|
| Status |
Public on May 23, 2023 |
| Title |
AME-d21, male, rep4 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
Sex: Male
genotype: WT, C57BL/6J
treatment: AME
time: d21
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ground livers from d0 and d21 male (n = 5) mice were used for total RNA isolation by using a miRNeasy Mini Kit (Qiagen) following the manufacturer’s instructions, including an on-column DNase I treatment. RNA was quantified spectrophotometrically. The integrity of RNA was assessed with an Agilent 2100 bioanalyzer in conjunction with the RNA 6000 Nano Kit (Agilent), and a RNA integrity number greater than or equal to nine was used.
RNA libraries were prepared by using 200 ng of total RNA according to the manufacturer’s instructions for the Illumina TruSeq RNA v2 kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base calling is performed using Illumina’s RTA version 2.5.2.
Quality control check via FastQC, read trimming using Trimmomatic
Sequence alignment using the MapRSeq3 package (using STAR)
read counting using the MapRseq3 package (using featureCounts)
Assembly: mm10
|
| |
|
| Submission date |
May 18, 2023 |
| Last update date |
May 23, 2023 |
| Contact name |
Robert H. Lane |
| Organization name |
Children's Mercy
|
| Street address |
2401 Gillham Rd
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64108 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE232811 |
Adverse maternal environments perturb hepatic DNA methylome and transcriptome prior to the adult-onset non-alcoholic fatty liver disease in mouse offspring [RNA-seq] |
| GSE232812 |
Adverse maternal environments perturb hepatic DNA methylome and transcriptome prior to the adult-onset non-alcoholic fatty liver disease in mouse offspring |
|
| Relations |
| BioSample |
SAMN35159345 |
| SRA |
SRX20430875 |
