|
| Status |
Public on Jan 18, 2023 |
| Title |
PAB14_4 |
| Sample type |
SRA |
| |
|
| Source name |
RNAseq analyses of the upper lobe of the right lung tissue
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: SD
tissue: lung
treatment method: pulmonary artery banding (PAB)
treatment age: postnatal day 1
test age: postnatal day 14
|
| Treatment protocol |
Newborn rats were anesthetized by brief hypothermia on crushed ice for approximately 3 minutes and then transferred to an ice bed to maintain anesthesia during the surgery. The operation was performed under the stereomicroscope in the supine position, including sternum clipping, thoracic cavity opening, pericardium incising, pulmonary artery quantitative constriction, thoracic cavity closing, etc. The constriction procedure which was only performed in the PAB group. After the surgery was completed, the rats were removed from the ice bed and placed on a heat plate of 37℃ to warm and wake up. The pups were not put back to their moms until they were absolutely conscious (around 3h after surgery).
|
| Growth protocol |
The suckling rats were breastfed by the mother rats and were housed in groups of 8-10 per cage, fed under the same conditions with free access to food and water, maintained in the 12h: 12h day: night cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lung tissue from the upper lobe of the right lung was rapidly removed from executed rat and flash frozen in -80℃ refrigerator , RNA was harvested using Trizol reagent.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
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| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected.We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10 and SnpEff software was used to annotation for the Variablesite).
Assembly: GCA_000001895.4
Supplementary files format and content: FPKM
|
| |
|
| Submission date |
Apr 26, 2022 |
| Last update date |
Jan 18, 2023 |
| Contact name |
Debao Li |
| E-mail(s) |
lidebao@sjtu.edu.cn
|
| Phone |
19956578645
|
| Organization name |
Shanghai Children's Medical Center
|
| Street address |
No. 1678 Dongfang Road, Tangqiao Street
|
| City |
Shanghai |
| ZIP/Postal code |
200127 |
| Country |
China |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE201522 |
Congenital heart disease associated bronchopulmonary dysplasia and its underlying mechanisms |
|
| Relations |
| BioSample |
SAMN27777322 |
| SRA |
SRX14998413 |
