|
Status |
Public on Jan 20, 2023 |
Title |
ZT(Lowest)_6month_KO |
Sample type |
SRA |
|
|
Source name |
Liver
|
Organism |
Mus musculus |
Characteristics |
tissue: Liver time: ZT(Lowest) age: 6month genotype: Egr1_KO
|
Extracted molecule |
polyA RNA |
Extraction protocol |
liver were removed, flash frozen on dry ice, and 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. mRNAs were enriched with poly-T oligo-attached magnetic beads using NEBNext First Strand Synthesis Reaction Buffer (5×) and then fragmented into small pieces. These cleaved RNA fragments were reverse-transcribed to create a cDNA library using Illumina's NEBNext® UltraTM RNA Library Prep Kit; the average insert size for the paired-end libraries was 300 bp (± 50 bp).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
tab-delimited text files include estimated counts for each sample
|
Data processing |
After sequencing and removal of low-quality reads that contained adaptor contamination, low-quality bases and undetermined bases using fastp software, the sequenced reads were aligned to the mouse genome(mm10) using HISAT2. FeatureCounts was used to determine the mRNA expression levels. Assembly: mm10 Supplementary files format and content: tab-delimited text files include estimated counts for each sample
|
|
|
Submission date |
Jan 20, 2023 |
Last update date |
Feb 15, 2023 |
Contact name |
Wang Haiquan |
E-mail(s) |
mg1835020@smail.nju.edu.cn
|
Phone |
+86-17865182827
|
Organization name |
Nanjing University
|
Street address |
Hankou Road
|
City |
Nanjing |
ZIP/Postal code |
250014 |
Country |
China |
|
|
Platform ID |
GPL13112 |
Series (1) |
GSE195456 |
Hepatic circadian gene expression in WT and liver specific Egr-1 knockout mice aged 2month, 6month and 12month |
|
Relations |
BioSample |
SAMN33214293 |
SRA |
SRX19315599 |