|
| Status |
Public on Aug 29, 2022 |
| Title |
lepb+ M. marinum 2 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryos
|
| Organism |
Danio rerio |
| Characteristics |
genotype: wild type
tissue: whole embryos
time: 5 days post fertilization
|
| Treatment protocol |
M. marinum infection
|
| Growth protocol |
Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://zfin.org).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Zebrafish larvae from lepb+ and lepbibl54 infected and control groups (15 pooled larvae/replicate, n=3) were resuspended and crushed in 0.5 ml of TRIzol Reagent.
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S/L) was used to process the samples. Briefly, mRNA was isolated from total RNA using oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation of the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with Fragment Analyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
150 nucleotides
Ding_Lepb++Mm vs lepb++ pvp_DEseq.xlsx, Ding_Lepb--Mm vs ++Mm_DEseq.xlsx
HTHCLDMXX_104090-002-005RR
|
| Data processing |
Sequencing data of zebrafish larvae were aligned and mapped to the zebrafish genome GRCz11 using CLC Genomics, and differential gene expression was analyzed using DESeq2 v1.21.1.
Gene Ontology (GO) term enrichment and KEGG pathway analysis were performed in DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/).
Assembly: the zebrafish genome GRCz11
Supplementary files format and content: tab-delimited text files include normalized read values per million for each Sample
|
| |
|
| Submission date |
Aug 24, 2022 |
| Last update date |
Aug 29, 2022 |
| Contact name |
Herman Pieter Spaink |
| E-mail(s) |
h.p.spaink@biology.leidenuniv.nl
|
| Phone |
31715275055
|
| Organization name |
Leiden University
|
| Department |
Institute of Biology
|
| Lab |
Molecular Cell Biology
|
| Street address |
Einsteinweg 55
|
| City |
Leiden |
| ZIP/Postal code |
2333 CC |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL24995 |
| Series (1) |
| GSE211981 |
Leptin mutation and mycobacterial infection lead non-synergistically to a similar metabolic syndrome |
|
| Relations |
| BioSample |
SAMN30480165 |
| SRA |
SRX17238368 |
