|
| Status |
Public on Sep 05, 2020 |
| Title |
Rat 13 Brain microRNA seq |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Rattus norvegicus |
| Characteristics |
animal number: 13
treatment: Whole Egg
strain: Lean
|
| Treatment protocol |
Animals were fed their respective diets, either Whole Egg or Casein.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue samples were homogenized on ice and total RNA was extracted using a Lexogen SPLIT RNA Extraction kit following the manufacturers instructions.
Libraries were prepared according to Lexogens instructions accompanying the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina and small RNA sequencing kits. Briefly, the Quantseq kit uses total RNA as input, hence no prior poly(A) enrichment or rRNA depletion is needed. Library generation starts with oligodT priming containing the Illumina-specific Read 2 linker sequence. After first strand synthesis the RNA is removed. Second strand synthesis is initiated by random priming and a DNA polymerase. The random primer contains the Illumina-specific Read 1 linker sequence. At this step Unique Molecular Identifiers (UMIs) can be introduced by exchanging the Second Strand Synthesis Mix 1 (SS1) from the standard QuantSeq FWD Kit with UMI Second Strand Synthesis Mix (USS). No purification is required between first and second strand synthesis. Second strand synthesis is followed by a magnetic bead-based purification step rendering the protocol compatible with automation. During the library amplification step sequences required for cluster generation are introduced. NGS reads are generated towards the poly(A) tail and directly correspond to the mRNA sequence. To pinpoint the exact 3’ end, Libraries were sequenced on the Illumina HiSeq 3000 following the manufacturer's protocols.
RNA-seq, miRNA-seq
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
microRNA seq
S4.xlsx
S3.xlsx
|
| Data processing |
Basecalls performed by the ISU DNA facility and data processing steps were followed according to the manufacturers guidelines here: https://www.lexogen.com/wp-content/uploads/2015/11/015UG009V0211_QuantSeq-Illumina.pdf
Briefly, fastq quality control tool FastQC was used to examine the quality of the sequencing run.
Next, adapters were trimmed using BBDUK and sequences were reanalyzed using FastQC
Reads were mapped to the RNO_6 genome using RNA STAR and read counts were simultaneously quantified using the --read-counts flag
Genome_build: RNO_6
Supplementary_files_format_and_content: mRNA DESEQ results.xlsx
Supplementary_files_format_and_content: mRNA Raw Reads.xlsx
Supplementary_files_format_and_content: microRNA DESEQ results.xlsx
Supplementary_files_format_and_content: microRNA Raw Reads.xlsx
|
| |
|
| Submission date |
Sep 04, 2020 |
| Last update date |
Sep 05, 2020 |
| Contact name |
Joe Webb |
| Organization name |
Iowa State University
|
| Lab |
Schalinske Lab
|
| Street address |
2302 Osborn drive, 220 Mackay Hall
|
| City |
Ames |
| State/province |
IA |
| ZIP/Postal code |
50010 |
| Country |
USA |
| |
|
| Platform ID |
GPL23945 |
| Series (1) |
| GSE157491 |
Influence of dietary whole egg on the transcriptome in Zucker Diabetic Fatty rats |
|
| Relations |
| BioSample |
SAMN16058485 |
| SRA |
SRX9075508 |
