|
| Status |
Public on Mar 06, 2015 |
| Title |
Control #3 Skeletal muscle |
| Sample type |
SRA |
| |
|
| Source name |
~Day 105 fetal skeletal muscle
|
| Organism |
Bos indicus x Bos taurus |
| Characteristics |
disease status: healthy
tissue: skeletal muscle
developmental stage: Day 105 fetus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At tissue collection, liver, skeletal muscle, brain, and kidney were well diced, mixed, and snap frozen in liquid nitrogen and stored at -80°C. Total RNA from fetal tissues was isolated using Trizol Reagent (Invitrogen) according to the manufacturer's instructions. RNA quality was determined by both spectrometry and agarose gel electrophoresis.
For each sample, 5μg RNA was submitted to the DNA core at University of Missouri, Columbia for RNAseq library preparation using Illumina TruSeq RNA sample preparation kit. Briefly, poly-A containing RNA was purified using magnetic beads with oligo-dT attached. The purified RNA was fragmented and used as a template for cDNA synthesis using random primers. In the following end-repair procedure, an "A" was added to the 3' end of the cDNA. The cDNA fragments with A-tailing were then ligated with T-tailing adaptors. PCR amplifications of cDNA fragments were followed to generate the final RNAseq library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Raw read counts of imprinted genes in skeletal muscle
|
| Data processing |
Base calling was perfomed using version 1.8 of the CASAVA package from Illumina
Adator sequences of the reads were removed with the use of FastqMcf program (version 1.04.636). Low quality reads were filtered out using DynamicTrim (version 1.13)
Reads were aligned using TopHat2 (version 2.0.10) with Bowtie2 scoring option (--score-min L,0,-0.2 --mp 6,6). Known splice junction from RefSeq and Ensembl were supplied for alignment
Cufflinks (version 2.1.1) was used to assembl the transcripts and assembled transcripts of each sample were merged into a single set of genes and transcripts using Cuffmerge (version 2.1.1)
Htseq (version 0.5.4) was used to make read counts for each imprinted genes and edgeR was used for differential gene expression analysis.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab deliminated text file of raw read counts of the imprinted genes in each tissue of each fetus
|
| |
|
| Submission date |
Nov 20, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Rocio Melissa Rivera |
| E-mail(s) |
riverarm@missouri.edu
|
| Phone |
5738826765
|
| Organization name |
University of Missouri, Columbia
|
| Department |
Division of Animal Sciences
|
| Street address |
920 East Campus Drive
|
| City |
Columbia |
| State/province |
MO |
| ZIP/Postal code |
65211 |
| Country |
USA |
| |
|
| Platform ID |
GPL21383 |
| Series (1) |
| GSE63509 |
Characterization of global loss of imprinting in overgrowth syndrome induced by assisted reproduction |
|
| Relations |
| BioSample |
SAMN03202928 |
| SRA |
SRX764732 |
