|
| Status |
Public on Apr 15, 2022 |
| Title |
0220L P3 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
age: 21 days
strain: C57/B6
treatment: Regular breastmilk
|
| Treatment protocol |
Neonatal mice was treated for 21 days with Triclosan at 120 ppm in the breastmilk of lactating females
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol. 1 ug of total RNA was used for the construction of sequencing libraries.
The sequencing library was prepared using the Illumina TruSeq RNA Sample Prep Kit (FC-122-1001; Illumina, San Diego, CA) with 1 ug of total RNA. The sequencing was performed on an NovaSeq 6000 sequencer in the IGM Genomics Center at UCSD.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Image deconvolution, quality value calculation, and the mapping of exon reads and exon junctions were performed at the UCSD sequencing core. Base calling was performed using bcl2fastq (v2.17.1.14; Illumina). RNA sequencing reads were aligned Q20 to the mice genome (mm10) with STAR (v2.2.0c)58 with default parameters, only uniquely alienable reads were used for downstream analysis. Gene expression values were calculated using HOMER by quantifying strand-specific reads across annotated gene exons (RefSeq) and reported as fragments per kilobase of exon per million mapped reads.
Assembly: mm10
Supplementary files format and content: One excel file containing results from all samples.
|
| |
|
| Submission date |
Apr 12, 2022 |
| Last update date |
Apr 15, 2022 |
| Contact name |
Andre Alberto Weber |
| E-mail(s) |
aaweber87@gmail.com
|
| Phone |
6192889420
|
| Organization name |
UCSD
|
| Street address |
9500 Gilman Dr. La Jolla
|
| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE200705 |
Lactational delivery of Triclosan promotes non-alcoholic fatty liver disease in newborn mice |
|
| Relations |
| BioSample |
SAMN27549630 |
| SRA |
SRX14835842 |
