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Sample GSM2611353 Query DataSets for GSM2611353
Status Public on Jun 28, 2017
Title s4001_HVNJMCCXX_L5
Sample type SRA
 
Source name chemically-induced cells from mouse fibroblasts
Organism Mus musculus
Characteristics strain: Mapttm2(EGFP)Klt/J
tissue: chemically-induced cells from mouse fibroblasts
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description #6 XEN-like colony (Figure S4A), #1 XEN-like colony (Figure S4B)
processed data file: Neuronal cell seq03.xls
s4001_HVNJMCCXX_L5
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
 
Submission date May 10, 2017
Last update date May 15, 2019
Contact name Yan-Tao Ma
E-mail(s) yantao.ma89@live.com
Organization name Peking University
Street address No. 5 Yiheyuan Road
City Beijing
ZIP/Postal code 100871
Country China
 
Platform ID GPL21273
Series (1)
GSE97721 Lineage Reprogramming of Fibroblasts into Functional Neurons and Hepatocytes via Chemically Induced XEN-like State
Relations
BioSample SAMN06925994
SRA SRX2794691

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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