|
| Status |
Public on May 01, 2016 |
| Title |
MP 2 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow progenitor
|
| Organism |
Mus musculus |
| Characteristics |
sample type: Lin-Sca-1-c-Kit+ mouse bone marrow cells
strain: FVB N/J
|
| Growth protocol |
GFP-labled APL cells were expanded in vivo via transplantation into syngeneic mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with AMBION AM1560 kit.
Following "TruSeq RNA Sample Preparation Guide".
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
HPC-2
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000 --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed using DEGseq function package in R program version 2.10.0
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample
|
| |
|
| Submission date |
Apr 26, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiang Zhu |
| E-mail(s) |
zhujiang@shsmu.edu.cn
|
| Organization name |
Shanghai institute of hematology
|
| Street address |
197, rui-jin 2nd Road
|
| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE46434 |
Expression data from GFP-labeled c-Kit+ mouse APL cells and normal Lin-Sca-1-c-Kit+ mouse bone marrow cells |
|
| Relations |
| BioSample |
SAMN02058598 |
| SRA |
SRX272199 |
