|
| Status |
Public on Jul 19, 2018 |
| Title |
Control_2 |
| Sample type |
SRA |
| |
|
| Source name |
Bladder urothelium
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6; 129S4
tissue: Bladder urothelium
age: Embryonic day 15.5
genotype: Control:Shhcre/+; Dnmt1flox/+
|
| Growth protocol |
Embryos generated by timed matings
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bladder urothelium separated from stroma by trypsin digestion. Dissected tissues were placed directly into RLT Plus lysis buffer (Qiagen) for later processing. For each batch of harvest, dissected tissues from multiple embryos were pooled into one lysate. Total RNA was purified from the RLT Plus lysates using the RNeasy Plus Micro Kit (Qiagen) according to manufacturer’s instructions.
The following is an excerpt from Hou et al, Sci Rep. 2015; 5:9570, the manuscript that details the protocol employed. Poly-A-tailed mRNA is isolated from total RNA using oligo-dT beads. Purified mRNA is then fragmented with heat in fragmentation buffer. First strand cDNA is then synthesized using random hexamer oligos containing partial Illumina 3′ adaptor sequence. After RNA removal, a modified oligo containing partial Illumina's 5′ adaptor is then ligated to the 5′ of the single stranded cDNA. The library is then amplified by PCR using oligos that contain full Illumina adaptor sequences and our in-house index sequences.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
jat063842
|
| Data processing |
Basecalls/demuxxing performed using Illumina bcl2fastq, v2.17.1.14
Reads were filtered and trimmed for adapters and quality.
Expression estimates were calculated using RSEM v1.2.3 with alignments by bowtie v0.12.9
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file with a table of Expected Counts expression estimates from the RSEM application
|
| |
|
| Submission date |
Jun 07, 2018 |
| Last update date |
Jul 19, 2018 |
| Contact name |
Chad Michael Vezina |
| Organization name |
University of Wisconsin-Madison
|
| Department |
Comparative Biosciences
|
| Street address |
1656 Linden Drive
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE115477 |
In vivo replacement of damaged bladder urothelium by Wolffian duct epithelial cells |
|
| Relations |
| BioSample |
SAMN09380099 |
| SRA |
SRX4180385 |
