|
| Status |
Public on Mar 01, 2021 |
| Title |
hDNMT3A_testis_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
testis
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: testis
strain: Sprague Dawley
age: 15 weeks
genotype/variation: hDNMT3A
development stage: adult
Sex: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
A2TR
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rattus_norvegicus.Rnor_6.0.89.chr using bowtie v1.0.1 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The expression level of each transcript was calculated using the fragments per kilobase of exon per million mapped reads (FPKM) method. Differentially expressed genes between two samples were identified based on a cutoff P value for per-gene variance less than 0.05 with conservative Bonferroni correction
Genome_build: Rattus_norvegicus.Rnor_6.0.89.chr
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Mar 25, 2019 |
| Last update date |
Mar 01, 2021 |
| Contact name |
Xiaoguo Zheng |
| E-mail(s) |
zxg@sagc.org.cn
|
| Phone |
+86-15021928432
|
| Organization name |
Shanghai Jiaotong University
|
| Street address |
145 Guangyuan Road
|
| City |
Shanghai |
| ZIP/Postal code |
200030 |
| Country |
China |
| |
|
| Platform ID |
GPL22396 |
| Series (1) |
| GSE128777 |
Transcriptome analysis of the brain and testis of the human-derived DNMT3A transgenic rat |
|
| Relations |
| BioSample |
SAMN11080375 |
| SRA |
SRX5488153 |
