|
| Status |
Public on Aug 03, 2019 |
| Title |
Oligodendrocyte intrinsic miR-27a controls myelination and remyelination |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The goal of this study was to understand miR-27a gene regulation in mouse OPCs
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| |
|
| Overall design |
Method- RNA isolated from biotin-tagged miRNA mimic (control and miR-27a)-transfected OPCs, as well as pulldown assays, were subjected to mRNA deep sequencing. RNA-seq libraries were prepared with Illumina’s TruSeq Stranded Total RNA with Ribo-Zero Globin kit and sequenced on HiSeq-2500 sequencer using Rapid Run v2, 100bp, Paired-end run. Post-sequencing, raw demultiplexed fastq paired end read files were trimmed of adapters and filtered using the program skewer to throw out any with an average phred quality score of less than 30 or a length of less than 36. Trimmed reads were then aligned using the HISAT2 aligner to the Mus musculus NCBI reference genome assembly (v GRCm38) and sorted using SAMtools. Aligned reads were counted and assigned to gene meta-features using the program featureCounts part of the Subread package. These count files were imported into the R programming language and were assessed for quality control, normalized, and analyzed using an in-house pipeline utilizing the edgeR Bioconductor library for differential gene expression testing.
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| |
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| Contributor(s) |
Tripathi A, Richardson B, Cameron M, Dutta R |
| Citation(s) |
31644912 |
| |
| Submission date |
Aug 02, 2019 |
| Last update date |
Nov 04, 2019 |
| Contact name |
Selva Baltan |
| E-mail(s) |
[email protected]
|
| Organization name |
Oregon Health and Science University
|
| Department |
Anesthesia and Perioperative Medicine (APOM)
|
| Street address |
3181 S.W. Sam Jackson Park Rd.
|
| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
|
| Samples (12)
|
| GSM4005103 |
Biotin OPC mir ctr 1 [Dutta_miRNA_Pulldown_Set_2_RandID_1_S1] |
| GSM4005104 |
Biotin OPC mir ctr 2 [Dutta_miRNA_Pulldown_Set_2_RandID_10_S10] |
| GSM4005105 |
Biotin OPC mir ctr 3 [Dutta_miRNA_Pulldown_Set_2_RandID_12_S12] |
| GSM4005106 |
Bioitin OPC mir27a 1 [Dutta_miRNA_Pulldown_Set_2_RandID_8_S8] |
| GSM4005107 |
Bioitin OPC mir27a 2 [Dutta_miRNA_Pulldown_Set_2_RandID_9_S9] |
| GSM4005108 |
Bioitin OPC mir27a 3 [Dutta_miRNA_Pulldown_Set_2_RandID_7_S7] |
| GSM4005109 |
Pull Bioitin OPC mirctr 1 [Dutta_miRNA_Pulldown_Set_2_RandID_11_S11] |
| GSM4005110 |
Pull Bioitin OPC mirctr 2 [Dutta_miRNA_Pulldown_Set_2_RandID_4_S4] |
| GSM4005111 |
Pull Bioitin OPC mirctr 3 [Dutta_miRNA_Pulldown_Set_2_RandID_5_S5] |
| GSM4005112 |
Pull Bioitin OPC mir27a 1 [Dutta_miRNA_Pulldown_Set_2_RandID_2_S2] |
| GSM4005113 |
Pull Bioitin OPC mir27a 2 [Dutta_miRNA_Pulldown_Set_2_RandID_3_S3] |
| GSM4005114 |
Pull Bioitin OPC mir27a 3 [Dutta_miRNA_Pulldown_Set_2_RandID_6_S6] |
|
| Relations |
| BioProject |
PRJNA558362 |
| SRA |
SRP217183 |
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