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| Status |
Public on Jan 01, 2020 |
| Title |
MEF_D8_GFP_1 |
| Sample type |
SRA |
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| Source name |
SKM secondary MEF
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| Organism |
Mus musculus |
| Characteristics |
sample stage: Day 8 of SKM MEF reprogramming
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| Growth protocol |
MEF cells are cultured in DMEM+10%FBS+1%NEAA, and mESCs and iPSCs are cultured in mESC medium. Reprogramming cells were cultured in mouse ES medium in presence of doxycycline.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For cultured cells, total RNA was extracted with RNeasy Plus mini kit (Qiagen, 74136) with QiaShredder (Qiagen, 79656). For sorted cells, samples at the indicated time points were collected and lysed in TRIzolTM Reagent (Invitrogen, 15596026).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB), according to the manufacturer’s instructions. A total amount of 2µg RNA per sample was used as input material for library preparation. The library fragments were purified with QiaQuick PCR kits (Oiagen, 28106), quality-controlled by Bioanalyzer 2100 and quantified by qPCR.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Total RNA of samples at the indicated times were used for sequencing. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) and then sequenced using Illumina HiSeq 2500 platform and 150 bp paired-end (PE150) reads were generated.
Before alignment, low quality reads and those containing adapter or poly-N were removed using FastQC. The remaining reads were mapped to the assembly mm9 genome using the default parameters in STAR (v2.5.1b) aligner. The read count files which produced by STAR have been merged into the gene expression file.
Genome_build: mm9
Supplementary_files_format_and_content: excel file include raw read count values for each Sample
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| Submission date |
Jul 01, 2018 |
| Last update date |
Jan 01, 2020 |
| Contact name |
Sheng Ding |
| E-mail(s) |
sheng.ding@gladstone.ucsf.edu
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| Organization name |
Gladstone Institute for Cardiovascular Disease
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| Lab |
Ding lab
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| Street address |
1650 Owens Street
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE98280 |
Function of Sox2 and Klf4 during SKM reprogramming |
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| Relations |
| BioSample |
SAMN09530308 |
| SRA |
SRX4328966 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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