 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 06, 2014 |
| Title |
sertoli upf2 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
testis
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: testis
age: post natal day 4
genotype: Upf2 KO
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Normal growth
|
| Extracted molecule |
total RNA |
| Extraction protocol |
P4 Testes were removed, frozen in RNA shield (Zymo), and RNA was harvested using Trizol reagent.mRNAs purified from 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using TOPHAT
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated and isoforms were assembled by using a protocol from Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: RPKM
|
| |
|
| Submission date |
Jun 11, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Yan |
| E-mail(s) |
wyan@medicine.nevada.edu
|
| Phone |
(775) 784-7765
|
| Organization name |
University of Nevada
|
| Department |
Physiology
|
| Lab |
Wei Yan Lab
|
| Street address |
1664 N. Virginia Street
|
| City |
reno |
| State/province |
NV |
| ZIP/Postal code |
89557 |
| Country |
USA |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN02850766 |
| SRA |
SRX590161 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
