|
| Status |
Public on Feb 24, 2021 |
| Title |
EPAS_MO_ 3 |
| Sample type |
SRA |
| |
|
| Source name |
Chick embryo derived trunk neural crest cells
|
| Organism |
Gallus gallus |
| Characteristics |
cell type: Trunk neural crest cells
modification: EPAS1 morpholino
age (hh stage): HH16
|
| Treatment protocol |
Embryos were injected and electroporated with morpholinos at stage HH10+.
|
| Growth protocol |
Embryos were allowed to grow in an incubator set at 37.5°C until stage HH16 was reached.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Ambion RNAqueous Micro Kit (AM1931)
Library was prepared according to TruSeq® Stranded mRNA Sample Preparation Guide (Part # 15031047 Rev. E) Modification of “Enrich DNA Fragment” step: from 15 to 13 PCR cycles.
TruSeq® Stranded mRNA Library Prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Demultiplexing: organized the FASTQ files based on the sample index information, and generated the statistics and reporting files. This task was performed using the bcl2fastq2 software with default settings
Raw Quality Control (QC): FastQC provided quality control analyses and checked on raw sequence data coming from the above Demultiplexing step of the pipeline.
Read Mapping: alignment of reads to the specified reference genome. This task was performed using the HISAT2 software package, and the reference genome sequence was from the Ensemble database, the Gallus Gallus 5.0, and the annotation (GTF) from the release 92.
Mapping QC: mapping quality control checked such as evaluating the distribution of reads mapped by the above mapping step.
Expression counts: assembled the alignments into full transcripts and quantified the expression levels of each gene and transcript. This task was performed using the StringTie software package.
DE analysis: Differentially expressed genes (DEG) analysis was performed using DESeq2.
Genome_build: Gallus Gallus 5.0,
Supplementary_files_format_and_content: tab-separated text files generated by StringTie software package; contains expression counts
|
| |
|
| Submission date |
Nov 13, 2019 |
| Last update date |
Feb 24, 2021 |
| Contact name |
Sofie Mohlin |
| E-mail(s) |
sofie.mohlin@med.lu.se
|
| Organization name |
Lund University
|
| Department |
Clinical Sciences
|
| Street address |
TCR, MV404:C3, Scheelevagen 8
|
| City |
Lund |
| ZIP/Postal code |
22363 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL27748 |
| Series (1) |
| GSE140319 |
Cancer associated HIF-2a governs trunk neural crest stemness |
|
| Relations |
| BioSample |
SAMN13279664 |
| SRA |
SRX7135249 |
