|
| Status |
Public on May 01, 2024 |
| Title |
NSD2∆IE RNA-seq 3 |
| Sample type |
SRA |
| |
|
| Source name |
colon
|
| Organism |
Mus musculus |
| Characteristics |
tissue: colon
genotype: NSD2{delta}IE
treatment: 16 weeks of HFCD
|
| Treatment protocol |
Intestinal-specific NSD2 knockout mice (NSD2∆IE) and controls (NSD2fl/fl) were treated with a 16-week HFCD diet
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent according to the instructions.
RNA purity and quantification were characterized using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA) and RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
NSD-3
|
| Data processing |
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads， clean reads for each sample were retained for subsequent analyses
The clean reads were mapped to the reference genome using HISAT2. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4.
PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jan 31, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
YIJIA ZHANG |
| E-mail(s) |
a15215572002@icloud.com
|
| Phone |
15215572002
|
| Organization name |
Beijing University of Chemical Technology
|
| Street address |
和平街道
|
| City |
北京市 |
| ZIP/Postal code |
100029 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE254667 |
Intestinal NSD2 aggravates hepatic steatosis during obesity through histone modifications [RNA-seq] |
|
| Relations |
| BioSample |
SAMN39688565 |
| SRA |
SRX23461595 |
