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Status |
Public on Feb 25, 2021 |
Title |
Epididyaml primary adipocytes - Prmt1 FKO_rep2 |
Sample type |
SRA |
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Source name |
Epididyaml primary adipocytes
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6N cell type: Epididyaml primary adipocytes genotype: Prmt1 adipocyte-specific KO
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA concentration was calculated by Quant-IT RiboGreen(Invitrogen, #R11490). To assess the integrity of the total RNA, samples are run on the TapeStation RNA screentape(Agilent). Only high-quality RNA preparations, with RIN greater than 7.0, were used for RNA library construction. A library was prepared with 1ug of total RNA for each sample by Illumina TruSeq mRNA Sample Prep kit (Illumina, Inc., San Diego, CA, USA). The first step in the workflow involves purifying the poly‐A containing mRNA molecules using poly‐T oligo‐attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using SuperScript II reverse transcriptase(Invitrogen) and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the indexing adapters. The products are then purified and enriched with PCR to create the final cDNA library. The libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA Library Quantificatoin kits for Illumina Sequecing platforms) and qualified using the TapeStation D1000 ScreenTape (Agilent Technologies, Waldbronn, Germany). Indexed libraries were then sequenced using the HiSeq4000 platform (Illumina,San Diego, USA) by the Macrogen Incorporated.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
KO-8
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Data processing |
We preprocessed the raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Mus musculus (mm10) using HISAT v2.1.0 HISAT utilizes two types of indexes for alignment (a global, whole-genome index and tens of thousands of small local indexes). These two types’ indexes are constructed using the same BWT (Burrows–Wheeler transform)/ a graph FM index (GFM) as Bowtie2. The reference genome sequence of Mus musculus (mm10) and annotation data were downloaded from the NCBI. And then, transcript assembly of known transcripts was processed by StringTie v1.3.4d. Expression abundance of transcript and gene were calculated as read count or FPKM value (Fragments Per Kilobase of exon per Million fragments mapped) per sample. Genome_build: mm10
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Submission date |
Feb 24, 2021 |
Last update date |
Feb 25, 2021 |
Contact name |
Seung-Hoi Koo |
E-mail(s) |
koohoi@korea.ac.kr
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Organization name |
Korea University
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Department |
Life Sciences
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Street address |
145 Anam-Ro, Seongbuk-Gu
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City |
Seoul |
ZIP/Postal code |
02841 |
Country |
South Korea |
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Platform ID |
GPL13112 |
Series (1) |
GSE167446 |
Quantitative Analysis of Wild Type and Prmt1 adipocyte-specific KO Epididymal primary adipocyte Transcriptomes |
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Relations |
BioSample |
SAMN18052439 |
SRA |
SRX10164290 |
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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