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| Status |
Public on Jun 18, 2024 |
| Title |
Blister gall Rep1 |
| Sample type |
SRA |
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| Source name |
Oak Gall
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| Organism |
Quercus robur |
| Characteristics |
tissue: Oak Gall
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| Growth protocol |
Tissue harvested from one mature oak tree
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted was carried out using a modified CTAB method (Pushkova et al., 2019, Barbier et al., 2019). 0.5ml of CTAB buffer (100mM Tris-HCL, pH9.5, 2% CTAB, 1.4M NaCl, 1% PEG 8000, 20mM EDTA, 2% PVP-40, 40mM DTT) and 2µl proteinase K was added to 50mg of ground tissue. This was incubated for 5 minutes at 65°C. 60µl of 10% SDS was then added, the tube inverted, and 1 volume of chloroform added. The samples were vortexed for 10 seconds, centrifuged (4°C, 5500xg,10 minutes). The aqueous phase was taken and mixed with an equal volume of chloroform. After centrifugation (room temperature, 14,000xg, 5 minutes), the aqueous phase was taken and precipitated overnight with 0.5 volumes of 7.5M Ammonium acetate and 2.5 volumes of ethanol. After extraction the RNA was treated with turbo DNAse (Invitrogen, AM2238) according to the manufacturer instructions.
mRNA library preparation (poly A enrichment)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
QC using fastqc and fastp
Sequence reads were trimmed for adaptor sequence / low-quality sequence using fastp with mean read quality of 20
kallisto used for mapping filtered paired end reads
trimmed sequence reads were mapped using kallisto v0.46.0
quantification and normalization were performed using kallisto software
Assembly: Reference transcriptome: Quercus robur downloaded from urgi.versailles.inra.fr
Supplementary files format and content: tab-delimited text file includes estimeated reads count for each sample calculated using kallisto
Supplementary files format and content: tab-delimited text file includes tpm value for each sample calculated using kallisto
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| Submission date |
Sep 27, 2023 |
| Last update date |
Jun 18, 2024 |
| Contact name |
Rupert Fray |
| Organization name |
University of Nottingham
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| Street address |
Sutton Bonington Campus
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| City |
Sutton Bonington |
| ZIP/Postal code |
LE12 5RD |
| Country |
United Kingdom |
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| Platform ID |
GPL33794 |
| Series (1) |
| GSE244168 |
Comparative transcriptome reprogramming in oak galls containing sexual or asexual generations of parasitoid wasps |
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| Relations |
| BioSample |
SAMN37565311 |
| SRA |
SRX21906603 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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