|
| Status |
Public on Mar 11, 2021 |
| Title |
KidD20_1 |
| Sample type |
SRA |
| |
|
| Source name |
adult female kidney
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
age: 9 weeks
dietary regimen: DRF
zeitgeber time in hours: ZT20
|
| Treatment protocol |
Animals were subjected to daytime-restricted feeding (DRF) or nighttime-restricted feeding (NRF) for 7 days
|
| Growth protocol |
Special pathogen-free (SPF) mice were purchased from Hunan SJT Laboratory Animal Co. and housed in a SPF barrier facility. C57BL/6J female mice at 7 weeks of age were grouped housed, and entrained to a 12h light:12h dark cycle with normal chow food and water ad libitum for 7 days before assigned to daytime-restricted feeding (DRF) and nighttime-restricted feeding (NRF) groups for additional 7 days.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tissues were dissected, flash frozen liquid nitrogen, and RNA was harvested using Trizol reagent.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at an appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. SOAPnuke:Version v1.5.2 Parameters -l 15 -q 0.2 -n 0.05
The clean reads were mapped to the reference genome using HISAT2. HISAT2: version: v2.0.4 Parameters：--phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Bowtie2 was applied to align the clean reads to the gene set. The expression level of gene was calculated by RSEM and represented as TPM. Bowtie2: version: v2.2.5 Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200 RSEM: version: v1.2.12
Genome_build: mm10/GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
May 20, 2020 |
| Last update date |
Mar 11, 2021 |
| Contact name |
Min-Dian Li |
| E-mail(s) |
mindianli@tmmu.edu.cn
|
| Organization name |
Southwest Hospital, Third Military Medical University (Army Medical University)
|
| Department |
Cardiology
|
| Lab |
The Center for Circadian Metabolism and Cardiovascular Disease
|
| Street address |
30 Gaotanyan Main Street
|
| City |
Chongqing |
| ZIP/Postal code |
400038 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (2) |
| GSE150385 |
Global circadian transcript profile of mouse peripheral tissues and brain entrained by inverted feeding |
| GSE151221 |
Global circadian transcript profile of mouse kidney entrained by inverted feeding |
|
| Relations |
| BioSample |
SAMN14832623 |
| SRA |
SRX8239169 |
