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| Status |
Public on Sep 17, 2020 |
| Title |
Pm_mantle_a |
| Sample type |
SRA |
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| Source name |
mantle tissue of the King Scallop
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| Organism |
Pecten maximus |
| Characteristics |
tissue: mantle
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were disrupted manually with a pestle in liquid nitrogen before RNA extraction using RNeasy universal kit (Qiagen).
Libraries were made at the Wellcome Sanger Institute. These were made according to their autoRNA library preparation process, with poly(A) pulldown, fragmentation, 1st and 2nd strand synthesis, end prep and ligation using the NEB Ultra II RNA custom kit (New England Biolabs, Massachusetts, United States) on an Agilent Bravo WS automation system (Agilent, California, United States). 14 rounds of PCR were used in library construction.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Initial trimming of poor quality sequence and residual Illumina adaptors with TrimGalore v0.6 at default parameters.
Reads were mapped using STAR 2.7 with the --quantMode GeneCounts option to a genome library of xPecMax.fa (produced using --sjdbOverhang 149)
Genome_build: GCA_902652985.1
Supplementary_files_format_and_content: Tab-delimtied STAR output of read counts
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| Submission date |
Mar 17, 2020 |
| Last update date |
Sep 18, 2020 |
| Contact name |
Katherine James |
| E-mail(s) |
[email protected]
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| Organization name |
Newcastle University
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| Department |
School of Computing
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| Street address |
Urban Sciences Building
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| City |
Newcastle upon Tyne |
| ZIP/Postal code |
NE1 7RU |
| Country |
United Kingdom |
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| Platform ID |
GPL28284 |
| Series (1) |
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| Relations |
| BioSample |
SAMN14390692 |
| SRA |
SRX7924984 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4417291_read_counts_Pm_mantle_a.tab.gz |
800.1 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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