|
| Status |
Public on Mar 01, 2018 |
| Title |
liver_zonation_12_KO |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
genotype: Gcg KO
feeding: Fed
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Liver were removed, flash frozen liquid nitrogen, and RNA was harvested using Trizol reagent. Total RNA was purified from all samples using MagMAX™-96 for Microarrays Total RNA Isolation Kit (Ambion by Life Technologies) according to manufacturer’s specifications. Genomic DNA was removed using MagMAX™Turbo™DNase Buffer and TURBO DNase from the MagMAX kit listed above (Ambion by Life Technologies). mRNA was purified from total RNA using Dynabeads mRNA Purification Kit (Invitrogen).
Strand-specific RNA-seq libraries were prepared using KAPA mRNA-Seq Library Preparation Kit (Kapa Biosystems).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample_12
|
| Data processing |
Illumina Casava 1.8.2 software used for basecalling.
Reads were decoded based on their barcodes. Read quality was evaluated using FastQC.
Reads were mapped to the reference genome (mouse: GRCm38) using using ArrayStudio® software (OmicSoft®, Cary, NC) allowing two mismatches.
RPKM calculated by ArrayStudio
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
|
| |
|
| Submission date |
Feb 15, 2018 |
| Last update date |
Mar 01, 2018 |
| Contact name |
Yurong Xin |
| E-mail(s) |
yurong.xin@regeneron.com
|
| Organization name |
Regeneron Pharmaceuticals, Inc.
|
| Street address |
777 Old Saw Mill River Road
|
| City |
Tarrytown |
| State/province |
NY |
| ZIP/Postal code |
10598 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE110672 |
Glucagon contributes to liver zonation in mice [Gcg KO] |
| GSE110674 |
Glucagon contributes to liver zonation in mice |
|
| Relations |
| BioSample |
SAMN08542283 |
| SRA |
SRX3702546 |
