|
| Status |
Public on Mar 11, 2015 |
| Title |
MiG-empty RNA-Seq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MiG-empty RNA-Seq
|
| Organism |
Mus musculus |
| Characteristics |
cell line: EML
tissue: bone marrow
cell type: basophil
atcc catalog number: CRL-11691
|
| Biomaterial provider |
ATCC
|
| Treatment protocol |
EML cells were transduced with either MSCV-IRES-GFP (MiG-empty) or with retroviral constructs encoding ASXL1(1-479) + BAP1 and expanded for 15 days post-transduction
|
| Growth protocol |
EML cells cultured under conditions recommended by ATCC. ATCC Cat # CRL-11691
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated and subjected to ribosomal depletion using Ribozero GOLD kit purchased from Epicentre.
RNA-seq library construction was carried out using 5500XL sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Description |
Ribosome-depleted RNA
processed data file: rna_express_lib1and2.xprs.txt; DESeq_results.txt
|
| Data processing |
RNA-seq reads were aligned using TopHat (version 2.0.9). Differential expression results were made with HTSeq and DESeq using genome version mm9 and Ensembl annotation (release 67, excluding non-protein coding transcripts). eXpress was used to obtain transcript-level expression estimates.
Genome_build: mm9
Supplementary_files_format_and_content: BED files with SICER calls, DESeq result file, eXpress result files
|
| |
|
| Submission date |
Feb 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Anjana Rao |
| E-mail(s) |
arao@liai.orgo
|
| Organization name |
La Jolla Institute for Allergy and Immunology
|
| Department |
Department of Signaling and Gene Expression
|
| Street address |
9420 Athena Circle
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL15907 |
| Series (1) |
| GSE65555 |
Cancer-associated ASXL1 mutations may act as gain-of-function mutations of the ASXL1-BAP1 complex |
|
| Relations |
| BioSample |
SAMN03326189 |
| SRA |
SRX864152 |
