|
| Status |
Public on Nov 24, 2020 |
| Title |
B5 |
| Sample type |
SRA |
| |
|
| Source name |
White adipose tissue (epididymal fat)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: White adipose tissue (epididymal fat)
age: 16 weeks age old
genotype: Mrp4 KO (Mrp4-/-)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
White adipose tissue (epididyma fat) were collected from mice, flash frozen on liquid nitrogen, and total RNA was harvested using Trizol reagent
RNA was purified using the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification,the RNA is fragmented into small pieces using divalent cations under elevated temperature.The cleaved RNA fragments are copied into first strand cDNA using reverset ranscriptase and random primers.This is followed by second strand cDNA synthesis using DNA PolymeraseI and RNaseH. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter.The products are then purifiedand enriched with PCR amplificat ion.We then quant ified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNAcircle), which gave the final library.DNA nanoballs(DNBs)were generated with the ssDNAcircle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100bp were read through on the BGISEQ-500platform for the following data analysis study.For this step, the BGISEQ-500 platform combines the DNAnanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Sequencing Reads Filtering was peroformed using SOAPnuke; version:v1.5.2; parameters: -l 15 -q 0.5 -n 0.1
Gene expresssion analysis was performed using 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 - X1000--no-mixed--no-discordant -p1-k200
Differetial gene expression analysis was performed using DEGseq: Parameters:FoldChange>=2 and Adjusted P value<=0.001; PossionDis: Parameters: Fold Change >= 2.00 and FDR <= 0.001
Data presented as FPKM
Genome_build: mm9
Supplementary_files_format_and_content: excel file
|
| |
|
| Submission date |
Nov 23, 2020 |
| Last update date |
Nov 24, 2020 |
| Contact name |
Jose E Manautou |
| E-mail(s) |
jose.manautou@uconn.edu
|
| Phone |
8604863852
|
| Organization name |
University of Connecticut
|
| Department |
Pharmaceutical Sciences
|
| Street address |
69 N Eagleville Rd, Room 517
|
| City |
Storrs |
| State/province |
Connecticut |
| ZIP/Postal code |
06269 |
| Country |
USA |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE162037 |
RNA Sequencing Analysis of wild type (WT) and Mrp4 knock out (Mrp4-/-) mice adipose tissue Transcriptomes |
|
| Relations |
| BioSample |
SAMN16878060 |
| SRA |
SRX9560788 |
