|
| Status |
Public on Jun 03, 2020 |
| Title |
Mp_Maize4 |
| Sample type |
SRA |
| |
|
| Source name |
Aphid fed on Zea mays
|
| Organism |
Myzus persicae |
| Characteristics |
line: Fed on Zea mays
treatment: No treatment
tissue: whole body
|
| Treatment protocol |
M. persicae on different plant species were kept separately in quarter cages. M. persicae population on B. rapa were originated from a single asexually female.
|
| Growth protocol |
M.persicae were reared in a SANYO versatile chamber with 14 he day/10 hr night
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit (250) from QIAGEN
Strand-specific libraries constructed using the Illumina TruSeq RNA Library Preparation kit following manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw fastq files were converted to fasta format.
Adapter sequences and reads less than 20 nt were trimmed using Trim Galore
Trimmed reads were aligned to the human genome (v.38) using HISAT2
Count matrix for genes was created using Kallisto
Differential expression analysis was done using the DESeq2 package available in R
Genome_build: Myzus persicae
|
| |
|
| Submission date |
Apr 11, 2019 |
| Last update date |
Jun 03, 2020 |
| Contact name |
Archana Singh |
| E-mail(s) |
archana.bhubioinfo@gmail.com
|
| Organization name |
Cambridge University
|
| Department |
Plant Science
|
| Street address |
Downing Street
|
| City |
Cambridge |
| State/province |
England |
| ZIP/Postal code |
CB23EA |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL26490 |
| Series (2) |
| GSE129667 |
An aphid lncRNA is a member of an aphid-specific family that translocates into plant and is a virulence factor [HostSwap Expt] |
| GSE129669 |
An aphid lncRNA is a member of an aphid-specific family that translocate into plant and is a virulence factor |
|
| Relations |
| BioSample |
SAMN11399152 |
| SRA |
SRX5670498 |
