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SRX13429825: WGS for enriched MHC of NA12878
1 ILLUMINA (Illumina NovaSeq 6000) run: 26.7M spots, 8G bases, 2.5Gb downloads

Design: Illumina sequencing for enriched MHC of NA12878
Submitted by: Fudan University, China
Study: Targeted haplotype-resolved assembly provides insights into allele-specific regulation of the MHC region
PRJNA789659 • SRP351160 • All experiments • All runs
show Abstracthide Abstract
We implemented targeted haplotype-resolved assembly of MHC region, amethod combining CRISPR/Cas9 targeted enrichment of high-molecular weight(HMW) MHC DNA, followed by 10x Genomics linked-reads sequencing and PacBiohigh-fidelity (HiFi) reads sequencing.Two fully phased haplotypeswith high accuracy and integrity were generated without using parent-child trioinformation. We further discovered and varied the allele-specific methylation andexpression events spanning the MHC region using the haplotype reference.
Sample: Illumina(MHC-1)
SAMN24146079 • SRS11330775 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: NA12878_PG1
Instrument: Illumina NovaSeq 6000
Strategy: WGS
Source: GENOMIC
Selection: PCR
Layout: PAIRED
Runs: 1 run, 26.7M spots, 8G bases, 2.5Gb
Run# of Spots# of BasesSizePublished
SRR1725093426,686,1308G2.5Gb2022-11-15

ID:
18578678

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  • SRR17250934 (1)
    SRA
  • E3 ubiquitin-protein ligase CHIP isoform a [Homo sapiens]
    E3 ubiquitin-protein ligase CHIP isoform a [Homo sapiens]
    gi|56181387|ref|NP_005852.2|
    Protein
  • Peripatopsis sedgwicki voucher NZAC:03005939 28S ribosomal RNA gene, partial seq...
    Peripatopsis sedgwicki voucher NZAC:03005939 28S ribosomal RNA gene, partial sequence
    gi|285029460|gb|GQ911164.1|
    Nucleotide
  • Formicidae sp. NZAC 03009293 voucher NZAC:03009293 28S ribosomal RNA gene, parti...
    Formicidae sp. NZAC 03009293 voucher NZAC:03009293 28S ribosomal RNA gene, partial sequence
    gi|983652912|gb|KT439721.1|
    Nucleotide
  • RecName: Full=Genome polyprotein; Contains: RecName: Full=Capsid protein C; AltN...
    RecName: Full=Genome polyprotein; Contains: RecName: Full=Capsid protein C; AltName: Full=Core protein; Contains: RecName: Full=Protein prM; Contains: RecName: Full=Peptide pr; Contains: RecName: Full=Small envelope protein M; AltName: Full=Matrix protein; Contains: RecName: Full=Envelope protein E; Contains: RecName: Full=Non-structural protein 1; Short=NS1; Contains: RecName: Full=Non-structural protein 2A; Short=NS2A; Contains: RecName: Full=Serine protease subunit NS2B; AltName: Full=Flavivirin protease NS2B regulatory subunit; AltName: Full=Non-structural protein 2B; Contains: RecName: Full=Serine protease NS3; AltName: Full=Flavivirin protease NS3 catalytic subunit; AltName: Full=Non-structural protein 3; Contains: RecName: Full=Non-structural protein 4A; Short=NS4A; Contains: RecName: Full=Peptide 2k; Contains: RecName: Full=Non-structural protein 4B; Short=NS4B; Contains: RecName: Full=RNA-directed RNA polymerase NS5; AltName: Full=Non-structural protein 5
    gi|81988679|sp|Q6YMS3.1|POLG_DEN3M
    Protein

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