|
| Status |
Public on Feb 01, 2015 |
| Title |
ALL211 d3 |
| Sample type |
SRA |
| |
|
| Source name |
ALL211 T-ALL cells
|
| Organism |
Mus musculus |
| Characteristics |
immunophenotype: GFPmid
treatment: 3 days Dox (shRNA shut-off)
cell source: splenocytes of leukemic recipient mice
cell type: T-ALL cells
|
| Treatment protocol |
Leukemic mice were untreated or treated with Dox for 3 days, resulting in shutdown of GFP-linked shRNA expression and restoration of endogenous Ikaros expression
|
| Growth protocol |
Spleen cells were isolated from leukemic mice and T-ALL cells were isolated using FACS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FACS sorted cell pellets were lysed and RNA prepared using QIAGEN RNeasy plus mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
batch date: Apr 22 2014
|
| Data processing |
Illumina CASAVA pipeline version 1.8.2 used for basecalling
Reads were aligned to the mouse genome by Rsubread version 1.14.0
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI exon annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files were written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene
|
| |
|
| Submission date |
Jan 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
smyth@wehi.edu.au
|
| Phone |
(+61 3) 9345 2326
|
| Fax |
(+61 3) 9347 0852
|
| URL |
http://www.wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
Bioinformatics
|
| Lab |
Smyth
|
| Street address |
1G Royal Pde
|
| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE64899 |
Expression profiling of mouse T-ALL (Vav-tTA;TRE-GFP-shIkaros primary leukemia ALL211) cells following Ikaros restoration |
| GSE64928 |
Expression profiling of mouse T-ALL (Vav-tTA;TRE-GFP-shIkaros primary leukemia) cells following Ikaros restoration |
|
| Relations |
| BioSample |
SAMN03283198 |
| SRA |
SRX840152 |
