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Status |
Public on Aug 21, 2017 |
Title |
Foxj3-ES rep1 |
Sample type |
SRA |
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Source name |
J1 ES cells
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Organism |
Mus musculus |
Characteristics |
cell line: J1 cell type: embryonic stem cell genotype: Foxj3 stable expressed
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction. RNA libraries were prepared for sequencing using IonProton,The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
F1
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Data processing |
Clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent of bases with qualities of <13. The clean reads were then aligned to mouse genome (version: mm10) using the MapSplice program (v2.1.6). In alignment, preliminary experiments were performed to optimize the alignment parameters (-s 22 -p 15 --ins 6 --del 6 --non-canonical). Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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.We applied DEseq algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) Fold Change>2 or <0.5; ii) FDR<0.05. Pathway analysis was used to find out the significant pathway of the differential genes according to KEGG database. We turn to the Fisher’s exact test to select the significant pathway, and the threshold of significance was defined by P-value and FDR. Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of unique genes in the significant or representative profiles of the differentially expressed gene in the experiment. We downloaded the GO annotations from NCBI (http://www.ncbi.nlm.nih.gov/), UniProt (http://www.uniprot.org/) and the Gene Ontology (http://www.geneontology.org/). Fisher’s exact test was applied to identify the significant GO categories and FDR was used to correct the p-values. We present Gene co-expression Networks to find the relations among genes. Gene co-expression Networks were built according to the normalized expression values of genes selected from genes in significant GO-terms. For each pair of genes, we calculate the Pearson Correlation and choose the significant correlation pairs (FDR<0.05) to constructed the network. Genome_build: mm10 Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …
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Submission date |
Sep 25, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Haibo Wu |
E-mail(s) |
[email protected]
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Organization name |
Northwest A&F University
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Street address |
3rd, Taicheng Road
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City |
Yangling |
ZIP/Postal code |
712100 |
Country |
China |
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Platform ID |
GPL13112 |
Series (1) |
GSE61748 |
Transcriptome analysis of Foxj3 or Zbtb18 stable expressed embryonic stem (ES) cell lines |
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Relations |
BioSample |
SAMN03079325 |
SRA |
SRX709944 |
Supplementary data files not provided |
SRA Run Selector |
Processed data are available on Series record |
Raw data are available in SRA |
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