708]


title: Periferal blood father [PL2733_Father]


title: Periferal blood mother [PL2730_Mother]


title: Extraembryonic mesoderm fetal biopsy [PL2733_EM3711]


title: Extraembryonic mesoderm fetal biopsy [PL2726_EM3707]


title: Periferal blood mother [PL2717_Mother]


title: Periferal blood father [PL2726_Father]


title: Extraembryonic mesoderm fetal biopsy [PL2730_EM3713]


title: Periferal blood father [PL2717_Father]


title: Chorionic villi fetal biopsy [PL2730_CV3713]


title: Extraembryonic mesoderm fetal biopsy [PL2717_EM3704]


title: Periferal blood mother [PL2728_Mother]


title: Extraembryonic mesoderm fetal biopsy [PL2712_EM3700]


title: Periferal blood mother [PL2727_Mother]


title: Periferal blood mother [PL2726_Mother]


title: Chorionic villi fetal biopsy [PL2726_CV3707]


title: Periferal blood mother [PL271_Mother]


title: Extraembryonic mesoderm fetal biopsy [PL271_EM1219]


title: Chorionic villi fetal biopsy [PL2711_CV3699]


title: Chorionic villi fetal biopsy [PL2717_CV3704]


title: Periferal blood father [PL2712_Father]


title: Chorionic villi fetal biopsy [PL271_CV1219]


title: Extraembryonic mesoderm fetal biopsy [PL2711_EM3699]


title: Periferal blood father [PL271_Father]


title: Periferal blood mother [PL2708_Mother]


title: Periferal blood mother [PL2712_Mother]


title: Periferal blood father [PL2708_Father]


title: Extraembryonic mesoderm fetal biopsy [PL2706_EM3691]


title: Extraembryonic mesoderm fetal biopsy [PL2708_EM3696]


title: Periferal blood father [PL2711_Father]


title: Extraembryonic mesoderm fetal biopsy [PL2701_EM3685]


title: Periferal blood mother [PL2706_Mother]


title: Chorionic villi fetal biopsy [PL2682_CV3669]


title: Chorionic villi fetal biopsy [PL2706_CV3691]


title: Periferal blood mother [PL2678_Mother]


title: Periferal blood father [PL2706_Father]


title: Periferal blood mother [PL2702_Mother]


title: Periferal blood father [PL2678_Father]


title: Periferal blood father [PL2702_Father]


title: Chorionic villi fetal biopsy [PL2712_CV3700]


title: Extraembryonic mesoderm fetal biopsy [PL2702_EM3686]


title: Periferal blood mother [PL2711_Mother]


title: Chorionic villi fetal biopsy [PL2666_CV3656]


title: Periferal blood father [PL2701_Father]


title: Periferal blood mother [PL2701_Mother]


title: Chorionic villi fetal biopsy [PL2701_CV3685]


title: Chorionic villi fetal biopsy [PL2702_CV3686]


title: Periferal blood mother [PL2682_Mother]


title: Extraembryonic mesoderm fetal biopsy [PL2662_EM3655]


title: Periferal blood father [PL2682_Father]


title: Extraembryonic mesoderm fetal biopsy [PL2682_EM3669]


title: Chorionic villi fetal biopsy [PL2678_CV3661]


title: Chorionic villi fetal biopsy [PL2708_CV3696]


title: Extraembryonic mesoderm fetal biopsy [PL2678_EM3661]


title: Periferal blood mother [PL2666_Mother]


title: Periferal blood father [PL2660_Father]


title: Periferal blood mother [PL2653_Mother]


title: Extraembryonic mesoderm fetal biopsy [PL2653_EM3643]


title: Periferal blood father [PL2666_Father]


title: Periferal blood mother [PL2662_Mother]


title: Periferal blood father [PL2662_Father]


title: Extraembryonic mesoderm fetal biopsy [PL2666_EM3656]


title: Periferal blood mother [PL2660_Mother]


title: Chorionic villi fetal biopsy [PL2653_CV3643]


title: Periferal blood mother [PL2652_Mother]


title: Periferal blood mother [PL2650_Mother]


title: Chorionic villi fetal biopsy [PL2660_CV3653]


title: Chorionic villi fetal biopsy [PL2662_CV3655]


title: Extraembryonic mesoderm fetal biopsy [PL2650_EM3642]


title: Periferal blood father [PL2653_Father]


title: Periferal blood father [PL2631_Father]


title: Periferal blood father [PL2652_Father]


title: Extraembryonic mesoderm fetal biopsy [PL2652_EM3644]


title: Periferal blood mother [PL2621_Mother]


title: Chorionic villi fetal biopsy [PL2650_CV3642]


title: Chorionic villi fetal biopsy [PL2652_CV3644]


title: Periferal blood mother [PL2631_Mother]


title: Extraembryonic mesoderm fetal biopsy [PL2621_EM3629]


title: Extraembryonic mesoderm fetal biopsy [PL2631_EM3632]


title: Chorionic villi fetal biopsy [PL2621_CV3629]


title: Periferal blood mother [PL2617_Mother]


title: Periferal blood father [PL2621_Father]


title: Chorionic villi fetal biopsy [PL2631_CV3632]


title: Extraembryonic mesoderm fetal biopsy [PL2660_EM3653]


title: Periferal blood father [PL2617_Father]


title: Chorionic villi fetal biopsy [PL2617_CV3627]


title: Extraembryonic mesoderm fetal biopsy [PL2617_EM3627]


title: Extraembryonic mesoderm fetal biopsy [PL2597_EM3619]


title: Periferal blood father [PL2597_Father]


title: Chorionic villi fetal biopsy [PL2597_CV3619]


title: Periferal blood mother [PL2597_Mother]


title: LW13 gradient syringe, below (expt3)

type: SRA

city: Salt Lake City

first: Aaron

middle: W

last: Puri

state: UT

address: 1390 Presidents Circle

country: USA

institute: University of Utah

description:
counts.csv
analysis.csv

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adapter sequences/low quality using Trimmomatic v.036 (KBase)
Trimmed sequence reads were mapped to the Methylomonas sp. LW13 genome using HISAT2 v2.1.0 (KBase)
Transcripts were assembled using StringTie v2.1.5 (KBase)
Differential expression matrix was created wusing DESeq2 v1.20.0 (KBase)
Assembly: CP033381.1
Supplementary files format and content: file contains FPKM values of each segment from each independent experiment
Supplementary files format and content: file contains DESeq2 expression matrix from pairwise agarose segment comparisons

molecule: total RNA

organism: Methylomonas sp. LW13

source_name: environmental isolate

growth_protocol: For each 10 mL syringe, 1 mL of LW13 cells was mixed with 5 mL NMS1 and 4 mL molten agarose (0.5% w/v, cooled to 55°C). The mixture was poured to the 8 mL marking of a 10 mL plastic Luer-Lok tip syringe fitted with a sterile PTFE filter tip. Solidified syringes were capped with a sterile 20 mm rubber butyl stopper and inlet and outlet needles were pierced through the rubber stopper, and 20 mL of 100% CH4 was flushed through the syringe headspace. Syringes were flushed daily with methane and incubated with the PTFE filter pointing up at 18°C.

extract_protocol:
Samples were frozen at -80°C until RNA extraction. Thawed aliquots were centrifuged and 600 µL of pre-warmed CTAB extraction buffer was added after removing supernatant. The CTAB buffer consisted of 2% CTAB, 2% polyvinylpyrrolidone 40, 2 M sodium chloride, 100 mM Tris-HCl (pH 8.0), and 20 mM EDTA. Zirconia glass beads were added, and samples were homogenized for 3 minutes at 30 Hz/sec using a bead beater. Samples were extracted twice with 600 µL chloroform-isoamyl alcohol (24:1), and the aqueous phase was mixed with isopropanol and incubated overnight at -20°C. Precipitates were centrifuged for 30 minutes at 16,100 x g at 4°C for 30 minutes and pellets were washed twice with cold 75% ethanol made with DEPC water. Air dried pellets were dissolved in 100 uL DEPC water and treated with DNase I (Ambion) at 37°C for 30 minutes. The DNase I was inactivated by extraction with three volumes of acid phenol:chloroform:IAA (125:24:1, pH 4.5) before pooling RNA from the same segment across all syringes in an overnight precipitation at -20°C in 1 volume isopropanol and 0.8 M LiCl. Precipitates were washed twice with cold 70% ethanol made with DEPC water, air dried, and resuspended in 50 uL DEPC water. Samples were re-purified using RNA Clean & Concentrator-5 (Zymo Research) to remove small RNAs.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep with rRNA Depletion kit

treatment_protocol: Agarose segments (2 mL) positioned above, at, and below the EPS band were extruded from each syringe through a 23-gauge needle into microcentrifuge tubes.

tag: cell line

value: environmental isolate

tag: genotype

value: WT

tag: treatment

value: below


title: LW13 gradient syringe, band (expt3)

description:
counts.csv
analysis.csv

value: band


title: LW13 gradient syringe, above (expt3)

description:
counts.csv
analysis.csv

value: above


title: Periferal blood mother [PL2596_Mother]


title: Periferal blood father [PL2596_Father]


title: Periferal blood mother [PL250_Mother]


title: Extraembryonic mesoderm fetal biopsy [PL2596_EM3616]


title: LW13 gradient syringe, below (expt2)

description:
counts.csv
analysis.csv


title: Chorionic villi fetal biopsy [PL2596_CV3616]


title: LW13 gradient syringe, above (expt1)

description:
counts.csv
analysis.csv


title: LW13 gradient syringe, below (expt1)

description:
counts.csv
analysis.csv


title: Chorionic villi fetal biopsy [PL250_CV816]


title: Extraembryonic mesoderm fetal biopsy [PL246_EM1048]


title: P14, replicate1, snRNA-seq

city: New York

first: Wei

last: Wang

state: New York

address: 1230 York Ave.

department: Bioinformatics Resource Center

institute: The Rockefeller University

description: 10X genomics

library_source: transcriptomic single cell

data_processing:
Sequenced reads were mapped to lab maintained ant genome assembly using cellranger version 7.0.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Ooceraea biroi

source_name: Antennal Clubs

extract_protocol:
Custom single nuclei extraction protocol for insect tissues.
10X Genomics 3' v3.1 kit

tag: developmental stage

value: Pupae aged 14 days

tag: cell type

value: Antennal Clubs


title: P14, replicate2, snRNA-seq

description: 10X genomics


title: Periferal blood father [PL2650_Father]


title: LW13 gradient syringe, above (expt2)

description:
counts.csv
analysis.csv


title: Periferal blood father [PL2452_Father]


title: Extraembryonic mesoderm fetal biopsy [PL250_EM816]


title: Periferal blood father [PL250_Father]


title: LW13 gradient syringe, band (expt2)

description:
counts.csv
analysis.csv


title: MGYPDa06_dsDNA_rep2

city: Ipswich

first: Zhiyi

last: Sun

state: MASSACHUSETTS

address: 240 County Road

department: Research

institute: New England Biolabs

library_source: genomic

data_processing:
basecalls were performed using Illumina RTA software and fastq files were generated from the BCL files using Picard’s basecallstofastq.
Reads were trimmed for adaptor sequence and low quality bases at the 3' end using the trim_galore program.
The trimmed read sequences were C to T converted and were then mapped to the a composite reference including E.coli and all the control sequences using the Bismark program with the default Bowtie2 settings.
The first 5 bp at the 5’ end of R2 reads were removed to reduce end-repair errors and aligned read pairs that shared the same alignment ends were regarded as PCR duplicates and were discarded.
The numbers of Ts (converted not methylated) and Cs (unconverted modified) of each covered cytosine position were then calculated from the remaining good quality alignments using Bismark methylation extractor.
Assembly: E. coli C2566, human hg38
Supplementary files format and content: tab-delimited text files include genomic coordinates, number of Cs and number of Ts and sequence contexts of covered cytosines.
Library strategy: SEM-seq

organism: Escherichia coli

source_name: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, and phage T4147

extract_protocol:
E. coli C2566 genomic DNA was purified using Monarch Genomic DNA Purification Kit (NEB Ipswich, MA), GM12878 genomic DNA was obtained from Coriell Cell Repositories (Camden, NJ).
Input DNA was sheared to 300 bp using the Covaris S2 instrument. Sheared material was transferred to a PCR strip tube to begin library construction. NEBNext DNA Ultra II Reagents (NEB, Ipswich, MA) were used according to the manufacturer’s instructions for end repair, A-tailing, and adaptor ligation. The custom made Pyrollo-dC adaptor (NEB Organic Synthesis Division, Ipswich MA), where all dCs are replaced with Pyrollo-dC, was used. The ligated samples were purified using NEBNext Sample Purification Beads  according to the manufacturer’s instructions. For ssDNA libraries, prior to deamination the DNA was denatured by heating at 90oC for 10 minutes followed by cooling for 2 minutes on ice. The DNA was then deaminated using 1 µL of PURExpress (NEB, Ipswich, MA) synthesized deaminase protein following manufacturer's recommendations for 1 hour at 37oC. Then 1 µL of Thermolabile Proteinase K (NEB, Ipswich, MA) was added and incubated for 30 min at 37oC followed by 10 min at 60oC. Then the library was amplified using NEBNext Q5U Master Mix (NEB, Ipswich, MA, USA). Paired-end sequencing of 150 cycles (2 x 75 bp) was performed for all the sequencing runs.
DNA sequencing of deaminated double-stranded and single-stranded DNA


title: LW13 gradient syringe, band (expt1)

description:
counts.csv
analysis.csv


title: MGYPDa06_ssDNA_rep2

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, and phage T4147


title: MGYPDa06_dsDNA_rep1


title: Periferal blood father [PL246_Father]

value: Male


title: LbDa01_ssDNA_rep2


title: MGYPDa06_ssDNA_rep1


title: Periferal blood mother [PL246_Mother]


title: LbDa01_dsDNA_rep2


title: Extraembryonic mesoderm fetal biopsy [PL2452_EM3591]


title: Chorionic villi fetal biopsy [PL2452_CV3591]


title: Periferal blood mother [PL2451_Mother]


title: HcDa01_ssDNA_rep2


title: LbDa01_ssDNA_rep1


title: HcDa01_ssDNA_rep1


title: Periferal blood father [PL2451_Father]

value: Father


title: Chorionic villi fetal biopsy [PL2451_CV3593]


title: Chorionic villi fetal biopsy [PL246_CV1048]


title: Periferal blood father [PL245_Father]

value: Periferal blood


title: LbDa01_dsDNA_rep1


title: Chorionic villi fetal biopsy [PL245_CV1081]

value: Product of conception


title: CseDa01_ssDNA_rep2


title: Periferal blood mother [PL2452_Mother]


title: Extraembryonic mesoderm fetal biopsy [PL241_EM806]

value: Extraembryonic mesoderm


title: Extraembryonic mesoderm fetal biopsy [PL245_EM1081]

value: Female


title: Periferal blood mother [PL245_Mother]


title: HcDa01_dsDNA_rep2


title: Periferal blood mother [PL241_Mother]


title: HcDa01_dsDNA_rep1


title: CseDa01_dsDNA_rep2


title: CseDa01_dsDNA_rep1


title: CseDa01_ssDNA_rep1


title: Extraembryonic mesoderm fetal biopsy [PL2451_EM3593]


title: CbDa01_ssDNA_rep2


title: Chorionic villi fetal biopsy [PL241_CV806]


title: CbDa01_ssDNA_rep1


title: CbDa01_dsDNA_rep1


title: Periferal blood father [PL2409_Father]


title: AvDa01_ssDNA_rep2


title: CbDa01_dsDNA_rep2


title: Chorionic villi fetal biopsy [PL2409_CV3584]


title: Periferal blood mother [PL2377_Mother]


title: AvDa01_ssDNA_rep1


title: AvDa01_dsDNA_rep1


title: Periferal blood father [PL2377_Father]


title: Extraembryonic mesoderm fetal biopsy [PL2377_EM3574]


title: Periferal blood father [PL241_Father]


title: AvDa01_dsDNA_rep2


title: Chorionic villi fetal biopsy [PL2377_CV3574]


title: Periferal blood mother [PL228_Mother]


title: StsDa01_ssDNA_rep2


title: Extraembryonic mesoderm fetal biopsy [PL228_EM1127]

value: ND


title: Periferal blood father [PL228_Father]


title: StsDa01_ssDNA_rep1


title: Chorionic villi fetal biopsy [PL228_CV1127]

value: Chorionic villi


title: PaDa02_ssDNA_rep1


title: PaDa02_ssDNA_rep2


title: PaDa02_dsDNA_rep1


title: Cd11_MGYPDa829_ssDNA_rep1


title: Periferal blood father [PL2261_Father]


title: Cd11_MGYPDa829_ssDNA_rep2


title: Periferal blood mother [PL2409_Mother]

value: Mother


title: Extraembryonic mesoderm fetal biopsy [PL2261_EM3545]


title: Cd11_MGYPDa829_dsDNA_rep2


title: Periferal blood father [PL2223_Father]


title: Periferal blood mother [PL2223_Mother]


title: SaDa03_ssDNA_rep2


title: SaDa03_ssDNA_rep1


title: Cd11_MGYPDa829_dsDNA_rep1


title: Extraembryonic mesoderm fetal biopsy [PL2223_EM3542]


title: Chorionic villi fetal biopsy [PL2223_CV3542]


title: SaDa03_dsDNA_rep2


title: Periferal blood mother [PL2194_Mother]


title: SaDa03_dsDNA_rep1


title: Extraembryonic mesoderm fetal biopsy [PL2194_EM3539]


title: MGYPDa03_ssDNA_rep1


title: PaDa02_dsDNA_rep2


title: Chorionic villi fetal biopsy [PL2194_CV3539]


title: MGYPDa03_dsDNA_rep2


title: Periferal blood mother [PL2178_Mother]


title: Chorionic villi fetal biopsy [PL2261_CV3545]


title: MGYPDa03_dsDNA_rep1


title: Periferal blood father [PL2178_Father]


title: Extraembryonic mesoderm fetal biopsy [PL2178_EM3538]


title: MGYPDa02_ssDNA_rep2


title: MGYPDa02_ssDNA_rep1


title: Chorionic villi fetal biopsy [PL2178_CV3538]


title: MGYPDa02_dsDNA_rep1


title: Periferal blood father [PL2137_Father]


title: MGYPDa02_dsDNA_rep2


title: Extraembryonic mesoderm fetal biopsy [PL2137_EM3531]


title: Periferal blood father [PL2194_Father]


title: BcDa01_ssDNA_rep2


title: Chorionic villi fetal biopsy [PL2137_CV3531]


title: BcDa01_ssDNA_rep1


title: MGYPDa03_ssDNA_rep2


title: Periferal blood mother [PL2130_Mother]


title: Periferal blood father [PL2130_Father]


title: BcDa01_dsDNA_rep2


title: Periferal blood mother [PL2115_Mother]


title: Extraembryonic mesoderm fetal biopsy [PL2130_EM3529]


title: Chorionic villi fetal biopsy [PL2130_CV3529]


title: Periferal blood father [PL2115_Father]


title: SaDa02_ssDNA_rep2


title: SaDa02_ssDNA_rep1


title: BcDa01_dsDNA_rep1


title: Periferal blood mother [PL2137_Mother]


title: Extraembryonic mesoderm fetal biopsy [PL2115_EM3528]


title: SaDa02_dsDNA_rep1


title: PpDa02_ssDNA_rep1


title: PpDa02_dsDNA_rep2


title: Periferal blood father [PL2087_Father]


title: Extraembryonic mesoderm fetal biopsy [PL2087_EM3520]


title: Chorionic villi fetal biopsy [PL2115_CV3528]


title: Chorionic villi fetal biopsy [PL2087_CV3520]


title: Periferal blood mother [PL2081_Mother]


title: SaDa02_dsDNA_rep2


title: MGYPDa01_ssDNA_rep1


title: MGYPDa01_ssDNA_rep2


title: PpDa02_dsDNA_rep1


title: MGYPDa01_dsDNA_rep2


title: EcDa04_ssDNA_rep2


title: MGYPDa01_dsDNA_rep1


title: PpDa02_ssDNA_rep2


title: Periferal blood father [PL2081_Father]


title: Extraembryonic mesoderm fetal biopsy [PL2081_EM3525]


title: Chorionic villi fetal biopsy [PL2081_CV3525]


title: EcDa04_dsDNA_rep2


title: Periferal blood mother [PL2074_Mother]


title: Periferal blood father [PL2074_Father]


title: EcDa04_ssDNA_rep1


title: EcDa04_dsDNA_rep1


title: HgDa01_ssDNA_rep1


title: Chorionic villi fetal biopsy [PL2074_CV3522]


title: HgDa01_dsDNA_rep2


title: Periferal blood mother [PL2087_Mother]


title: Extraembryonic mesoderm fetal biopsy [PL2074_EM3522]


title: Periferal blood father [PL2030_Father]


title: AcDa01_ssDNA_rep2


title: AcDa01_ssDNA_rep1


title: Extraembryonic mesoderm fetal biopsy [PL2030_EM3512]


title: Chorionic villi fetal biopsy [PL2030_CV3512]


title: Periferal blood mother [PL203_Mother]


title: AcDa01_dsDNA_rep2


title: AcDa01_dsDNA_rep1


title: Periferal blood father [PL203_Father]


title: SET2 HMGA1 KD rep3

city: BALTIMORE

first: Linda

last: Resar

state: Maryland

address: 720 Rutland Avenue

department: Department of Medicine / Division of Hematology

institute: Johns Hopkins University

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into FASTQ files, trimmed, and de-multiplexed using Illumina's bcl2fastq 2.17 software
Alignment was performed using Bowtie 2.2.1 with the default parameter to the GRCh37/hg19 genome assembly (NCBI) with TopHat using strand-specific parameters.
Feature and read summarization was performed using Feature Counts from the Subread package.
Log2 fold changes and false discovery rates (FDRs) were determined with DESeq2 in R with an adjusted P value of <0.05 considered significant
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

source_name: SET2 HMGA1 KD

growth_protocol: DAMI cells (ATCC, CRL-9792) were cultured in RPMI 1640 medium (Corning) supplemented with 10% fetal bovine serum (Sigma) and SET-2 cells (DSMZ, CVCL_2187) were cultured in RPMI 1640 supplemented with 20% FBS.

extract_protocol:
Cell pellets were stored in Trizol after which RNA was isolated (RNeasy mini kits; Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lentivirus is concentrated using Amicon Ultra-15 Centrifugal Filter Unit (sigma) at 4,000 × g for 0.5 hours, 4 °C. The virus pellet was resuspended in a fresh medium, and stored at −80°C until use. For lentivirus transduction, we used magnetic nanoparticles.

value: leukemic cells

tag: disease state

value: MPN/AML

value: shHMGA1 lentivirus infected


title: SET2 HMGA1 KD rep2


title: HgDa01_ssDNA_rep2


title: Extraembryonic mesoderm fetal biopsy [PL203_EM1090]


title: Chorionic villi fetal biopsy [PL203_CV1090]


title: SET2 HMGA1 KD rep1


title: SET2 TRC rep2

source_name: SET2 TRC

value: Control lentivirus infected


title: Chorionic villi fetal biopsy [PL2019_CV3509]


title: Periferal blood father [PL2019_Father]


title: SET2 TRC rep1


title: Extraembryonic mesoderm fetal biopsy [PL2019_EM3509]


title: Periferal blood mother [PL2030_Mother]


title: Periferal blood mother [PL2016_Mother]


title: DAMI HMGA1 KD rep3

source_name: DAMI HMGA1 KD

value: DAMI


title: DAMI HMGA1 KD rep2


title: HgDa01_dsDNA_rep1


title: Periferal blood father [PL2016_Father]


title: DAMI HMGA1 KD rep1


title: Extraembryonic mesoderm fetal biopsy [PL2016_EM3507]


title: DAMI TRC rep3

source_name: DAMI TRC


title: Chorionic villi fetal biopsy [PL2016_CV3507]


title: DAMI TRC rep2


title: SET2 TRC rep3


title: Periferal blood mother [PL1973_Mother]


title: Periferal blood mother [PL2019_Mother]


title: DAMI TRC rep1


title: Periferal blood father [PL1973_Father]


title: Extraembryonic mesoderm fetal biopsy [PL1973_EM3492]


title: Chorionic villi fetal biopsy [PL1973_CV3492]


title: MYBPC3 G115* T112-mech. 1

city: Fujisawa City

first: Yuya

last: Fujiwara

state: Kanagawa Prefecture

address: 2-26-1 Muraokahigashi

country: Japan

institute: Kyoto University

data_processing:
Illumina bcl2fastq (v2.17.14) were performed for converting fastq files and separation by samples with default setting
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v1.12) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.2.5), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (2.5.3a)
HTSeq (0.11.2) were perfomed for counting reads with the GENCODE (version 27) annotation gtf file.
Assembly: To normalized read counts, R (v4.1.2) and its package DESeq2 (1.34.0) were performed.
Supplementary files format and content: GRCh38

source_name: 1390D4 hiPSCs, NHDF

growth_protocol: ECTs were mainteined StemPro-34 SFM supplimented with  2 mM L-Glutamine, 0.4 mM monothioglycerol, 50 µg/mL ascorbic acid, 150 µg/mL Transferrin and 5 ng/mL VEGF

extract_protocol:
ECTs were lysised using QIAzo (Qiagen)l and RNA was purified using miRNeasy  purification Kit (Qiagen) following the manufacturer's instructions.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (illumina) following manufacturer's protocols.

treatment_protocol: For ECTs construction, Dissociated  hiPS-CMs were mixed with  NHDFs in  collagen medium which is composed of 1 mg/mL collagen type I neutralized with NaOH and 11 % GeltrexTM LDEV-Free reduced growth factor basement membrane matrix (Invitrogen Corporation). After  one week culture, ECTs were treated with DMSO and 3μM T112 with or without 10% elongation stimulation at 1Hz for eight days.

value: 1390D4 hiPSCs, NHDF

value: engineered cardiac tissue

value: MYBPC3 G115*

value: T112 with mechanical stimulation (10% elongation, 1Hz)


title: MYBPC3 G115* T112-mech. 3


title: MYBPC3 G115* T112-mech. 2


title: Periferal blood mother [PL1965_Mother]


title: MYH7 R719Q T112-mech. 2

value: MYH7 R719Q


title: MYH7 R719Q T112-mech. 1


title: MYH7 R719Q T112-mech. 3


title: Periferal blood mother [PL2261_Mother]

value: Periferal blood


title: Periferal blood father [PL1965_Father]

value: Male

value: Father


title: Extraembryonic mesoderm fetal biopsy [PL2409_EM3584]

value: Female

value: Product of conception

value: Extraembryonic mesoderm


title: Periferal blood father [PL1941_Father]


title: Chorionic villi fetal biopsy [PL1965_CV3501]

value: Chorionic villi


title: WT T112-mech. 3

value: WT


title: WT T112-mech. 2


title: Periferal blood mother [PL1941_Mother]

value: Mother


title: WT T112-mech. 1


title: Extraembryonic mesoderm fetal biopsy [PL1941_EM3488]


title: T3 T112-mech. 2

value: TNNI1-EmGFP, TNNI3-mCheery


title: Periferal blood mother [PL1896_Mother]


title: Periferal blood father [PL1896_Father]


title: T3 T112-mech. 1


title: Extraembryonic mesoderm fetal biopsy [PL1896_EM3472]


title: T3 DMSO-mech. 3

value: DMSO with mechanical stimulation (10% elongation, 1Hz)


title: T3 DMSO-mech. 2


title: Chorionic villi fetal biopsy [PL1941_CV3488]


title: Chorionic villi fetal biopsy [PL1896_CV3472]


title: T3 DMSO-mech. 1


title: T3 T112-static 3

value: T112 in static condition


title: Periferal blood mother [PL1892_Mother]


title: T3 T112-mech. 3

value: 1390D4 hiPSCs, NHDF


title: I11550_inflam_72h

city: Kiel

first: Kristina

last: Schlicht

address: Düsternbrooker Weg 17

country: Germany

institute: UKSH Kiel

data_processing:
Raw FastQ files were aligned, quality controlled and transformed into read counts using the Nextflow nfcore/RNAseq pipeline
Read counts were analyzed in R v3.6.2 via edgeR and DeSEQ2 packages.
Differential expression analysis (DEA) was done in edgeR using the Quasi-Likelihood F-test function with multi-level contrasting.
Contrasts in the main analysis were modeled for the effect of HBO under inflammation and normal conditions at 24h and 72h.
Assembly: GRCh37
Supplementary files format and content: raw_counts.txt: tab-deliminated file includes raw read counts of all samples, samples in columns

growth_protocol: After getting the patients’ informed consents, free gingiva samples were surgically obtained from five randomly recruited healthy individuals (n=5; suppl. table 1), during elective interventions. Cells were isolated, cultured and STRO-1 immunomagnetically sorted (anti-STRO-1 Alexa 647, BioLegend, San Diego, USA and anti-Alexa microbeads; Miltenyi Biotec, Bergisch-Gladbach, Germany). Subsequently, cultures of STRO-1+ sorted G-MSCs [25] were purified by single colony selection.

extract_protocol:
RNeasy Kit (Qiagen)
TruSeq Stranded mRNA Library Prep Workflow

treatment_protocol: Third passage G-MSCs were preconditioned in the following four groups and re-ceived a single treatment at 24h or a double treatment over 72h (US-Navy treatment protocol, table 9): 2.3. Control-Group: Basic Medium HBO-group: basic medium supplemented with hyperbaric oxygen (100% O2, [Hüllmann Gas, Hans Hüllmann GmbH, Kiel, Germany], 90min, 2-3bar). Inflammatory-group: basic medium supplemented with inflammatory cytokines (IL-1β [1ng/ml], TNF-α [10ng/ml] and IFN-γ [100ng/ml]). HBO/inflammatory-group: basic medium with hyperbaric oxygen (100% O2, [Hüllmann Gas], 90min, 2-3bar) and inflammatory cytokines (IL-1β [1ng/ml], TNF-α [10ng/ml] and IFN-γ [100ng/ml]). Media were renewed every second day. To create hyperbaric conditions, samples were placed in a HBO-chamber system (Testcom200/20, Haux-Life-Support, Karls-bad-Ittersbach, Germany), nitrogen layers were exhausted, through applying pure O2, and the pressure of 2-3 bar was built-up, following an established protocol composed of compression (10 minutes), supplementation of isobaric oxygen (90 minutes) and finally decompression (10 minutes). Pneumatic use of pure oxygen is prohibited due to its high reactivity (IGV-SH-07S-Rev1). Instead, samples were placed in a compressed air chamber and received constant oxygen ventilation through individually constructed covers.

value: Gingiva

value: Gingival Mesenchymal Stem/Progenitor Cells

tag: individual

tag: culture medium

value: inflam

value: untreated

tag: time


title: T3 T112-static 2

value: engineered cardiac tissue


title: Periferal blood father [PL1892_Father]

value: Male

value: Periferal blood


title: I11549_control_72h

value: control


title: I11542_O2_inflam_72h

value: HBO


title: I11541_HBO_control_72h


title: T3 T112-static 1


title: I11548_inflam_72h


title: I11547_control_72h


title: T3 DMSO-static 3

value: DMSO in static condition


title: Chorionic villi fetal biopsy [PL1892_CV3471]

value: Product of conception

value: Chorionic villi


title: T3 DMSO-static 2


title: Periferal blood mother [PL1873_Mother]

value: Female

value: Mother


title: I11536_inflam_24h


title: I11535_control_24h


title: I11539_HBO_control_72h


title: T3 DMSO-static 1

value: TNNI1-EmGFP, TNNI3-mCheery


title: I11529_HBO_control_24h


title: I11534_inflam_24h


title: Airway T helper cells from dog allergen challenged mice

city: Solna

first: Chris

middle: Andrew

last: Tibbitt

state: non-US

address: Biomedicum C7,, Tomtebodavägen 16

country: Sweden

institute: KI

data_processing:
RNA-seq reads were aligned to the NCBI Build 37 (UCSC mm10-3) of the mouse genome using TopHat (Trapnell et al., 2009). The resulting alignments were processed by Cufflinks to evaluate the expression of transcripts from RefSeq.
Assembly: mm10-3

organism: Mus musculus

source_name: bronchoalveolar lavage

extract_protocol:
T helper cells were purified from the bronchoalveolar lavage of mice sensitized and challenged with dog allergen extracts. The BAL was kept cold and processed rapidly. Cells were stained for CD4, CD3, Siglec-    F and B220. CD4+  CD3+ SiglecF−  B220− cells were sorted into pure FCS using a BD FACSAria Fusion. Cells were washed and resuspended in cold PBS. Single cells were isolated with the droplet- based microfluidic system Chromium (10x Genomics).
10X 5' gene expression and TCR libraries were prepared using the method described by the manufacturer

value: bronchoalveolar lavage

value: T helper cell


title: I11528_HBO_inflam_24h

value: Gingiva


title: Extraembryonic mesoderm fetal biopsy [PL1873_EM3461]

value: Extraembryonic mesoderm


title: I11533_control_24h

value: Gingival Mesenchymal Stem/Progenitor Cells


title: Extraembryonic mesoderm fetal biopsy [PL1892_EM3471]


title: Chorionic villi fetal biopsy [PL1873_CV3461]


title: Periferal blood mother [PL1824_Mother]


title: Msl3 floxed Conditional Knockout Testes at P45, biological replicate 3

city: Albany

first: Paolo

middle: Emanuele

last: Forni

state: NY

address: 1400 Washington Avenue

department: Biology

institute: University at Albany

description: Sample 6 - MSL3cKO_3

data_processing:
STAR was used to align RNA-seq libraries to the reference genome.
DESeq2 was used for differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: ReadsPerGene.out.tab files include gene counts. Column 1: gene ID; Column 2: counts for unstranded RNA-seq; Column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes); Column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse).

source_name: Testes

extract_protocol:
3 Msl3 floxed conditional knockout mice and 3 Msl3 wild-type mice were euthanized by CO2 at P45 and testes were isolated. Extraction of total RNA was performed according to manufacturer instructions of the Thermo Fisher PureLink™ RNA Mini Kit.
Library preparation and sequencing were conducted by the Center of Functional Genomics (CFG) (https://www.albany.edu/genomics/ngs.html , Albany, NY).
Single-end, 75bp.

value: Testes

tag: strain

value: MSL3 cKO

tag: age

value: postnatal day 45


title: Msl3 floxed Conditional Knockout Testes at P45, biological replicate 2

description: Sample 5 - MSL3cKO_2


title: I11540_HBO_inflam_72h

value: inflam


title: Periferal blood father [PL1824_Father]

value: Male

value: Father

value: Periferal blood


title: Msl3 floxed Conditional Knockout Testes at P45, biological replicate 1

description: Sample 4 - MSL3cKO_1


title: Msl3 Wild-type Testes at P45, biological replicate 3

description: Sample 3 - MSL3WT_3

value: MSL3 WT


title: I11530_HBO_inflam_24h

value: HBO


title: Periferal blood father [PL1873_Father]


title: Extraembryonic mesoderm fetal biopsy [PL1824_EM3446]

value: Product of conception


title: Chorionic villi fetal biopsy [PL1824_CV3446]

value: Chorionic villi


title: Msl3 Wild-type Testes at P45, biological replicate 2

description: Sample 2 - MSL3WT_2


title: Msl3 Wild-type Testes at P45, biological replicate 1

description: Sample 1 - MSL3WT_1


title: I11527_HBO_control_24h

value: control


title: Periferal blood father [PL1809_Father]


title: Periferal blood mother [PL1809_Mother]

value: Female

value: Mother


title: arteriolar smooth muscle cell, sorting, rep5

city: Shanghai

first: Dong-Dong

last: Zhang

state: Shanghai

address: 130 Dong'an Road

country: China

institute: Fudan University

description:
aSMC5
Raw_gene_counts_matrix.txt

data_processing:
Ubuntu terminal environment in minutes with Windows Subsystem for Linux (WSL), v 20.04.4. Conda for managing and deploying applications, environments and packages in RNA-Seq, v 4.14.0.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim-galore, v 0.6.7  (parameter: --quality score 25, --cores 4, --phred 33, --length 35, --stringency 3).
Trimmed sequence reads were processed to Quality control using FastQC, v 0.11.9  and MultiQC, v 1.13.
Trimmed sequence reads were mapped to GrCM38 using Salmon index, and then were genetic quantified using Salmon quant, v 1.4.0.
Read count extraction and matrix were performed using tximport package in R, v 4.1.0.
Assembly: Grcm38
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: cerebral arteriole

growth_protocol: The transgenic mice, including SMACreER:Ai47, SMACreER:Ai14 and hGFAPCreER:Ai14, were bred, then for cell sorting.

extract_protocol:
RNA was harvested using RNeasy plus mini kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Ovation RNA-Seq system V2 and Ovation Ultralow system V2 (NuGEN) following manufacturer's protocols.

treatment_protocol: Using the Ai47 or Ai14 reporter mice, the EGFP or tdtomato positive cells labeling aSMCs or astrocytes were acquired by fluorescence-activated cell sorting (FACS), then for RNA extraction.

value: cerebral arteriole

value: arteriolar smooth muscle cell

value: sorting


title: Periferal blood mother [PL1800_Mother]


title: arteriolar smooth muscle cell, sorting, rep6

description:
aSMC6
Raw_gene_counts_matrix.txt


title: Extraembryonic mesoderm fetal biopsy [PL1809_EM3438]

value: Extraembryonic mesoderm


title: arteriolar smooth muscle cell, sorting, rep4

description:
aSMC4
Raw_gene_counts_matrix.txt


title: Chorionic villi fetal biopsy [PL1809_CV3438]


title: arteriolar smooth muscle cell, sorting, rep3

description:
aSMC3
Raw_gene_counts_matrix.txt


title: KD_SAP30BP_rep1

first: Hong

last: Cheng

state: State

address: 320 Yue Yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology, CAS.

description: 2x150 paired-end sequence reads

data_processing:
The raw pair-end reads were preprocessed to remove the adapters with cutadapt (v.3.5), the quality of the resulting files was evaluated using FastQC (v.0.11.9). Reads were firstly mapped to rRNA sequences which derived from NCBI, and then reads that were not mapped to rRNA sequences were aligned to the human genome (hg38) with GENCODE v32 gene annotation using STAR aligner (v.2.7.9a). Spike in reads are normalized by DESeq2 R package using estimateSizeFactorsfunction.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene raw counts for each Sample

source_name: hela

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

extract_protocol:
RNA-seq: RNA was harvested using TRIzol reagent (life technologies). 1 ug of total RNA was used for the construction of sequencing libraries.
stranded cDNA libraries were generated with VAHTS Universal V8 RNA-seq Library Prep Kit  (Vazyme) according to the manufacturer’s instructions.

treatment_protocol: RNA-seq: All cells were  grown to 80% confluence in 12-well plate before addition of dTAG13 prepared and added (200nM for 2, 6, 12, 24 hr) to cell culture medium.

value: hela

value: uterine cervix


title: KD_SAP30BP_rep2

description: 2x150 paired-end sequence reads


title: KD_U1C_rep1

description: 2x150 paired-end sequence reads


title: KD_U1C_rep2

description: 2x150 paired-end sequence reads


title: arteriolar smooth muscle cell, sorting, rep2

description:
aSMC2
Raw_gene_counts_matrix.txt


title: KD_LUC_rep1

description: 2x150 paired-end sequence reads

value: siLUC(siNC)


title: KD_LUC_rep2

description: 2x150 paired-end sequence reads


title: arteriolar smooth muscle cell, sorting, rep1

description:
aSMC1
Raw_gene_counts_matrix.txt


title: NHA_D28_Rep3

city: San Francisco

first: I-Li

last: Tan

state: California

address: 1650 Owens St

institute: Gladstone Institutes

data_processing:
MAGeCK (Li et al. 2014)
Supplementary files format and content: The MAGeCk_all_samples_counts.xlsx file contains the sgRNA sequences in the library, the raw and normalized read count for MAGeCK RRA analysis, and the log2 fold change of sgRNA representation from day 28 (D28) compared to day 1 (T0).
Supplementary files format and content: The MAGeCk_RRA.zip file contains the results of RRA analysis using MAGeCk.

source_name: NHA

extract_protocol:
gDNA were extracted using Quick-DNA Miniprep Plus Kit (Zymo Research #D4068).
NGS libraries were constructed using a two-step PCR protocol. In the first step, PCR was conducted with primers containing partial Illumina adaptors to amplify the sgRNA cassettes. Subsequently, a second PCR was performed to attach full Illumina adaptors and barcode the samples.

value: NHA

value: Normal human astrocyte


title: NHA_D28_Rep1


title: Extraembryonic mesoderm fetal biopsy [PL1965_EM3501]


title: Periferal blood father [PL1800_Father]

value: Male

value: Father

value: Periferal blood


title: NHA_D28_Rep2


title: Extraembryonic mesoderm fetal biopsy [PL1800_EM3429]

value: Product of conception


title: NHA_T0_Rep1


title: SF11411_D28_Rep3

value: Hypermutated GBM


title: NHA_T0_Rep2


title: Chorionic villi fetal biopsy [PL1800_CV3429]

value: Chorionic villi


title: CD24 high control 3

city: Boston

first: Samuel

middle: P

last: Rowbotham

state: MA

address: 185 Cambridge Street

institute: Massachusetts General Hospital

data_processing:
Sequence quality evaluated using FASTQC
Reads filtered and trimmed with Atropos
High quality reads mapped to mouse genome using Bowtie2
Filtered properly paired reads with high mapping quality MAPQ10>10
Peaks called using de-duplicated uniquely mapped reads with MACS2
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: bed

source_name: Lung

extract_protocol: Corces et al. Nat. Methods 2017

value: Lung

value: CD31/45- Epcam+ Sca-1+ Cd24hi

value: adult 6-12 weeks

value: Vehicle


title: CD24-  control 3


title: Periferal blood father [PL180_Father]

source_name: Periferal blood


title: CD24 low control 3

value: CD31/45- Epcam+ Sca-1+ Cd24lo


title: CD24 high G9ai 3


title: Periferal blood mother [PL180_Mother]

value: Female

value: Mother


title: SF11411_D28_Rep1


title: SF11411_D28_Rep2


title: SF11411_T0_Rep3


title: SF11411_T0_Rep2


title: Chorionic villi fetal biopsy [PL180_CV1075]


title: SF11411_T0_Rep1


title: Periferal blood mother [PL1790_Mother]


title: CD24- G9ai 3


title: NHA_T0_Rep3


title: CD24 low G9ai 3


title: Periferal blood father [PL1790_Father]


title: Muscle, TRCO30a

city: Burwood

first: Danielle

last: Hiam

state: Vic

address: 221 Burwood Hwy

department: IPAN

country: Australia

institute: Deakin University

data_processing:
Reads underwent quality check with FastQC (v0.11.9); Kallisto (v0.46.1) was used to map reads to the human reference genome (HomoSapien GRCh38) and to generate transcript counts.
Assembly: HomoSapien GRCh38
Supplementary files format and content: 3col.tsv- Long format of aligned raw gene counts
Supplementary files format and content: GeneCounts_ RAW DATA.csv- Wide format of aligned raw gene counts

source_name: vastus lateralis muscle

growth_protocol: Satellite cells were isolated by dissociation with 0.05% trypsin/EDTA (Life Technologies). Cells were plated on a flask coated with extracellular matrix (ECM; Sigma-Aldrich, Castle Hill, Australia) and allowed to proliferate to 70% confluence before passaging. Myoblasts were maintained in proliferation media [Ham’s F-10 medium (Life Technologies) containing 20% FBS, 25 ng/mL fibroblast growth factor (bFGF; Promega), 1% penicillin streptomycin, and 0.5% amphoteromycin (Life Technologies)] at 37°C and 5% CO2. Cells were passaged by mechanical disturbance twice and then frozen down in proliferation media and 10% DMSO. Upon thawing, cells were passaged once before myoblasts were purified using CD56+ Microbeads (Miltenyi Biotec) to eliminate fibroblasts and other cell populations as per manufacturer instructions. At 70-80% confluence cells were seeded into 6 well plates and were allowed to differentiate by replacing proliferation media to differentiation media [DMEM (Life Technologies) containing 2% HS (New Zealand origin; Gibco, Life Technologies) and 1% penicillin/streptomycin. Medium was replaced every 48hours.

extract_protocol:
RNA was extracted from human primary cells using AllPrep RNA/RNA/miRNA universal kit (Qiagen) according to manufacturer instructions
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol

treatment_protocol: On day five of differentiation, myotubes were transfected with either 20nM of miR-30a or miR-30c mimics or 20 nM of a mimic scramble (mirVana™ miRNA mimics, ThermoFisher) using Lipofectamine® RNAiMAX Transfection Reagent (Ambion, Life Technologies) diluted 16.7X in Opti-MEM I Reduced serum medium (Life Technologies). This solution was added to differentiation medium at a 10x dilution. After 24 h transfection cells were harvested for RNA

value: vastus lateralis muscle

value: Skeletal muscle primary cells

tag: Sex

value: MALE

tag: age of donor

value: Day 5 Differentiation

value: 24h 20nM of miR-30a


title: Muscle, TRCO30c

value: 24h 20nM of miR-30c


title: Muscle, TRCOSCRAM

value: 24h 20nM of mimic scramble


title: CD24 high control 2


title: Muscle, SAALSCRAM

value: FEMALE


title: Extraembryonic mesoderm fetal biopsy [PL1790_EM3436]

source_name: Extraembryonic mesoderm

value: Male

value: Product of conception

value: Extraembryonic mesoderm


title: CD24 low control 2

value: Lung


title: CD24-  control 2

value: adult 6-12 weeks


title: Chorionic villi fetal biopsy [PL668_CV1642 methylation]

hyb_protocol: From each sample 300 ng of DNA was bisulfite-converted using the EZ DNA Methylation Kit (Zymo Research, CA, USA) according to the manufacturer’s instructions

scan_protocol: Illumina Infinium™ MethylationEPIC v1.0 BeadChip (Illumina, CA, USA).

data_processing: Data preprocessing was carried out using the RnBeads R package. Briefly, the data were normalized with subset-quantile within array normalization (SWAN) and poor-quality sites/samples were removed based on the greedycut algorithm (detection p-value threshold: 0.05). Further sites were removed: (i) sites on the sex chromosomes, (ii) sites in close proximity to SNPs, (iii) sites with missing values in more than 10% of samples, (iv) sites not in a CpG context. Additional sample quality control, namely sex prediction and SNP probe analysis, was carried out using the sEst42 package and RnBeads respectively.

label: cy3, cy5

source_name: Chorionic villi

label_protocol: Standard Illumina Protocol

value: Chorionic villi fetal biopsy


title: Muscle, FI730c


title: Chorionic villi fetal biopsy [PL1790_CV3436]

value: Chorionic villi


title: Muscle, SAAL30a


title: Muscle, SAAL30c


title: Muscle, FI7SCRAM


title: Extraembryonic mesoderm fetal biopsy [PL668_EM1642 methylation]

value: Female

value: Extraembryonic mesoderm fetal biopsy


title: Muscle, FI730a

value: vastus lateralis muscle


title: Periferal blood mother [PL1783_Mother]

value: Mother

value: Periferal blood


title: CD24 high G9ai 2

value: CD31/45- Epcam+ Sca-1+ Cd24hi


title: Muscle, FI630a

value: Skeletal muscle primary cells

value: Day 5 Differentiation

value: 24h 20nM of miR-30a


title: CD24 low G9ai 2

value: CD31/45- Epcam+ Sca-1+ Cd24lo


title: Chorionic villi fetal biopsy [PL150_CV794 methylation]


title: Extraembryonic mesoderm fetal biopsy [PL2409_EM3584 methylation]


title: Periferal blood father [PL1783_Father]

value: Male

value: Father


title: Muscle, FI6SCRAM

value: FEMALE

value: 24h 20nM of mimic scramble


title: Muscle, SG19330c

value: MALE

value: 24h 20nM of miR-30c


title: Extraembryonic mesoderm fetal biopsy [PL150_EM794 methylation]


title: CD24- G9ai 2

value: Lung

value: adult 6-12 weeks


title: Muscle, SG19330a


title: CD24 high control 1

value: Vehicle


title: Muscle, SG19130c

value: vastus lateralis muscle


title: Extraembryonic mesoderm fetal biopsy [PL180_EM1075 methylation]

value: Female

value: Extraembryonic mesoderm fetal biopsy


title: Chorionic villi fetal biopsy [PL2409_CV3584 methylation]

value: Chorionic villi fetal biopsy


title: Chorionic villi fetal biopsy [PL2712_CV3700 methylation]


title: Extraembryonic mesoderm fetal biopsy [PL2717_EM3704 methylation]


title: Chorionic villi fetal biopsy [PL1783_CV3431]

value: Product of conception

value: Chorionic villi


title: Chorionic villi fetal biopsy [PL180_CV1075 methylation]


title: CD24 low control 1


title: Extraembryonic mesoderm fetal biopsy [PL1783_EM3431]

value: Extraembryonic mesoderm


title: Muscle, SG19130a

value: Skeletal muscle primary cells

value: Day 5 Differentiation

value: 24h 20nM of miR-30a


title: Periferal blood mother [PL1776_Mother]

value: Mother

value: Periferal blood


title: N-IP for MeRIP-seq

city: Jinan

first: baoxia

last: cui

address: Wenhua

institute: Qilu Hospital of Shandong Univerity

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0)
The m6A peaks were identified using exomePeak R package
Assembly: mm10
Supplementary files format and content: peak files
Library strategy: MeRIP-seq

source_name: Human normal cervical tissue

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
Briefly, the concentration of total RNA was measured by Qubit

value: Human normal cervical tissue

value: IP


title: Muscle, SG191SCRAM

value: MALE

value: 24h 20nM of mimic scramble


title: CD24-  control 1

value: Lung

value: adult 6-12 weeks

value: Vehicle


title: N-Input for MeRIP-seq

value: Input


title: Periferal blood father [PL1776_Father]

value: Male

value: Father


title: Extraembryonic mesoderm fetal biopsy [PL1776_EM3430]

value: Product of conception


title: CC3-Input for MeRIP-seq

source_name: Human cervical cancer tissue

value: Human cervical cancer tissue


title: CC2-Input for MeRIP-seq


title: CD24 high G9ai 1

value: CD31/45- Epcam+ Sca-1+ Cd24hi


title: Chorionic villi fetal biopsy [PL2617_CV3627 methylation]

value: Female

value: Chorionic villi fetal biopsy


title: CD24 low G9ai 1

value: CD31/45- Epcam+ Sca-1+ Cd24lo


title: Extraembryonic mesoderm fetal biopsy [PL2712_EM3700 methylation]

value: Extraembryonic mesoderm fetal biopsy


title: Chorionic villi fetal biopsy [PL2717_CV3704 methylation]


title: Chorionic villi fetal biopsy [PL1776_CV3430]

value: Chorionic villi


title: CC1-IP for MeRIP-seq

value: IP


title: CC3-IP for MeRIP-seq


title: Muscle, SG193SCRAM

value: vastus lateralis muscle

value: Skeletal muscle primary cells

value: MALE

value: Day 5 Differentiation


title: Periferal blood mother [PL1758_Mother]

value: Mother

value: Periferal blood


title: CC1-Input for MeRIP-seq

value: Input


title: Periferal blood father [PL1758_Father]

value: Male

value: Father


title: Patient Vitamin D N5 M3, ADT

city: Montpellier

first: Eric

last: Thouvenot

address: 141 rue de la Cardonille

country: France

institute: IGF

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-20" in barcodes.tsv.gz

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting, cell-surface protein counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Further analysis was performed with Seurat v4.3.0 using the aggregated counts.
The quality of the raw data was assessed using FastQC (v0.11.9) from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer). Contaminant screening was done using FastQ Screen (v0.15.1).
Assembly: GRCh38
Supplementary files format and content: CellRanger output files:  barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

source_name: Blood

extract_protocol:
Live lymphocytes from 5 vitamin D-treated MS patients and 5 placebo-treated MS patients.
Construction of gene expression (GEX) libraries and cell-surface protein expression (CellSurface) libraries were performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 3’ Reagent Kits (v3.1 single index) with Feature Barcoding technology for Cell Surface Protein protocol, 10x Genomics, https://www.10xgenomics.com/support/single-cell-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry-with-feature-barcoding-technology-for-cell-surface-protein) by MGX platform (IGF, Montpellier, France).

value: Blood

value: Lymphocytes

value: PBMC

value: Vitamin D

tag: library type

value: ADT


title: Extraembryonic mesoderm fetal biopsy [PL180_EM1075]

data_processing:
The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. We subsequently fed these data into haplarithmisis (Zamani Esteki et al. 2019, Nature medicine).
Image data was analyzed using Genomestudio with genotyping module (Illumina). Subsequently, genotype calls (AA,AB,BB,or NC (no call), SNP B-allele frequency values, LogR.

tag: gender

value: Female

value: Product of conception

value: Extraembryonic mesoderm


title: CD24- G9ai 1

value: Lung

value: adult 6-12 weeks


title: Patient Vitamin D N5 M3, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-20" in barcodes.tsv.gz

value: mRNA


title: T12_CP-1892

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
STAR aligner algorithm was used to aligned the fastq files to the mouse mm10 reference genome.
Resulting BAM files were sorted and indexed using Samtools. Quality control was completed using Picard.
Salmon was used to determine the transcript read counts
The resulting data was upper quantile normalized
Upper quantile normalized data was log2 transformed
Assembly: mm10
Supplementary files format and content: Tab-delimited text file of gene expression matrix (82 samples, genes as rows)
Supplementary files format and content: Tab-delimited text file of gene expression matrix (82 samples, upper quantile normalized, genes as rows)

source_name: Mammary Tumor

extract_protocol:
Cryopreserved tumors were homogenized using a tissue homogenizer. The RNeasy Mini Kit (#74104, Qiagen) was used to iolate the RNA according to the manufacturer's protocol
The Agilent Bioanalyzer was used to asses the mRNA quality and libraries for mRNA-seq were constructed using total RNA and the Illumina TruSeq mRNA sample preparation kit

value: Mammary Tumor

value: BALB/c


title: Patient Vitamin D N5 J0, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-18" in barcodes.tsv.gz


title: Extraembryonic mesoderm fetal biopsy [PL1758_EM3428]

first: Rick

last: Essers

address: P. Debyelaan 25

institute: Maastricht University Medical Centre (MUMC+)

extract_protocol: Genomic DNA was extracted using a standard phenol-chloroform extraction method that allows for the isolation of up to 900 ng DNA from the tissues. Likewise, genomic DNA was extracted from peripheral blood of parents using the standard phenol-chloroform method.

tag: family member


title: T12_CP-1891

tag: tissue


title: Patient Vitamin D N5 J0, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-18" in barcodes.tsv.gz

tag: cell line


title: Muscle, FI630c

value: vastus lateralis muscle

value: Skeletal muscle primary cells

value: FEMALE

value: Day 5 Differentiation

value: 24h 20nM of miR-30c


title: CC2-IP for MeRIP-seq

value: Human cervical cancer tissue

value: IP


title: Patient Vitamin D N4 M3, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-16" in barcodes.tsv.gz

value: Blood

value: Lymphocytes

value: PBMC

value: Vitamin D


title: T12_CP-1890


title: Patient Vitamin D N4 M3, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-16" in barcodes.tsv.gz


title: Periferal blood mother [PL1744_Mother]

value: Female

value: Mother

value: Periferal blood


title: Patient Vitamin D N4 J0, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-13" in barcodes.tsv.gz

value: mRNA


title: Patient Vitamin D N4 J0, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-13" in barcodes.tsv.gz

value: ADT


title: MMTV-PYMT_CP-3730

value: Mammary Tumor

value: FVB


title: Periferal blood father [PL1744_Father]

value: Male

value: Father


title: MMTV-PYMT_CP-3617


title: Patient Vitamin D N3 M3, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-14" in barcodes.tsv.gz


title: Patient Vitamin D N3 M3, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-14" in barcodes.tsv.gz


title: Patient Vitamin D N3 J0, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "11" in barcodes.tsv.gz


title: Extraembryonic mesoderm fetal biopsy [PL1744_EM3422]

value: Product of conception

value: Extraembryonic mesoderm


title: Patient Vitamin D N3 J0, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "11" in barcodes.tsv.gz


title: MMTV-PYMT_CP-3616


title: Chorionic villi fetal biopsy [PL1744_CV3422]

value: Chorionic villi


title: MMTV-PYMT_CP-3054


title: Patient Vitamin D N2 M3, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-6" in barcodes.tsv.gz


title: Patient Vitamin D N2 J0, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-4" in barcodes.tsv.gz


title: MMTV-PYMT_CP-3053


title: Patient Vitamin D N2 J0, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-4" in barcodes.tsv.gz


title: Periferal blood mother [PL1710_Mother]


title: MMTV-NEU_CP-3614


title: Patient Vitamin D N1 M3, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-9" in barcodes.tsv.gz


title: Periferal blood father [PL1710_Father]


title: MMTV-NEU_CP-3613


title: Chorionic villi fetal biopsy [PL1758_CV3428]


title: Extraembryonic mesoderm fetal biopsy [PL1710_EM3596]


title: Patient Vitamin D N1 J0, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-7" in barcodes.tsv.gz


title: Patient Vitamin D N1 J0, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-7" in barcodes.tsv.gz


title: Patient Placebo N5 M3, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-10" in barcodes.tsv.gz

value: Placebo


title: Patient Vitamin D N2 M3, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-6" in barcodes.tsv.gz

value: Blood


title: Extraembryonic mesoderm fetal biopsy [PL1710_EM3253]


title: MMTV-NEU_CP-3612


title: Patient Placebo N5 J0, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-8" in barcodes.tsv.gz

value: Lymphocytes


title: Patient Placebo N5 M3, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-10" in barcodes.tsv.gz

value: PBMC


title: Patient Placebo N5 J0, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-8" in barcodes.tsv.gz


title: MMTV-NEU_CP-3052


title: Patient Placebo N4 M3, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-19" in barcodes.tsv.gz


title: Patient Placebo N4 M3, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-19" in barcodes.tsv.gz


title: MMTV-NEU_CP-1291


title: MMTV-NEU_CP-3051


title: MMTV-NEU_CP-1290


title: Patient Placebo N4 J0, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-17" in barcodes.tsv.gz


title: Patient Placebo N3 J0, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-12" in barcodes.tsv.gz


title: Chorionic villi fetal biopsy [PL1710_CV3253]


title: Patient Placebo N3 M3, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-15" in barcodes.tsv.gz


title: Chorionic villi fetal biopsy [PL1710_CV3399]


title: Chorionic villi fetal biopsy [PL1710_CV3596]


title: MMTV-NEU_CP-1289


title: Periferal blood mother [PL1701_Mother]


title: Patient Placebo N4 J0, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-17" in barcodes.tsv.gz


title: Patient Placebo N3 M3, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-15" in barcodes.tsv.gz


title: Patient Vitamin D N1 M3, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-9" in barcodes.tsv.gz

value: Vitamin D


title: Patient Placebo N3 J0, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-12" in barcodes.tsv.gz


title: Patient Placebo N2 M3, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-5" in barcodes.tsv.gz


title: KPB1-A_CP-3059


title: Extraembryonic mesoderm fetal biopsy [PL1710_EM3399]


title: Patient Placebo N2 M3, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-5" in barcodes.tsv.gz


title: Periferal blood father [PL1701_Father]


title: Patient Placebo N2 J0, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-3" in barcodes.tsv.gz


title: Extraembryonic mesoderm fetal biopsy [PL1701_EM3396]

value: Female


title: KPB1-A_CP-3042


title: Patient Placebo N2 J0, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-3" in barcodes.tsv.gz


title: Patient Placebo N1 M3, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-2" in barcodes.tsv.gz


title: Chorionic villi fetal biopsy [PL1701_CV3396]


title: Patient Placebo N1 M3, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-2" in barcodes.tsv.gz


title: Patient Placebo N1 J0, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
suffix "-1" in barcodes.tsv.gz


title: E0771_CP-4292


title: Periferal blood mother [PL1682_Mother]

value: Mother


title: Patient Placebo N1 J0, GEX

description:
GEX (3'mRNA) library : read1 contains cell barcode and UMI; read2 file contains transcript
suffix "-1" in barcodes.tsv.gz


title: Periferal blood father [PL1682_Father]

value: Periferal blood


title: E0771_CP-4291


title: 9263_CP-3853

value: BALB/c


title: PAD_3.2

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software version 5.0.0 and 6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: grch38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skeletal muscle

extract_protocol:
For isolation of cells for scRNAseq, and in less than 2 hours after collection and preservation in ice-cold hypothermic preservation solution (HypoThermosol® FRS Preservation Solution, H4416 Sigma-Aldrich) , samples were minced in a petri dish on ice using scissors and a surgical blade. Minced samples were transferred into a digestion buffer (4 mL digestion buffer per 100 mg of muscle) containing 2 mg/ml Dispase II (D4693 Sigma-Aldrich) and 2 mg/ml Collagenase IV (17104019 Thermo Fisher Scientific) in HBSS buffer (14025100 Thermo Fisher Scientific) at 37°C for 25-30 minutes, with gentle shaking every 3-5 minutes. After digestion, the reaction was stopped by adding an equal volume of 20% heat inactivated FBS (10500064 Thermo Fisher Scientific) 1mM EDTA (E177 VWR Life Science) in HBSS (14025100 Thermo Fisher Scientific) and the suspension was passed through a 100-µm cell strainer (800100 Bioswisstec) and a 40-µm cell strainer (352340 Falcon). Cell suspension was centrifuged at 500 g for 5 minutes at 4°C and the supernatant discarded. The pellet was resuspended in 1 mL of ACK Lysing Buffer (A1049201 Thermo Fisher Scientific) for red blood cell lysis for 2 minutes at room temperature. After incubation, the reaction was stopped with 4 mL of 10% heat inactivated FBS (10500064 Thermo Fisher Scientific) in HBSS buffer (14025100 Thermo Fisher Scientific). Cell suspension was centrifuged at 500 g for 5 minutes at 4°C and the pellet resuspended in 0.5% BSA (A1391 PanReac AppliChem) in DPBS (14190250 Thermo Fisher Scientific) containing 1mM EDTA (E177 VWR Life Science) for FACS. Calcein Violet (65-0854-39 Thermo Fisher Scientific) was added directly to the cell suspension at 1:1000 dilution 10 minutes before sorting.
Metabolically active (Calcein+) human muscle mononuclear cells were FACS sorted and loaded into the 10X Chromium Next GEM Chip G, aiming the recovery of ~10000 cells per sample. scRNAseq libraries were generated according to 10X Chromium Next Gem Single Cell 3’ Reagent Kits v3.1 (CG000204 Rev D) and sequenced on the Illumina Novaseq 6000 system

value: Skeletal muscle

value: male

value: PAD


title: PAD_3.1

description: 10x Genomics


title: Control_4

description: 10x Genomics

value: Control


title: PAD_4.1

description: 10x Genomics


title: PAD_4.2

description: 10x Genomics


title: Chorionic villi fetal biopsy [PL1682_CV3398]

city: Maastricht


title: PAD_2.2

description: 10x Genomics


title: Extraembryonic mesoderm fetal biopsy [PL1682_EM3398]


title: 9263_CP-3851

value: Mammary Tumor


title: 9263_CP-3852


title: Periferal blood mother [PL1681_Mother]


title: E0771_CP-4299


title: Control_3.1

description: 10x Genomics


title: Control_3.2

description: 10x Genomics


title: 9263_CP-3554


title: Control_2

description: 10x Genomics


title: PAD_1.2

description: 10x Genomics


title: Control_1

description: 10x Genomics


title: 9263_CP-3552


title: SEMseq_10pg

data_processing:
basecalls were performed using Illumina RTA software and fastq files were generated from the BCL files using Picard’s basecallstofastq.
Reads were trimmed for adaptor sequence and low quality bases at the 3' end using the trim_galore program.
The trimmed read sequences were C to T converted and were then mapped to the a composite reference including E.coli and all the control sequences using the Bismark program with the default Bowtie2 settings.
The first 5 bp at the 5’ end of R2 reads were removed to reduce end-repair errors and aligned read pairs that shared the same alignment ends were regarded as PCR duplicates and were discarded.
The numbers of Ts (converted not methylated) and Cs (unconverted modified) of each covered cytosine position were then calculated from the remaining good quality alignments using Bismark methylation extractor.
Assembly: E. coli C2566, human hg38
Supplementary files format and content: tab-delimited text/bed files include genomic coordinates, number of Cs and number of Ts and sequence contexts of covered cytosines.
Library strategy: SEM-seq


title: Chorionic villi fetal biopsy [PL1681_CV3393]

value: Male

value: Product of conception


title: SEMseq_cfDNA_rep2


title: SEMseq_cfDNA_rep1


title: Periferal blood mother [PL167_Mother]


title: 9263_CP-3058


title: 4T1_CP-4063


title: PAD_2.1

description: 10x Genomics


title: Periferal blood father [PL1681_Father]

value: Father


title: Periferal blood father [PL167_Father]


title: SEMseq_50ng_rep2


title: mice treated with CCl4 in combination with injection of AAV8-shRNA-lncHELF2#, biological rep3

city: Tianjin

first: Kun

address: Qixiangtai Road NO.22

department: Department of Histology and Embryology

institute: Tianjin medical university

data_processing:
basecalls performed using BGISEQ-500
SOAPnuke was used to get the "clean reads"
Mapping clean reads to hg19 whole genome using BWA
Bowtie2 was used to get mapping ratio
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: TPM

growth_protocol: 8 weeks old Balb/c male background were used in CCl4-induced liver fibrosis model

extract_protocol:
RNA of liver tissues were  isolated useing Trizol reagent. Total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer
The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: For CCl4-induced mouse liver fibrosis model, the AAV8 virus was injected via the tail vein 4 weeks after the first injection of CCl4 (1x10`12 pfu/mouse) . After treatment with CCl4 for 8 weeks, all mice were sacrificed under anesthesia with 3% sodium pentobarbital (45 mg/kg, ip).

value: Balb/c

value: liver

value: 8 weeks old

tag: genotype


title: mice treated with CCl4 in combination with injection of AAV8-shRNA-lncHELF2#, biological rep2


title: Extraembryonic mesoderm fetal biopsy [PL167_EM945]

value: Extraembryonic mesoderm


title: 4T1_CP-4062


title: Chorionic villi fetal biopsy [PL167_CV945]

value: Chorionic villi


title: SAP30BP_RNAseq_dTAG_24h_R1

description: 2x150 paired-end sequence reads

data_processing:
The raw pair-end reads were preprocessed to remove the adapters with cutadapt (v.3.5), the quality of the resulting files was evaluated using FastQC (v.0.11.9). Reads were firstly mapped to rRNA sequences which derived from NCBI, and then reads that were not mapped to rRNA sequences were aligned to the human genome (hg38) with GENCODE v32 gene annotation using STAR aligner (v.2.7.9a). Spike in reads are normalized by DESeq2 R package using estimateSizeFactors function.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene raw counts for each Sample

extract_protocol:
RNA-seq: RNA was harvested using TRIzol reagent (life technologies). 1 ug of total RNA was used for the construction of sequencing libraries.   TT-seq: Six in vitro transcribed spike-in RNAs were added to 100ug  total RNA per sample. This was followed by fragmentation by 1M NAOH and biotinylation of the 4sU-containing RNA with 200 µg/ml HPDP-biotin, and then  purified the nascent RNA with  Dynabeads™ MyOne™ Streptavidin T1 (thermo). The 4sU-labeled RNA was eluted  with 100 mM DTT and then purified and concentrated with the RNeasy MinElute Cleanup Kit (Qiagen).
stranded cDNA libraries were generated with VAHTS Universal V8 RNA-seq Library Prep Kit  (Vazyme) according to the manufacturer’s instructions.

treatment_protocol:
RNA-seq: All cells were  grown to 80% confluence in 12-well plate before addition of dTAG13 prepared and added (200nM for 2, 6, 12, 24 hr) to cell culture medium.
TT-seq: 20 million cells were treated per biological replicate sample. Following the specified treatment (dTAG13 or DMSO for 2 hours), we supplemented the treatment medium with 1mM 4-thiouridine (4sU) and metabolically labeled the cells for 15 min. The cells were lysed in Trizol reagent (life technologies).

value: hela

value: uterine cervix

tag: treatment


title: Extraembryonic mesoderm fetal biopsy [PL1681_EM3393]


title: SEMseq_50ng_rep1

first: Zhiyi

address: 240 County Road

institute: New England Biolabs

extract_protocol:
E. coli C2566 genomic DNA was purified using Monarch Genomic DNA Purification Kit (NEB Ipswich, MA), GM12878 genomic DNA was obtained from Coriell Cell Repositories (Camden, NJ).
Input DNA was sheared to 300 bp using the Covaris S2 instrument. Sheared material was transferred to a PCR strip tube to begin library construction. NEBNext DNA Ultra II Reagents (NEB, Ipswich, MA) were used according to the manufacturer’s instructions for end repair, A-tailing, and adaptor ligation. The custom made Pyrollo-dC adaptor (NEB Organic Synthesis Division, Ipswich MA), where all dCs are replaced with Pyrollo-dC, was used. The ligated samples were purified using NEBNext Sample Purification Beads  according to the manufacturer’s instructions. For ssDNA libraries, prior to deamination the DNA was denatured by heating at 90oC for 10 minutes followed by cooling for 2 minutes on ice. The DNA was then deaminated using 1 µL of PURExpress (NEB, Ipswich, MA) synthesized deaminase protein following manufacturer's recommendations for 1 hour at 37oC. Then 1 µL of Thermolabile Proteinase K (NEB, Ipswich, MA) was added and incubated for 30 min at 37oC followed by 10 min at 60oC. Then the library was amplified using NEBNext Q5U Master Mix (NEB, Ipswich, MA, USA). Paired-end sequencing of 150 cycles (2 x 75 bp) was performed for all the sequencing runs.
DNA sequencing of deaminated double-stranded and single-stranded DNA


title: SAP30BP_RNAseq_dTAG_12h_R1

description: 2x150 paired-end sequence reads


title: mice treated with CCl4 in combination with injection of AAV8-shRNA-lncHELF2#, biological rep1


title: PAD_1.1

description: 10x Genomics


title: 9263_CP-3553


title: mice treated with CCl4 in combination with injection of AAV8-shRNA-lncHELF1#, biological rep3


title: 4T1_CP-4045


title: Periferal blood father [PL166_Father]

value: Periferal blood


title: 4T1_CP-4044

value: BALB/c


title: mice treated with CCl4 in combination with injection of AAV8-shRNA-lncHELF1#, biological rep2


title: SAP30BP_RNAseq_dTAG_6h_R1

description: 2x150 paired-end sequence reads


title: mice treated with CCl4 in combination with injection of AAV8-shRNA-lncHELF1#, biological rep1


title: 4T1_CP-4061


title: mice treated with CCl4 in combination with injection of AAV8-NC, biological rep3


title: SAP30BP_RNAseq_dTAG_0h_R1

description: 2x150 paired-end sequence reads


title: Chorionic villi fetal biopsy [PL166_CV1054]


title: CDK11_RNAseq_dTAG_24h_R2

description: 2x150 paired-end sequence reads


title: Periferal blood mother [PL166_Mother]

value: Female

value: Mother


title: 2336_CP-3524


title: 2336_CP-3995


title: Periferal blood mother [PL164_Mother]


title: Periferal blood father [PL164_Father]


title: Extraembryonic mesoderm fetal biopsy [PL166_EM1054]


title: 2336_CP-3522


title: CDK11_RNAseq_dTAG_24h_R1

description: 2x150 paired-end sequence reads


title: mice treated with CCl4 in combination with injection of AAV8-NC, biological rep2

value: male


title: mice treated with CCl4 in combination with injection of AAV8-NC, biological rep1


title: CW_transplanted_iVO_Spike_ECD_3

city: Tokyo

first: Norikazu

last: Saiki

address: 1-5-45 Yushima, Bunkyo-ku

department: Institute of Research

institute: Tokyo Medical and Dental University

data_processing:
From the sequencing output, quality control, alignment reads on hg19 (hg19_AmpliSeq_Transcriptome_21K_v1.bed), read counts and the normalization (reads per million, RPM) for each gene were obtained using the Torrent ampliSeqRNA plugin (hg19 AmpliSeq Transcriptome ERCC v1) in Torrent Suite Software v5.2.1. To exclude mouse tissue-derived reads, mapping and alignment was performed using a custom reference sequence with mouse Refseq.
Data scaling of AmpliSeq count data were performed by converting into Log2(RPM+1) or z-score.
Scaled dataset were first subjected to gene functional classification and pathway enrichment analysis by GSEA ver.4.3.1. Gene set for each pathway derived from the Molecular Signatures Database (MSigDB) ver.7.
Network map of connections among pathways were generated by Enrichment Map implemented in Cytoscape ver.3.9.1 using significantly enriched geneset with a nominal p value <0.05 and FDR <25%.
Assembly: hg19
Supplementary files format and content: RPM values for each Sample

source_name: Transplanted human induced vascular organoid (iVO) under cranial window

growth_protocol: The 8-d-differentiated cells for iVHEC (from Kusabira orange [KO]-expressing iPSCs) were isolated using CD34 immunomagnetic beads (Miltenyi Biotec) according to the manufacturer’s protocol. 8.75 × 104 CD34-positive cells mixed with 1.25 × 104 CD34-negative cells (7:1) were suspended in 100 μl of SEDM. The cell suspension was pipetted into a well (1 × 105 cells per well) of Ultra-Low Attachment 96-well plates and incubated at 37°C in a humidified atmosphere containing 5% CO2 for 4 days. The 4-d-cultured iPSC-vascular organoids were transplanted on the mouse cortex under a cranial window of 9- to 16-week-old mice as described previously (Takebe et al., 2014).

extract_protocol:
Graft was stabilized by immersion in RNAlater and then I to beads pre-filled tube and added lysis buffer of NucleoSpin RNA Plus XS (MACHEREY-NAGEL). Tissue homogenization was performed by SHAKE MASTER tissue disrupter (BMS Japan) for 2.5 min and total RNA was extracted by NucleoSpin RNA Plus XS.
A cDNA library was generated from 10 ng of total RNA, using a SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific). Amplification, primer digestion, and adapter ligation were performed using an Ion AmpliSeq Transcriptome Human Gene Expression Kit (Thermo Fisher Scientific). The cDNA library was purified using Agencourt AMPure XP Reagent (Beckman Coulter) and quantified using Ion Library TaqMan Quantitation Kit (Thermo Fisher Scientific), followed by dilution to 75 pM with water and pooled equally.

treatment_protocol: Mice were tail vein injected with recombinant SARS-CoV-2 Spike-ECD protein (1 μg/mouse; GenScript) or recombinant peptide containing only poly-His and FLAG solution in saline.

value: LifeAct reporter iPSC line

value: Human vascular organoid

value: SARS-CoV-2 Spike-ECD


title: CW_transplanted_iVO_Spike_ECD_2

value: Transplanted human induced vascular organoid (iVO) under cranial window


title: CDK11_RNAseq_dTAG_12h_R2

description: 2x150 paired-end sequence reads


title: CDK11_RNAseq_dTAG_12h_R1

description: 2x150 paired-end sequence reads


title: Extraembryonic mesoderm fetal biopsy [PL164_EM825]

value: Product of conception


title: 2336_CP-3523

value: Mammary Tumor


title: SAP30BP_RNAseq_dTAG_2h_R1

description: 2x150 paired-end sequence reads


title: CW_transplanted_iVO_Spike_ECD_1


title: 2336_CP-3996


title: 2250_CP-3981


title: CDK11_RNAseq_dTAG_6h_R2

description: 2x150 paired-end sequence reads


title: Periferal blood mother [PL1618_Mother]


title: CDK11_RNAseq_dTAG_6h_R1

description: 2x150 paired-end sequence reads


title: CW_transplanted_iVO_Control_Peptide_3

value: Control peptide


title: 2250_CP-3539


title: CDK11_RNAseq_dTAG_2h_R2

description: 2x150 paired-end sequence reads


title: 2250_CP-3538


title: CW_transplanted_iVO_Control_Peptide_2


title: Extraembryonic mesoderm fetal biopsy [PL1618_EM3345]


title: 2250_CP-3982


title: CDK11_RNAseq_dTAG_2h_R1

description: 2x150 paired-end sequence reads


title: 2250_CP-3537


title: CW_transplanted_iVO_Control_Peptide_1


title: Periferal blood mother [PL1595_Mother]


title: CDK11_RNAseq_dTAG_0h_R2

description: 2x150 paired-end sequence reads


title: 2250_CP-2827


title: Periferal blood father [PL1595_Father]

value: Male

value: Father


title: Chorionic villi fetal biopsy [PL1618_CV3345]

value: Chorionic villi


title: iVO SARS-CoV-2 B.1.617.2  infected 4 dpi 4

data_processing:
From the sequencing output, quality control, alignment reads on hg19 (hg19_AmpliSeq_Transcriptome_21K_v1.bed), read counts and the normalization (reads per million, RPM) for each gene were obtained using the Torrent ampliSeqRNA plugin (hg19 AmpliSeq Transcriptome ERCC v1) in Torrent Suite Software v5.2.1.
Data scaling of AmpliSeq count data were performed by converting into Log2(RPM+1) or z-score.
Scaled dataset were first subjected to gene functional classification and pathway enrichment analysis by GSEA ver.4.3.1. Gene set for each pathway derived from the Molecular Signatures Database (MSigDB) ver.7.
Network map of connections among pathways were generated by Enrichment Map implemented in Cytoscape ver.3.9.1 using significantly enriched geneset with a nominal p value <0.05 and FDR <25%.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPM values for each Sample

source_name: LifeAct reporter iPSC line

growth_protocol: The 8-d-differentiated cells for iPSC-derived venous hemogenic endothelial cell were seeded on growth factor-reduced matrigel (Corning) pre-coated 48-well culture plates at 8.0 × 104 cells / well and cultured with StemPro 34 SFM supplemented with 5 ng/mL VEGF, 30 ng/mL bFGF, and 10 mM ROCK inhibitor (Y276932). Capillary-like structures were confirmed overnight and replaced with a same medium minus the ROCK inhibitor. After 24 hrs of culture, iVOs were used for SARS-CoV-2 infection assay.

extract_protocol:
Total RNA was extracted from cultured cells, using a PureLink RNA Mini Kit (Thermo Fisher Scientific).
A cDNA library was generated from 10 ng of total RNA, using a SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific). Amplification, primer digestion, and adapter ligation were performed using an Ion AmpliSeq Transcriptome Human Gene Expression Kit (Thermo Fisher Scientific). The cDNA library was purified using Agencourt AMPure XP Reagent (Beckman Coulter) and quantified using Ion Library TaqMan Quantitation Kit (Thermo Fisher Scientific), followed by dilution to 75 pM with water and pooled equally.

treatment_protocol: iVOs were infected with SARS-CoV-2 at 1x105 TCID50/mL for 2 hr.

value: human induced vascular organoid (iVO)

value: SARS-CoV-2 infection


title: 2250_CP-3056


title: Chorionic villi fetal biopsy [PL164_CV825]


title: 2250_CP-2622


title: 12NNK-GAL4 in-vitro ligation-PCR library 1st

first: Shuai

last: Li

state: Tianjin

address: Huanhuxi Road

institute: Tianjin Tumor Hospital

description: Library: 12NNK random peptide  library; FACS Rounds: first (1st); Strategy: piggyBac-in-vitro ligation-PCR (template 10ng)

data_processing:
PE reads were assigned to samples based on barcodes.
Reads were filtered by QIIME quality filters.
Clean reads were merged by FLASH software.
Assembly: NA
Supplementary files format and content: fasta files, containing nucleotide sequence of the library, were generated for each sample.

molecule: other

growth_protocol: HEK293T cells were maintained in DMEM (CORNING) supplemented with 10% FBS (CORNING) and 1% penicillin-streptomycin solution (CORNING) at 37℃ with 5% CO2.

extract_protocol:
The positive cell genome was extracted after flow sorting.Genomic DNAs were extracted with a TaKaRa MiniBEST Universal Genomic DNA Extraction Kit Ver. 5.0 (TaKaRa).  High-fidelity KOD-Plus-Neo DNA polymerase was used to amplify the sequences containing the degenerate codons.
PCR products were subjected to sequencing library construction by using TruSeq® DNA PCR-Free Sample Preparation Kit (Illumina).

treatment_protocol: For the transfection of piggyBac-in-vitro ligation library, HEK293T cells were plated in 6-well plates the day before transfection, and reached a 70~80% confluency on the day of transfection. piggyBac-in-vitro ligation library dsDNAs (1 μg/well) were co-transfected with hyperactive piggyBac transposase expression vector (1 μg/well) into HEK293T cells using Lipofectamine 2000. For the transfection of piggyBac-in-vitro ligation-PCR library, HEK293T cells were plated in 10-cm dishes the day before transfection, and reached a 70~80% confluency on the day of transfection. Library dsDNAs (6 μg/dish) and hyperactive piggyBac transposase expression vector (6 μg/dish) were co-transfected into HEK293T cells using Lipofectamine 2000. Forty-eight hours after transfection, a 10-day selection with puromycin was performed.For the identification of novel transcriptional activator peptide, HEK293T cells were plated in 10-cm dishes the day before transfection, and reached a 70-80% confluency on the day of transfection. Library dsDNAs with the promoter-GAL4-XTEN-<NNK>12-PAS expression cassette (6 μg/dish) and hyperactive piggyBac transposase expression vector (6 μg/dish) were co-transfected into HEK293T cells using Lipofectamine 2000. Forty-eight hours after transfection, a 5-day selection with puromycin was performed. The obtained cells with successful genomic integration were re-seeded into eight 10-cm dishes and transfected with pG5egfp vector (6 μg/dish). Forty-eight hours after transfection, cells were harvested for the following FACS sorting.

value: Human embryonic kidney


title: 2250_CP-2621

value: BALB/c


title: CDK11_RNAseq_dTAG_0h_R1

description: 2x150 paired-end sequence reads

value: hela

value: uterine cervix


title: Extraembryonic mesoderm fetal biopsy [PL1595_EM3335]

value: Extraembryonic mesoderm


title: Periferal blood father [PL1618_Father]

value: Periferal blood


title: 12NNK-GAL4 in-vitro ligation-PCR library 2nd

description: Library: 12NNK random peptide  library; FACS Rounds: second (2nd); Strategy: piggyBac-in-vitro ligation-PCR (template 10ng)


title: Chorionic villi fetal biopsy [PL1595_CV3335]


title: iVO SARS-CoV-2 B.1.617.2  infected 4 dpi 1

value: LifeAct reporter iPSC line


title: Periferal blood mother [PL158_Mother]

value: Female

value: Mother


title: iVO SARS-CoV-2 B.1.617.2  infected 4 dpi 5


title: 2250_CP-2620


title: 2250_CP-2203


title: Periferal blood father [PL158_Father]


title: iVO Mock 4 dpi 5

value: Mock


title: 12NNK-GAL4 in-vitro ligation-PCR library inital

description: Library: 12NNK random peptide  library; FACS Rounds: inital (0); Strategy: piggyBac-in-vitro ligation-PCR (template 10ng)


title: 3NNK-EGFP in-vitro ligation-PCR (10ng) library-diluted 100 times 2nd

description: Library: 3NNK EGFP-chromophore-randomized library (65-67) 100 times dilution; FACS Rounds: second (2nd); Strategy: piggyBac-in-vitro ligation-PCR (template 10ng)


title: 2225_CP-4012

value: Mammary Tumor


title: 3NNK-EGFP in-vitro ligation-PCR (10ng) library-diluted 100 times 1st

description: Library: 3NNK EGFP-chromophore-randomized library (65-67) 100 times dilution; FACS Rounds: first (1st); Strategy: piggyBac-in-vitro ligation-PCR (template 10ng)


title: iVO Mock 4 dpi 4


title: Extraembryonic mesoderm fetal biopsy [PL158_EM995]

value: Product of conception


title: Chorionic villi fetal biopsy [PL158_CV995]


title: iVO SARS-CoV-2 B.1.617.2  infected 4 dpi 3


title: 3NNK-EGFP in-vitro ligation-PCR (10ng) library-diluted 100 times inital

description: Library: 3NNK EGFP-chromophore-randomized library (65-67) 100 times dilution; FACS Rounds: inital (0); Strategy: piggyBac-in-vitro ligation-PCR (template 10ng)


title: 3NNK-EGFP in-vitro ligation-PCR (10ng) library 2nd

description: Library: 3NNK EGFP-chromophore-randomized library (65-67); FACS Rounds: second (2nd); Strategy: piggyBac-in-vitro ligation-PCR (template 10ng)


title: 2225_CP-4011


title: iVO Mock 4 dpi 3


title: iVO Mock 4 dpi 2


title: iVO SARS-CoV-2 B.1.617.2  infected 4 dpi 2


title: iVO Mock 4 dpi 1


title: 2225_CP-3843


title: Periferal blood father [PL1547_Father]

value: Male


title: 3NNK-EGFP in-vitro ligation-PCR (10ng) library 1st

description: Library: 3NNK EGFP-chromophore-randomized library (65-67); FACS Rounds: first (1st); Strategy: piggyBac-in-vitro ligation-PCR (template 10ng)


title: 2225_CP-3844


title: 2225_CP-3748


title: 3NNK-EGFP in-vitro ligation-PCR (10ng) library inital

description: Library: 3NNK EGFP-chromophore-randomized library (65-67); FACS Rounds: inital (0); Strategy: piggyBac-in-vitro ligation-PCR (template 10ng)


title: Extraembryonic mesoderm fetal biopsy [PL1547_EM3323]


title: 2225_CP-3747


title: Chorionic villi fetal biopsy [PL1547_CV3323]


title: RBM25_IP-1

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina NovaSeq 6000 software used for basecalling.
Adaptors and low-quality bases were sheared using FASTX-Toolkit (Version 0.0.13) and reads less than 16 nt were filtered after discarding more than 2-N bases from raw sequencing reads.
Cleaned reads were mapped to the mRatBN7.2 genome with four mismatches using HISAT2. Reads with unique mapping were utilized to calculate fragments per kilobase of transcript per million fragments mapped (FPKM) value for each gene.
After reads were aligned onto the genome, we analysed the unique reads binding regions of RBM25 on genome using “ABLIRC” strategy.
Assembly: mRatBN7.2 genome
Supplementary files format and content: tab-delimited text files include peak information for each group.

organism: Rattus

extract_protocol:
H9C2 cells were irradiated once for 400 mJ/cm2 and lysed in ice-cold wash buffer. Cells lysis was performed in cold Wash buffer (1×PBS, 0.1% SDS, 0.5% NP-40, and 0.5% sodium deoxycholate) supplemented with a 200 U/mL RNase inhibitor (Takara) and protease inhibitor cocktail (Roche) and incubate on ice for 30 min. Clear cell lysate by centrifugation at 10,000 rpm for 10 min at 4°C. Add RQ I (Promega, 1U/μl) to a final concentration of 1 U/μl and incubate in a water bath for 30 min at 37 °C. Immediately afterward, a stop solution was added to the lysates to quench DNase. The mixture was then vibrated vigorously and centrifuged at 13,200 rpm at 4 ℃ for 20 min to remove cell debris. Then RNA digestion by MNase (Thermo Scientific) was performed.
cDNA libraries were prepared with the SMARTer Stranded Total RNA-Seq Kit version 2 (634413;Takara/Clontech) according the manufacturer’s procedure. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina NovaSeq system for 150 nt paired-end sequencing.

value: IP


title: Periferal blood mother [PL150_Mother]


title: 3NNK-EGFP in-vitro ligation-PCR (1ng) library 2nd

description: Library: 3NNK EGFP-chromophore-randomized library (65-67); FACS Rounds: second (2nd); Strategy: piggyBac-in-vitro ligation-PCR (template 1ng)


title: 2225_CP-3569


title: 3NNK-EGFP in-vitro ligation-PCR (1ng) library 1st

description: Library: 3NNK EGFP-chromophore-randomized library (65-67); FACS Rounds: first (1st); Strategy: piggyBac-in-vitro ligation-PCR (template 1ng)


title: RBM25_input-2

value: input


title: 2225_CP-3568


title: Periferal blood father [PL150_Father]

value: Father


title: Periferal blood mother [PL1547_Mother]


title: RBM25_input-1


title: 3NNK-EGFP in-vitro ligation library 2nd

description: Library: 3NNK EGFP-chromophore-randomized library (65-67); FACS Rounds: second (2nd); Strategy:piggyBac-in-vitro ligation


title: 3NNK-EGFP in-vitro ligation-PCR (1ng) library inital

description: Library: 3NNK EGFP-chromophore-randomized library (65-67); FACS Rounds: inital (0); Strategy: piggyBac-in-vitro ligation-PCR (template 1ng)


title: Extraembryonic mesoderm fetal biopsy [PL150_EM794]


title: H9C2_RBM25_3

description:
expressed_gene_FPKM.txt
expressed_gene_reads.txt

data_processing:
Adaptors and low-quality bases were sheared using FASTX-Toolkit (Version 0.0.13) and reads less than 16 nt were filtered after discarding more than 2-N bases from raw sequencing reads.
Cleaned reads were mapped to the mRatBN7.2 genome with four mismatches using HISAT2. Reads with unique mapping were utilized to calculate fragments per kilobase of transcript per million fragments mapped (FPKM) value for each gene.
The R Bioconductor package DESeq2 (Love, Huber et al. 2014) was utilized to screen   out the differentially expressed genes (DEGs). The P value <0.05 and fold change>1.5 or   < 2/3 were set as the cut-off criteria for identifying DEGs.
Assembly: mRatBN7.2 genome
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using Nanodrop One (Thermo). RNA integrity was further verified by 1.5% agarose gel electrophoresis.  For each sample, 1 μg of total RNA was used for RNA-seq library preparation by KAPA Stranded mRNA-Seq Kit for Illumina® Platforms (#KK8544). Polyadenylated mRNAs were purified by VAHTS mRNA capture Beads (N401-01) and Fragmented. Fragmented mRNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to Diluted Roche Adaptor (KK8726). After purification of ligation product and size fractioning to 300-500bps , the ligated products were amplified and purified, quantified and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) is not amplified, allowing strand-specific sequencing.
For high-throughput sequencing, the libraries were applied to Illumina Novaseq 6000 system for 150 nt paired-end sequencing.

value: RBM25 overexpression


title: H9C2_RBM25_2


title: Chorionic villi fetal biopsy [PL150_CV794]

value: Chorionic villi


title: 2225_CP-3055

value: BALB/c


title: 2224_CP-3756


title: 3NNK-EGFP in-vitro ligation library inital

description: Library: 3NNK EGFP-chromophore-randomized library (65-67); FACS Rounds: inital (0); Strategy: piggyBac-in-vitro ligation

value: Human embryonic kidney


title: 3NNK-EGFP in-vitro ligation library 1st

description: Library: 3NNK EGFP-chromophore-randomized library (65-67); FACS Rounds: first (1st); Strategy: piggyBac-in-vitro ligation


title: H9C2_RBM25_1


title: Periferal blood mother [PL142_Mother]


title: 2NNK-BFP in-vitro ligation library 2nd

description: Library: 2NNK EGFP-chromophore-randomized library (65-66); FACS Rounds: second (2nd); Strategy: piggyBac-in-vitro ligation


title: RBM25_IP-2


title: 2224_CP-3755


title: H9C2_Ctrl_3

value: control plasmid


title: Periferal blood father [PL142_Father]


title: 2NNK-EGFP in-vitro ligation library 2nd


title: Extraembryonic mesoderm fetal biopsy [PL142_EM1018]

value: ND

value: Extraembryonic mesoderm


title: 2224_CP-3754


title: 2224_CP-2168


title: Chorionic villi fetal biopsy [PL142_CV1018]


title: 2225_CP-3567


title: Periferal blood mother [PL1400_Mother]

value: Periferal blood


title: 2NNK in-vitro ligation library inital

description: Library: 2NNK EGFP-chromophore-randomized library (65-66); FACS Rounds: inital (0); Strategy: piggyBac-in-vitro ligation


title: 2208_ROSEN-12


title: 2208_CP-4048