 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 18, 2017 |
| Title |
jaki_stage1_rep_01 |
| Sample type |
SRA |
| |
|
| Source name |
Programmed somatic cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: a hybrid background of B6;CBATg ( Pou5f1-EGFP) 2Mnn/J x B6D2F1/J mice
cell type: mouse embryonic fibroblasts (MEFs)
time point: day 3
agent: Jaki
passage: P1
|
| Treatment protocol |
The RNA samples were collected from the reprogrammed cells at 18 days after retroviral Oct4, Klf4, Sox2, and cMyc (OKSM) transduction of OG-MEFs cultured in LIF containing medium and treated either with the specific Jak inhibitor I (Jaki)[34,43] or DMSO as the control (Ctl) starting at day 3 of viral infection (named hereafter DMSO-Stage 1 (S1) or Jaki-S1, respectively), or from induced colonies picked at day 21 and expanded one more passage (p2) (named hereafter DMSO-Stage 2 (S2) or Jaki-S2, respectively)
|
| Growth protocol |
The reprogramming medium was a 1:1 mix of KSR-ESC medium containing 76% KO-DMEM, 20% KSR, 1% 100x glutamax, 1% 100x non-essential amino acids, and 0.5x penicillin/streptomycin (Invitrogen), and supplemented with 1% 100x β-mercaptoethanol and 1,000 U/ml LIF (Millipore, Billerica, MA, USA), and Serum- ESC medium with 76% DMEM, 20% ESC-qualified FBS from Hyclone (Fisher Scientific, Pittsburg, PA, USA), 1% 100x glutamax, 1% 100x non-essential amino acids, 0.5x penicillin/streptomycin, 1% 100x β-mercaptoethanol, and 1,000 U/ml LIF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from reprogrammed cells with different treatments using RNeasy Mini kit (Qiagen, Valencia, CA)
500 ng of rRNA-depleted total RNA from each sample was used to prepare the RNA sequencing library following the manufacturer’s instructions by SOLiD Total RNA-seq Kit (Life Technologies, Grand Island, NY). Finally, sequencing libraries were quantified by using Agilent 2100 bioanalyzer and then barcoded, multiplexed, and sequenced on a 5500xl Genetic Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Description |
jaki_stage1_0
|
| Data processing |
Sequencing adapters were trimmed using Cutadapt and low quality reads were pre-filtered by FASTX-Toolkit before mapping. The quality of reads after filtering was examined using fastQC.
All filtered reads were aligned to mouse reference genome (GRCm38/mm10) by Tophat (v2.0.10) using SAMtools (v0.1.18) and Bowtie (v2.1.0) with default parameters
Individual mapped reads were fed to Cufflinks (v1.2.1) to contruct transcriptome models and any novel genes and transcripts that did not fit the supplied gene models were also assembled.
Cuffmerge was used to converge individual transcriptome to produce a master gene model.
Cufflinks was run to calculate Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) by using RefSeq genes as reference
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Mar 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiuchun Tian |
| E-mail(s) |
[email protected]
|
| Organization name |
University of connecticut
|
| Department |
Animal Science
|
| Street address |
1390 Storrs Road, ABL220D
|
| City |
Storrs |
| State/province |
CT |
| ZIP/Postal code |
06269 |
| Country |
USA |
| |
|
| Platform ID |
GPL15907 |
| Series (1) |
| GSE97261 |
Jak/Stat3 regulated global gene expression dynamics during late-stage reprogramming process |
|
| Relations |
| BioSample |
SAMN06670828 |
| SRA |
SRX2693042 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
