|
| Status |
Public on Mar 18, 2011 |
| Title |
layer_reads |
| Sample type |
SRA |
| |
|
| Source name |
layer skeletal muscle at embryonic 10 days
|
| Organism |
Gallus gallus |
| Characteristics |
breed: White Leghorn
|
| Treatment protocol |
skeletal muscles (pectoralis) were collected from broilers and layers at E10 stage, immediately frozen in liquid nitrogen, and stored at -80°C until RNA isolation.
|
| Growth protocol |
Meat-type broiler eggs (commercial Arbor Acres) and egg-type layer eggs (White Leghorn) were incubated at 37.5°C for 10 days (E10).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from skeletal muscles using the Trizol reagent (Invitrogen) and precipitated overnight at -20°C. Approximately 20 μg of Total RNA from broiler and layer chickens were submitted to Beijing Genomics Institute (BGI) for Solexa sequencing. In brief, the sequencing was performed as follows: total RNA was fractionated by polyacrylamide gel electrophoresis (PAGE), to enrich for molecules in the range of 16-30 nt, and ligated with proprietary adapters. Following adaptor ligation, the RNA was reverse transcribed for cDNA synthesis. The cDNA was amplified with 15 PCR cycles to produce sequencing libraries that were subjected to sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
short RNA
|
| Data processing |
0. Run Solexa pipeline
Data were deposited in *.fastq files (.fq format)
1. Filter low quality reads and trimming adaptors
Data were deposited in *_clean_reads_16-30.txt files
File format: one line for one read, delimited by tab.
Column1 is the raw read.
Column2 is the corresponding quality.
Column3 is the length of read after trimming adaptor.
Column4 is the number of error base localizing in trimmed adaptor.
Column5 is the read after trimming adapter
4. Group all identical sequence reads together
Data were deposited in all_nr.fas (.fasta format)
For each id:
eg. >nr1 26(bp) L:1 B:0
>id reads-length L:reads-number-in-layer B:reads-number-in-broiler
5. Map reads to the UCSC chicken genome galGal3 by ZOOM with perfect match.
Data were deposited in all_nr_ZOOM_mm0.bed (BED format)
Column1 is the chromosome.
Column2 is the start position.
Column3 is the end position.
Column4 is the name. eg. nr136536_L0_B1 id_L(reads number in layer)_B(reads number in broiler)
Column5 is the reads length.
Column6 is the strand.
|
| |
|
| Submission date |
Mar 18, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Tingting Li |
| E-mail(s) |
litt@hsc.pku.edu.cn
|
| Phone |
+86-10-82801585
|
| Organization name |
Peking University
|
| Department |
Medical informatics
|
| Street address |
38 Xueyuan Rd
|
| City |
Beijing |
| ZIP/Postal code |
100191 |
| Country |
China |
| |
|
| Platform ID |
GPL10223 |
| Series (2) |
| GSE20942 |
Characterization of miRNA transcriptome of skeletal muscle from broiler and layer chicken lines by deep sequencing |
| GSE20992 |
Systematic analysis of miRNA transcriptome of skeletal muscle identifies novel miRNAs and differentially expressed miRNAs in divergent skeletal muscle growth rates of broiler and layer chickens |
|
| Relations |
| SRA |
SRX017843 |
| BioSample |
SAMN00010218 |
