|
| Status |
Public on Dec 31, 2018 |
| Title |
Dnmt1cKO_urogenital epithelium_2 |
| Sample type |
SRA |
| |
|
| Source name |
E15.5 Urogenital epithelium
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue type: Urogenital epithelium
age: E15.5
genotype (experimental group): Dnmt1cKO
|
| Treatment protocol |
None
|
| Growth protocol |
Embryos generated by timed matings
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Urogenital epithelium 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 |
mUGE_b3_rep1
jat_063818_0100650__S27_L005
jat_063818_0100692__S27_L004
|
| 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 |
Oct 10, 2018 |
| Last update date |
Dec 31, 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) |
| GSE121086 |
Comparison of DNA methyltransferase-1 (Dnmt1) deleted urogenital sinus epithelium compared to wildtype urogenital sinus epithelium |
|
| Relations |
| BioSample |
SAMN10228296 |
| SRA |
SRX4824521 |
