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| Status |
Public on Aug 27, 2018 |
| Title |
Poly(A)+ RNA-seq from H226 cells expressing doxycycline-inducible Control (non-targeting) and p63-targeting shRNAs |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
To determine the impact of ΔNp63α knockdown on steady-state mRNA levels, we performed poly(A)-enriched RNA-seq analysis of lung squamous cell carcinoma line H226 (inducible shControl and shp63) in the presence of 1µg/mL doxycycline to induce shRNA expression.
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| Overall design |
Poly(A)+ RNA for two independent biological replicates was purified from H226 cells (inducible shControl and shp63) incubated treated for six days with 1 µg/mL doxycycline. a TruSeq Stranded mRNA Library Prep Kit (Illumina). Libraries were sequenced on an Illumina HiSeq 2000 system at the University of Colorado Cancer Center Genomics and Microarray Core facility. Reads were aligned (TopHat2) to the Human reference genome (GRCh37/hg19) and gene-level counts (HTseq-count) were used for differential expression analysis (DESeq2).
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| Contributor(s) |
Abraham CG, Pandey A, Galbraith MD, Espinosa JM |
| Citation(s) |
30232004 |
| |
| Submission date |
Mar 09, 2018 |
| Last update date |
Mar 27, 2019 |
| Contact name |
Matthew D Galbraith |
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Department |
Pharmacology & Linda Crnic Institute for Down Syndrome
|
| Street address |
RC1-N, Mail Stop 8303, Rm. P18-6114 12800 E. 19th Ave.
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (4)
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| GSM3035185 |
H226 shControl, 6 days doxycycline, replicate 1 |
| GSM3035186 |
H226 shControl, 6 days doxycycline, replicate 2 |
| GSM3035187 |
H226 shp63, 6 days doxycycline, replicate 1 |
| GSM3035188 |
H226 shp63, 6 days doxycycline, replicate 2 |
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| This SubSeries is part of SuperSeries: |
| GSE111635 |
sgRNA cassette sequencing and RNA-seq from H226 cells expressing doxycycline-inducible Control (non-targeting) and p63-targeting shRNAs |
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| Relations |
| BioProject |
PRJNA437576 |
| SRA |
SRP134235 |
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