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Sample GSM3498119 Query DataSets for GSM3498119
Status Public on Dec 01, 2018
Title Deficient-rep2-cold
Sample type SRA
 
Source name inguinal white adipose tissue_Oct3 deficient_4C
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: inguinal white adipose tissue
genotype: Oct3 deficient
age: 3-month-old
Extracted molecule total RNA
Extraction protocol WAT were removed, flash frozen on dry ice, and RNA was harvested using using the RNeasy Lipid Mini Kit (Qiagen, Hilden, Germany).
Quality of RNA was analyzed using the Agilent 2100 (Agilent Technologies, Palo Alto, Calif.). The poly-A-containing mRNA was purified by using poly-T oligo-attached magnetic beads. Purified mRNA was fragmented into small pieces using divalent cations under elevated temperature. RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA polymerase I and RNase H. A single 'A' base was added to cDNA fragments and the adapter was subsequently ligated. The products were then purified and enriched with PCR amplification. PCR yield was quantified by Qubit and samples were pooled together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and had 50 bp of single end read through the BGISEQ-500 platform. The DNA nanoball-based nanoarrays and stepwise sequencing were combined using Combinational Probe-Anchor Synthesis Sequencing Method and analyzed.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Description Deficient-2
Data processing BaseCall1.1.0 software was used for basecalling.
SOAPnuke 1.5.2 software was used for data filtering steps
HISAT2 v2.0.4 software was used for read alignment
RSEM v1.2.12 software was used for abundance measurement
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
 
Submission date Nov 30, 2018
Last update date Dec 03, 2018
Contact name wenxin song
E-mail(s) songwenxincpu@163.com
Organization name Tsinghua university
Street address Hai Dian, Beijing
City Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL23479
Series (1)
GSE123181 Next Generation Sequencing Facilitates Quantitative Analysis of Control and Oct3 Deficient Adipose Transcriptomes
Relations
BioSample SAMN10505402
SRA SRX5084675

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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