|
| Status |
Public on Dec 09, 2017 |
| Title |
iPS(RNAseq)-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
induced pluripotent stem cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: iPSCs cells
passages: 5-8
|
| 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.
|
| |
|
| 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
|
| |
|
| 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 |
SAMN06191983 |
| SRA |
SRX2452309 |
