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| Status |
Public on May 22, 2024 |
| Title |
Green ringtail possum (Sample1772) |
| Sample type |
SRA |
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| Source name |
kidney
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| Organism |
Pseudochirops archeri |
| Characteristics |
tissue: kidney
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extractions for WGS libraries were done using DNeasy blood & tissue kit
The Hi-C libraries were prepared following the in situ Hi-C strategy (Rao, Huntley et al., 2014). Briefly, cells or tissue were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads. Afterward DNA was handled according to standard Illumina library construction protocol. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo-) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3 end. After adapter ligation DNA was PCR amplified with Illumina primers and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on various Illumina instruments following the manufacturer's protocols. Fpr the tammar wallaby, a short insert-size PCR-free DNA-Seq library was prepared following the ClaSeek protocol.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
w2rap/Juicer/3D-DNA/JBAT
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| Data processing |
Short-read assembly using w2rap (Clavijo, 2017); Hi-C-guided genome assembly (Juicer, 3D-DNA, JBAT); RagTag assembler (Alonge et al., 2022) for Dactylopsila trivirgata and Distoechurus pennatus
Assembly: Generated as part of the study
Supplementary files format and content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly; RagTag assisted assemblies for Dactylopsila trivirgata and Distoechurus pennatus
Library strategy: In situ Hi-C; ClaSeek PCR-free DNA-Seq.
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| Submission date |
Feb 23, 2024 |
| Last update date |
May 22, 2024 |
| Contact name |
Olga Dudchenko |
| E-mail(s) |
Olga.Dudchenko@bcm.edu
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| Organization name |
Baylor College of Medicine
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| Street address |
1 Baylor Plaza
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL34234 |
| Series (1) |
| GSE256507 |
Emx2 underlies the development and evolution of marsupial gliding membranes |
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| Relations |
| BioSample |
SAMN40044684 |
| SRA |
SRX23714667 |
| SRA |
SRX23714670 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8102041_Pseudochirops_archeri_HiC.fasta.gz |
994.4 Mb |
(ftp)(http) |
FASTA |
SRA Run Selector |
| Raw data are available in SRA |
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