|
| Status |
Public on Aug 18, 2017 |
| Title |
WT_dmso_n2 |
| Sample type |
SRA |
| |
|
| Source name |
Cultured cortical neurons
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wildtype
treatment: dmso
|
| Treatment protocol |
At 7 DIV, neurons were treated for 24 hours with vehicle, Jq1, or THZ1.
|
| Growth protocol |
Neurons were grown in Neurobasal media supplemented with B27, Glutamax, and Pen/Strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified from neurons using Qiagen RNAeasy kit
Purified DNA was prepared for sequencing with the TruSeq RNA sample Prep Kit (Illumina) as per manufacturer's instructions. Libraries were sequenced on NextSeq500 (Illumina) with 75bp single reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
WT_dmso_n2
|
| Data processing |
Data was aligned using Tophat2 (2.1.0) with mm9 as a reference genome
Samtools (version 0.1.19) was used to sort bam files
TDF files were generated by IGVtools (2.3.67) count function with processed bam files as input
HTSeq (0.6.1) was used to generate counts and DESeq2 was used for comparing conditions for differential expression
Genome_build: mm9
Supplementary_files_format_and_content: tdf
Supplementary_files_format_and_content: DESeq data: WTvKO.deseq2.csv
Supplementary_files_format_and_content: count data for dmso and Jq1 treated WT and KO
|
| |
|
| Submission date |
May 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Erica Korb |
| Organization name |
University of Pennsylvania
|
| Lab |
Korb Lab
|
| Street address |
3400 Civic Center Boulevard
|
| City |
Philadelphia |
| State/province |
PENNSYLVANIA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE81803 |
RNA-sequencing in WT and Fmr1-/- (KO) neurons treated with Jq1 and THZ |
| GSE81912 |
Fragile X Syndrome causes epigenetic disruptions treatable with BET inhibitor Jq1 |
|
| Relations |
| BioSample |
SAMN05171550 |
| SRA |
SRX1797701 |
