|
| Status |
Public on Mar 16, 2020 |
| Title |
OFT-banded heart 3 |
| Sample type |
SRA |
| |
|
| Source name |
Heart
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: Heart
age: HH29
sample type: outflow tract
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hearts were removed, flash frozen in liqid nitrogen, and RNA was harvested using Trizol reagent. NEBNext Ultra directional RNA library Prep Kit for Illumina (NEB#E7420S/L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols for paired end sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RPKM_OFT-banded_chick_heart_RNA_Seq.txt
|
| Data processing |
Base-calling done with cl2fastq, Illumina standard processing
Compressed FASTQ files were trimmed to filter reads for adapter and low quality bases, then mapped to galGal4 reference genome using Tophat (https://ccb.jhu.edu/ software/tophat/index.shtml) to known gene exon coordinates
Alignment counts were recorded in BAM format with only uniquely mapped read alignment hits (47-90 x 106) having a quality score of MAPQ ≥ 20 used. Htseq-count was used for generation of count tables.
Read counts were then normalised using FPKM.Genes with average FPKM values <1 were filtered from the FPKM data before gene regulation was assessed using DESeq adjusted p-values (FDRs).
Genome_build: galGal4
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample...
|
| |
|
| Submission date |
Sep 26, 2018 |
| Last update date |
Mar 16, 2020 |
| Contact name |
Chrysostomos Perdios |
| Organization name |
The University of Nottingham
|
| Department |
Medical School
|
| Lab |
C5
|
| Street address |
Queen's Medical Centre, Derby Road
|
| City |
Nottingham |
| State/province |
Nottinghamshire |
| ZIP/Postal code |
NG7 2UH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19787 |
| Series (1) |
| GSE120498 |
Characterisation of the outflow tract banded heart utilising RNA sequencing to direct functional analysis |
|
| Relations |
| BioSample |
SAMN10132215 |
| SRA |
SRX4740934 |
