|
| Status |
Public on Jan 31, 2023 |
| Title |
LS007 genomic HiC |
| Sample type |
SRA |
| |
|
| Source name |
juvenile whole leaf
|
| Organism |
Lathyrus sativus |
| Characteristics |
tissue: juvenile whole leaf
genotype: LS007
treatment: sand/vermiculite/perlite, growth chamber
time: 4 weeks after imbibing
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
cross-linked, Phase Genomics extraction
Phase Genomics proprietary
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
HiC data used for assembly scaffolding
|
| Data processing |
FastQC
Kontaminant pipeline (removing contaminants using sortmerna v2.0)
Trimmed sequence reads (trim_galore v 0.4.1)
read mapping using Kallisto
Assembly: Rbp1.0 grasspea assembly that is published with manuscript
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jan 29, 2023 |
| Last update date |
Jan 31, 2023 |
| Contact name |
Martin Vickers |
| E-mail(s) |
martin.vickers@jic.ac.uk
|
| Organization name |
John Innes Centre
|
| Street address |
Colney Ln
|
| City |
Norwich |
| State/province |
Norfolk |
| ZIP/Postal code |
NR4 7UH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL33069 |
| Series (1) |
| GSE223956 |
Sequence data for annotation and scaffolding of the Lathyrus sativus LS007 Rbp1.0 genome assembly |
|
| Relations |
| BioSample |
SAMN32953636 |
| SRA |
SRX19210597 |
