|
| Status |
Public on Aug 17, 2016 |
| Title |
Control #1 Placenta |
| Sample type |
SRA |
| |
|
| Source name |
Placenta of day ~105 conceptus
|
| Organism |
Bos indicus x Bos taurus |
| Characteristics |
tissue: placenta
developmental stage: four day ~105 conceptus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol Reagent (Invitrogen) according to the manufacturer's instructions. Semen DNA was isolated using phenol chloroform method.
RNAseq libraries were prepared 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. Two DNAseq libraries (one with 350bp target insert size, the other with 550bp target insert size) were prepared using Illumina TruSeq DNA PCR-Free Sample Preparation Kit according to the manufacturer’s instructions (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Bos indicus X Bos taurus F1 hybrid
|
| 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 3.3.1)
DNAseq read pairs were aligned to the bovine reference genome assembly UMD3.1 using Bowtie2 (version 2.2.3)
Genome Analysis Tool Kit (version 3.3-0) and SAMtools mpileup (version 0.1.19) were used for SNP calling from the uniquely aligned DNAseq reads
A pseudo Bos indicus genome was generated by editing the reference allele (UMD3.1; i.e. Bos taurus) with the SNPs identified in the Bos indicus sire. A diploid genome was generated by combining the Bos taurus and the pseudo Bos indicus FASTA files.
RNAseq reads of the Bos indicus X Bos taurus F1 conceptuses were aligned to the diploid genome using HISAT2 (version: 2.0.0) and BWA mem (version:0.7.7)
Cufflinks (version: 2.2.1) and Cuffmerge (version: 2.2.1) were used to assemble transcripts from the uniquely aligned RNAseq reads
RNAseq read counts for each gene model were generated using Htseq-count (version: 0.5.4) and read counts were normalized using edgeR (version: 3.8.6)
SNPiR pipeline (Piskol et al., 2013) was adapted to identify SNPs in RNAseq data. The parental-allele-origin of the RNA variants were assigned accoding to the Bos indicus sire DNAseq reads
Allele-specific read counts for SNPs in the same gene were aggregated for allele-specific expression analyes.
Genome_build: UMD3.1
Supplementary_files_format_and_content: The SNPs of the Bos indicus sire used to assgin allele-origin of the RNAseq reads from the Bos indicus X Bos taurus F1 hybrids, allele-sepcific read counts of the monoallelically expressed genes identified in this study
|
| |
|
| Submission date |
Jan 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Rocío Melissa Rivera |
| E-mail(s) |
riverarm@missouri.edu
|
| Organization name |
University of Missouri, Columbia
|
| Department |
Animal Sciences
|
| Street address |
920 East Campus Drive, ASRC 164
|
| City |
Columbia |
| State/province |
MO |
| ZIP/Postal code |
65211 |
| Country |
USA |
| |
|
| Platform ID |
GPL21383 |
| Series (1) |
| GSE77389 |
Global assessment of imprinted gene expression in the bovine conceptus by next generation sequencing |
|
| Relations |
| BioSample |
SAMN04448266 |
| SRA |
SRX1553598 |
