 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 21, 2020 |
| Title |
miRNA SS2 |
| Sample type |
SRA |
| |
|
| Source name |
spleen
|
| Organism |
Gallus gallus |
| Characteristics |
Sex: female
treatment: 2,000 plaque-forming units (PFU) of the MDV-GA strain
d.p.i: 55-d-old
sample_group: survivor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted from spleen tissues by Trizol (Invitrogen, CA) according to the manufacturer¡¯s instruction.
A total of 3 ¦Ìg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext? Multiplex Small RNA Library Prep Set for Illumina? (NEB, USA.) following the manufacturer¡¯s recommendations and index codes were added to attribute sequences to each sample.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
SS2
|
| Data processing |
Reads containing adapter, poly-N, and low-quality bases at high proportion were removed to obtain clean reads
Short reads were aligned to reference genome using Burrows-Wheeler Aligner (BWA) with ¡®aln¡¯ and ¡®samse¡¯ options and default parameters
Annotated chicken miRNAs file was downloaded from miRbase (http://www.mirbase.org/index.shtml)
Reads counts that assigned to genome were computed by FeatureCounts (0.18.1)
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: Tab-delimited text files include readcount of each Sample
|
| |
|
| Submission date |
Oct 08, 2019 |
| Last update date |
Jan 21, 2020 |
| Contact name |
lulu wang |
| E-mail(s) |
B20183040319@cau.edu.cn
|
| Phone |
15010583049
|
| Organization name |
China Agricultural University
|
| Street address |
Malianwa
|
| City |
Beijing |
| ZIP/Postal code |
100000 |
| Country |
China |
| |
|
| Platform ID |
GPL19005 |
| Series (1) |
| GSE138601 |
Genome-wide studies of microRNAs in Marek's tumorigenesis in Chicken (miRNA-Seq) |
|
| Relations |
| BioSample |
SAMN12995059 |
| SRA |
SRX6965770 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
