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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 28, 2017 |
| Title |
s39-P17_HVNJMCCXX_L5 |
| Sample type |
SRA |
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| Source name |
chemically-induced cells from mouse fibroblasts
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| Organism |
Mus musculus |
| Characteristics |
strain: Mapttm2(EGFP)Klt/J
tissue: chemically-induced cells from mouse fibroblasts
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each sample was isolated using the RNeasy Plus Mini Kit (QIAGEN).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
chemically-induced XEN-like cells
processed data file: Neuronal cell seq03.xls
s39-P17_HVNJMCCXX_L5
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| Data processing |
The transcriptome reads were mapped using the TopHat2 program.
The gene expression level was calculated by using FPKM method.
Genome_build: mm10
Supplementary_files_format_and_content: fpkm_tracking files including FPKM values for the analysis of gene expression
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| Submission date |
May 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yan-Tao Ma |
| E-mail(s) |
yantao.ma89@live.com
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| Organization name |
Peking University
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| Street address |
No. 5 Yiheyuan Road
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE97721 |
Lineage Reprogramming of Fibroblasts into Functional Neurons and Hepatocytes via Chemically Induced XEN-like State |
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| Relations |
| BioSample |
SAMN06926010 |
| SRA |
SRX2794708 |
| 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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