|
| Status |
Public on Sep 01, 2021 |
| Title |
65E1_d12ChGFP |
| Sample type |
SRA |
| |
|
| Source name |
Day 12 naivex2 mCherry+/GFP+
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6; 129S4-Tg(Tet1-mCherry)B37Koh x B6;CBA-Tg(Pou5f1-EGFP)2Mnn/J
Stage: Stage IV reprogramming intermediate
genotype: Tg(mCherry)/wt; Tg(GFP)/wt
gender: male
|
| Growth protocol |
1x105 to 3x106 cells in each reprogramming intermediate fraction ( mCherry+ and mCherry+/GFP+) were sorted from three independent lines as biological replicates. iPSC samples were passaged 6-7 times on feeders in KSR media, then feeder-depleted and harvested for RNA.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was purified using TRIzol (Cat.#15596026,Invitrogen) and RNeasy mini kit (Cat#74004, Qiagen).
300 ng of RNA was used for library preparation using the KAPA stranded mRNA-seq kit (Cat#07692193001, Roche) according to the manufacturer’s instructions (V5.17). KAPA single-indexed adapters (Cat#08005699001, Roche) were added to the A-tailed cDNA for library amplification with 14 cycles of PCR. The final library was purified by using Agencourt AMPure XP beads (Cat#A63881, Beckman Coulter) to size select fragments of 200-300 bp.
stranded RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
sequencing_1st batch
biological replicate_1
countMatrix_by_FeatureCounts_1.count
|
| Data processing |
Illumina Casava2.18 software used for basecalling and demultiplexing
Index-trimmed single-end 75bp reads were aligned to the mouse reference genome (mm10) by using Hisat2 (v2.1.0)
Gene-level read count matrix was summarized from mapped reads by using featureCounts (v1.5.3; http://bioinf.wehi.edu.au/featureCounts/)
Count matrix was imported into the R Bioconductor DESeq2 package (v1.18.1) for differential gene expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: text file provide count information
|
| |
|
| Submission date |
Sep 11, 2018 |
| Last update date |
Sep 01, 2021 |
| Contact name |
Kian Peng Koh |
| E-mail(s) |
kian.koh@kuleuven.be
|
| Organization name |
KULeuven
|
| Street address |
Herestraat 49, O&N IV - box 804
|
| City |
Leuven |
| State/province |
Select... |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE119830 |
Gene expression profiling of late reprogramming stages during in vitro reprogramming of mouse embryonic fibroblasts (MEFs) to induced pluripotent stem cells (iPSCs) |
| GSE119831 |
Dynamics of Tet1 and Oct4 gene activation identify temporally distinct late stages in reprogramming of induced pluripotency |
|
| Relations |
| BioSample |
SAMN10034672 |
| SRA |
SRX4671387 |
