|
| Status |
Public on Dec 13, 2019 |
| Title |
Spleen LSCe from mice transplanted with shEvi1 (clone #44)-transduced LCLSK-MA9, treated with atRA |
| Sample type |
SRA |
| |
|
| Source name |
leukemic stem cell enriched cells (LSCe)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
shrn: shEvi1
agent: atRA
age: 10-12 weeks
tissue: Spleen
|
| Treatment protocol |
LSCe were treated with 1 µM atRA or the corresponding amount of DMSO for another 24 h.
|
| Growth protocol |
LSCe (Venus+ RFP+ lineage (CD11b, CD3, Ter119, B220, Gr1) negative, c-Kit+, Sca-1-, CD34+, CD16/CD32+ cells) were isolated from spleen by flow cytometry and allowed to recover for 24 h in IMDM medium containing 10% FBS, 1% L-Glutamine, 50 ng/ml mSCF, 10 ng/ml mIL-3, 10 ng/ml mTPO, 10 ng/ml mFlt3L, and 10 ng/ml mIL-6.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using QIAshredder 50 columns (Qiagen) and the RNeasy Mini Kit 50 including DNase treatment (Qiagen) according to the manufacturer’s protocol.
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library concentrations were determined with the Qubit Fluorometric Quantitation system and the size distribution was assessed using the Experion Automated Electrophoresis System. Sequencing libraries were pooled, diluted, and sequenced on an Illumina HiSeq 4000 using 50 bp single read chemistry.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
shEvi1_ATRA_0
|
| Data processing |
Adapters were removed and reads were cropped at 65 bp using Trimmomatic (0.36)
Sequencing quality was checked using FASTQC (0.11.5)
Reads were mapped using STAR aligner (2.6.0c) on mouse genome version mm10 (UCSC) with RefSeq gene annotation and index with 100 bp splice junction overhang
HTSeq was used to quantify raw gene counts according to mm10refGene.gtf
Genome_build: mm10
Supplementary_files_format_and_content: raw counts for all samples are summarized as tab delimited txt file
|
| |
|
| Submission date |
Dec 03, 2018 |
| Last update date |
Dec 13, 2019 |
| Contact name |
Rotraud Wieser |
| E-mail(s) |
rotraud.wieser@meduniwien.ac.at
|
| Organization name |
Medical University of Vienna
|
| Department |
Clinic of Medicine I
|
| Street address |
Waehringer Guertel 18-20
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE123255 |
All-trans retinoic acid enhances, and a pan-RAR antagonist counteracts, the stem cell promoting activity of EVI1 in acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN10516999 |
| SRA |
SRX5088397 |
