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Series GSE99784 Query DataSets for GSE99784
Status Public on Jun 08, 2017
Title Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Nrl-/- Retinal Transcriptomes
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: To identify the role of glycosylation of dentin matrix protein1 (DMP1), S89G-DMP1 point mutation mouse model was created with changing S89 to glycine(S89G). RNA sequencing were performed to compare the transcriptome differences between the neural stem cells or astrocytes separated form S89G-DMP1 and WT mice.
Methods: mRNA profiles of astrocytes and neural stem cell separated from S89G-DMP1 and WT were generated by RNA sequencing. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat2(for astrocytes) or with HISAT2o (for neural stem cells).
Results: Differential expression analyses with DESeq2 use raw read counts: 762 transcripts were downregulated and 991 transcripts were up-regulated in S89G-DMP1 astrocytes; 475 transcripts were downregulated and 343 transcripts were up-regulated in S89G-DMP1 neural stem cells. All the differential expressed genes were used for Heatmap analysis and KEGG or GO enrichment analyses.
Conclusions: Our study represents the detailed transcriptome changes of astrocytes and neural stem cells with deglycosylated DMP1.
Overall design mRNA profiles of astrocytes and neural stem cells separated from adult (10-week-old) S89G-DMP1 or WT mice were generated by RNA sequencing using Illumina.
Contributor(s) Jing B, Liu J
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Submission date Jun 07, 2017
Last update date May 15, 2019
Contact name Bo Jing
Phone +8613122776193
Organization name 同济大学医学院
Street address 同济大学医学院713
City 上海
State/province 上海
ZIP/Postal code 200092
Country China
Platforms (2)
GPL16417 Illumina MiSeq (Mus musculus)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (8)
GSM2652207 S89G-AST
GSM2652208 WT-AST
GSM2652209 S89G-NSC-Trip1
BioProject PRJNA389593
SRA SRP108781

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Supplementary file Size Download File type/resource
GSE99784_AST_fpkm.xls.gz 526.4 Kb (ftp)(http) XLS
GSE99784_AST_readcount.xls.gz 224.4 Kb (ftp)(http) XLS
GSE99784_NSC_TPM.csv.gz 765.1 Kb (ftp)(http) CSV
GSE99784_NSC_count.csv.gz 326.3 Kb (ftp)(http) CSV
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Processed data are available on Series record

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