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Status |
Public on Dec 01, 2018 |
Title |
Deficient-rep2-cold |
Sample type |
SRA |
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Source name |
inguinal white adipose tissue_Oct3 deficient_4C
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 tissue: inguinal white adipose tissue genotype: Oct3 deficient age: 3-month-old
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
BGISEQ-500 |
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Description |
Deficient-2
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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
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Submission date |
Nov 30, 2018 |
Last update date |
Dec 03, 2018 |
Contact name |
wenxin song |
E-mail(s) |
songwenxincpu@163.com
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Organization name |
Tsinghua university
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Street address |
Hai Dian, Beijing
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City |
Beijing |
ZIP/Postal code |
100084 |
Country |
China |
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Platform ID |
GPL23479 |
Series (1) |
GSE123181 |
Next Generation Sequencing Facilitates Quantitative Analysis of Control and Oct3 Deficient Adipose Transcriptomes |
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Relations |
BioSample |
SAMN10505402 |
SRA |
SRX5084675 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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