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| Status |
Public on Jan 11, 2022 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Bat3-/- BMDC Transcriptomes I |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived WT or Bat3 KO BMDC transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
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| Overall design |
Methods: BMDC mRNA profiles of wild-type (WT) and Bat3 KO mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
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| Contributor(s) |
Subramanian A, Lambden C |
| Citation(s) |
35275752 |
| Submission date |
Mar 24, 2021 |
| Last update date |
Apr 13, 2022 |
| Contact name |
Ayshwarya Subramanian |
| E-mail(s) |
subraman@broadinstitute.org
|
| Organization name |
Broad Institute
|
| Department |
Klarman Cell Observatory
|
| Street address |
415 Main Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (1) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE169664 |
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Bat3-/- BMDC Transcriptomes |
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| Relations |
| BioProject |
PRJNA716971 |
| SRA |
SRP311973 |
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