|
| Status |
Public on May 22, 2017 |
| Title |
Hhex-deleted LSK cells rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Bone marrow
cell type: LSK (Lin-Sca+Kit+)
genotype: Hhex deletion
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from sorted LSK cells using the RNeasy Kit (Qiagen, Valencia CA).
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were mapped to mouse genome mm9 using Subread. Only uniquely mapped reads were retained. Mapped reads were assigned to mouse RefSeq genes using featureCounts. NCBI RefSeq mouse annotation build 37.2 was used. Genes were removed from analysis if they failed to achieve a RPKM (reads per kilo exonic bases per million mapped reads) value of 0.5 or greater in at least two libraries.
Counts were converted to log2 counts per million, quantile normalized and precision weighted with the ‘voom’ function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. A false discovery rate cutoff of 0.1 was applied when calling differentially expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file including normalized log2-RPKM expression values of genes.
|
| |
|
| Submission date |
Aug 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Shi |
| E-mail(s) |
Wei.Shi@onjcri.org.au
|
| Organization name |
Olivia Newton-John Cancer Research Institute
|
| Street address |
145 Studley Road
|
| City |
Heidelberg |
| State/province |
Victoria |
| ZIP/Postal code |
3084 |
| Country |
Australia |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE86209 |
Hhex regulates HSC self-renewal and stress hematopoiesis via repression of Cdkn2a |
|
| Relations |
| BioSample |
SAMN05715191 |
| SRA |
SRX2065896 |
