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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 28, 2017 |
| Title |
CiPSCs rep2_RNA-seq |
| Sample type |
SRA |
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| Source name |
Chemical induced pluripotent stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Chemical induced pluripotent stem cells from mouse fibroblasts
gender: male
passage: 5-10
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| Treatment protocol |
The feeder layers were removed on gelatin-coated plates before collecting cells.
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| Growth protocol |
Mouse ESCs, 4F-iPSCs and CiPSCs were maintained on feeder layers of mitomycin C-treated MEFs in an ESC culture medium containing DMEM high glucose (Gibco),15%fetal bovine serum (FBS,Gicco), 1% GlutaMAXTM-I (Invitrogen), 1% nonessential amino acids (NEAA, Invitrogen), sodium pyruvate, 0.055 mM 2-mercaptoethanol (Invitrogen), 1%penicillin-streptomycin (Invitrogen) ,1,000 U/ml leukemia inhibitory factor (LIF, Millipore) and supplemented with 2i (3 μM CHIR99021 and 1 μM PD0325901)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was collected using the TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Illumina software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 genome assembly using Tophat v2.0.13 with default parameters
Uniquely mapped pairs were retained using the following commond: samtools view -hf 0x2 accepted_hits.bam |perl -ne 'print if (/^@/||/NM:i:(\d+)/ &&$1<5);'|samtools view -bS - >paired_uniq.bam
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a Cufflinks v2.2.1. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files include FPKM values for each Sample
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| Submission date |
Dec 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Hu |
| E-mail(s) |
hujian5241@126.com
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| Organization name |
Tongji University
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| Street address |
1239,Siping Road
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| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE92983 |
Reprogramming methods influence DNA methylation and expression patterns of mouse induced pluripotent stem cells [RNA-seq] |
| GSE92985 |
Reprogramming methods influence DNA methylation and expression patterns of mouse induced pluripotent stem cells |
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| Relations |
| BioSample |
SAMN06189289 |
| SRA |
SRX2448838 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2441459_CiPSCs_rep2.fpkm_tracking.gz |
776.1 Kb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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