|
| Status |
Public on Jun 01, 2016 |
| Title |
testes1 |
| Sample type |
SRA |
| |
|
| Source name |
testes
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: testes
|
| Biomaterial provider |
Ambion
|
| Extracted molecule |
total RNA |
| Extraction protocol |
commerically available Human Testes Total RNA - Ambion AM7972
Sperm RNA was isolated and purified using a modified RNeasy (Qiagen) protocol and finally the RNA quality assessed for DNA contamination as described in paper
A total of 2 ng of unfractionated input RNA was reverse transcribed and the resulting cDNA amplified using SeqPlex RNA Amplification (Sigma-Aldrich Co.) allowing for the use of samples with low quantity of spermatozoa
Amplified primer dimers were removed prior to library construction using Agencourt AMPure XP (Beckman Coulter) and libraries were constructed with 50 ng of amplified cDNA using Encore NGS Library System I (Nugen, Inc.).
4bp inline Illumina index primers allowed for multiplexing of samples
Paired-end sequencing (2x51 + 6Index) was performed using an Illumina HiSeq 2500 sequencer
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
sequencing date: 01/9/2013
|
| Data processing |
Basecalling Illumina RTA 1.17.21.3
demultiplexing (Casava 1.8.2, Illumina)
Alignment to hg19 +18S/28S rRNA using Bowtie39 (v. 2.2.3.0) and splice junction mapper Tophat38 (v.2.0.12)
FPKM coverage for each of 2 testes samples was calcuated based on aligned BAM files using Genomatix Expression Analysis for RNA seq (v3.30126)
Genome_build: hg19
Supplementary_files_format_and_content: Testes-2samples-RPKM.txt - contains FPKM values (Genomatix) for 23180 annotated transcripts (isoform with highest expression)
|
| |
|
| Submission date |
Jun 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Krawetz |
| E-mail(s) |
steve@compbio.med.wayne.edu
|
| Phone |
313-577-6770
|
| Organization name |
Wayne State University School of Medicine
|
| Department |
Center for Molecular Medicine and Genetics
|
| Lab |
C.S. Mott Center for Human Growth and Development
|
| Street address |
275 E. Hancock
|
| City |
Detroit |
| State/province |
MI |
| ZIP/Postal code |
48201 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE69434 |
The protein and transcript profiles of human semen |
|
| Relations |
| BioSample |
SAMN03754346 |
| SRA |
SRX1045004 |
