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Sample GSM3425841 Query DataSets for GSM3425841
Status Public on Dec 31, 2018
Title Dnmt1cKO_urogenital epithelium_3
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_b4_rep1
jat_063819_0100651__S28_L005
jat_063819_0100693__S28_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 SAMN10228295
SRA SRX4824522

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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