|
| Status |
Public on Nov 29, 2017 |
| Title |
15917_B-ALSK-non-2 |
| Sample type |
SRA |
| |
|
| Source name |
Lin-Sca-1+c-kit+ (LSK) cells
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: BCR-ABL negative
cell type: LSK
tissue origination: bone marrow
|
| Extracted molecule |
total RNA |
| Extraction protocol |
LSK cells from non-induced and induced CML mice were sorted and total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Valencia, CA).
Illumina small RNA-seq protocol (TruSeq Small RNA Sample Prep kit) with some modifications.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample 4
LSK-non-2
Processed data file: miRNA.txt
|
| Data processing |
Adapter was trimmed using cutadapt.
Reads were aligned to mm9 genome using Bowtie.
Expression value of miRNAs in miRBase v18 was counted using customized R script.
Count data were normalized by TMM method using "edgeR" package.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: miRNA.txt: Tabular file containing raw counts.
|
| |
|
| Submission date |
Nov 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiwei Wu |
| E-mail(s) |
[email protected]
|
| Organization name |
City of Hope National Medical Center
|
| Department |
Computational and Quantitative Medicine
|
| Street address |
1500 E. Duarte Rd.
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE107431 |
Small RNA deep sequencing using Illumina HiSeq2500 |
|
| Relations |
| BioSample |
SAMN08104976 |
| SRA |
SRX3426416 |
