|
| Status |
Public on Nov 01, 2015 |
| Title |
Mouse_Adult_Testes_Asb1_AO34(Het)_mRNA |
| Sample type |
SRA |
| |
|
| Source name |
Mouse_Adult_Testes_Asb1_AO34(Het)_mRNA
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: Asb1 +/-
age: adult
Sex: male
tissue: testes
molecule subtype: messenger RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse, rat and rabbit testes were homogenized as described in Lau et al, Science. 2006 Jul 21;313(5785):363-7., and this extract was used only for the Mili (Piwil2) IP experiments. For total RNA, testes were pulverized into powder while frozen and thawed into Tri-reagent solution to extract RNA according to the manufacterur (MRC) instructions
Small RNA libraries were constructed using the custom protocol described in Matts et al. Methods Mol Biol. 2014;1093:123-36. Messenger RNA libraries were constructed with the Epicentre ScriptSeq v2 kits.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The adapter sequence based on the standard Illumina linkers were only removed on the small RNA reads. The full sequence of this adapter linker is CGTCGTATGCCGTCTTCTGCTTGT.
The linker sequence was first removed by fastx_clipper program from FASTX Toolkit(0.0.13) with the parameters: "-a CGTCGTATGCCG -M 9 -n -l 20"
The shorter linkers on remaining reads were removed by searching for where the last 2 to 8 base pairs matches perfactly to the first 2 to 8 base pairs of the adapter sequence (CGTCGTATGCCG)
The final filtering step removed reads if its entire sequence contained more than 12 base pairs of poly(A/C/G/T).
No additional processing was performed on mRNA reads.
Supplementary_files_format_and_content: text files of sequences for each RNA read
|
| |
|
| Submission date |
Oct 21, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
NELSON LAU |
| E-mail(s) |
[email protected]
|
| Organization name |
Boston University School of Medicine
|
| Department |
Biochemistry
|
| Street address |
72 E Concord St K219, Dept of Biochemistry
|
| City |
BOSTON |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE62556 |
The evolution of genic piRNA cluster loci expression patterns |
|
| Relations |
| BioSample |
SAMN03121869 |
| SRA |
SRX737161 |
