|
| Status |
Public on Apr 06, 2021 |
| Title |
RORaDN-3 |
| Sample type |
SRA |
| |
|
| Source name |
neutrophils
|
| Organism |
Danio rerio |
| Characteristics |
cell type: neutrophils
genotype: RORa-dominant negative
|
| Treatment protocol |
Transgenic lines expressing RORa-dominant negative or mcherry were used.
|
| Growth protocol |
zebrafish were grow in circulating system
|
| Extracted molecule |
total RNA |
| Extraction protocol |
tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing.
miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145-160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Clontech Laboratories, Inc.).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina Novaseq 6000.
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the zebrafish genome using STAR (v2.5) RNA-seq aligner with the following parameter “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to genes using featureCounts (from subread v1.5.1) with the following parameters: for Samples 1-5: “-s 1 –Q 10”, for Samples 6-11, "-p -Q 10".
The data was filtered using read count per million (CPM) > 0.5 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: GRCz11
Supplementary_files_format_and_content: Raw counts and differential analysis
|
| |
|
| Submission date |
Apr 05, 2021 |
| Last update date |
Apr 06, 2021 |
| Contact name |
Qing Deng |
| E-mail(s) |
qingdeng@purdue.edu
|
| Phone |
765-494-0423
|
| Organization name |
Purdue University
|
| Department |
Department of Biological Sciences
|
| Street address |
915 W. State Street
|
| City |
West Lafayette |
| State/province |
Indiana |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL24995 |
| Series (1) |
| GSE171501 |
RORa is required for neutrophil migration |
|
| Relations |
| BioSample |
SAMN18619432 |
| SRA |
SRX10514122 |
