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Status |
Public on Dec 09, 2017 |
Title |
OSK-cJun-D3(RNAseq)-rep1 |
Sample type |
SRA |
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Source name |
reprogramming cells
|
Organism |
Mus musculus |
Characteristics |
cell type: reprogramming cells day of reprogramming: day3
|
Treatment protocol |
MEFs were reprogrammed as previously described2. Briefly, MEFs within 2 passages were plated at 2*104 per well (12 well plate) and then infected with retrovirus generated from PlatE cells. Infected cells were cultured in iCD1 medium or ESC medium (DMEM, 15% (v/v) FBS, penicillin/streptomycin (GIBCO), NEAA, GlutaMAX, LIF (10 ng/ml)). iPSC colonies were picked and then maintained as described above for ESCs. A step-by-step protocol describing the reprogramming procedure in this study can be found at the Nature Protocol Exchange3. shRNAs were transfected into cells by Lenti virus.
|
Growth protocol |
ESCs cells and iPSCs cells were cultured in N2B27+2i+LIF medium, MEF cells were cultured in 10% FBS medium
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was prepared with TRIzol. For quantitative PCR, cDNAs were synthesized with ReverTra Ace (Toyobo) and oligo-dT (Takara), and then analyzed by qPCR with Premix Ex Taq (Takara). For RNA-seq, TruSeq RNA Sample Prep Kit (RS-122-2001, Illumina) was used for library construction and the sequencing was done using a NextSeq 500 High Output Kit v2 (75 cycles) (FC-404-1005, Illumina), according to the manufacturers instructions.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
bcl2fastq conversion software v2.17 used for basecalling. RNAseq reads were aligned to the mm10 genome assembly using rsem with options --bowtie2 --bowtie2-sensitivity-level very_sensitive expected_count were extract from the sample_name.genes.results and merged together to get a big table RNAseq data was normalized by EDAseq Genome_build: mm10 Supplementary_files_format_and_content: tsv file was generated form normalized RNAseq data, it include all samples' RNAseq data
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Submission date |
Dec 30, 2016 |
Last update date |
May 15, 2019 |
Contact name |
dongwei Li |
E-mail(s) |
li_dongwei@gibh.ac.cn
|
Organization name |
Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences
|
Department |
South China Institute for Stem Cell Biology and Regenerative Medicine
|
Lab |
Duanqing Pei lab
|
Street address |
190 Kai Yuan Avenue, Science Park
|
City |
Guangzhou |
State/province |
Guangdong province |
ZIP/Postal code |
510530 |
Country |
China |
|
|
Platform ID |
GPL19057 |
Series (2) |
GSE93027 |
Chromatin Open/Close Logic in Cellular Reprogramming [RNA-Seq] |
GSE93029 |
Chromatin Open/Close Logic in Cellular Reprogramming |
|
Relations |
BioSample |
SAMN06191976 |
SRA |
SRX2452316 |