|
| Status |
Public on Apr 07, 2020 |
| Title |
RNA_LSK_BMT_RKO_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: bone marrow
cell type: LSK
genotype: RKO
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq experiments were performed using LSK or CMP cells obtained from WT-, SKO-, RKO-, or DKO-transplanted mice.
RNA was extracted using RNeasy Mini Kit (QIAGEN) or NucleoSpin RNA XS (Macherey-Nagel). Libraries for RNA-seq were prepared using the NEBNext Ultra RNA Library Prep kit for Illumina (New England BioLabs) and were subjected to sequencing using HiSeq 2500 instrument (Illumina) with a standard 125-bp paired-end protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNA_LSK_BMT_cpm.txt
|
| Data processing |
RNA-seq experiments were performed in three or more biological replicates. The sequencing reads were aligned to the mouse reference genome (mm9) using STAR7 (v2.5.3).
Reads on each gene were counted with featureCounts (v1.5.3) from Subread package, and edgeR package in R was used to identify the differentially expressed genes with FDR threshold of 0.05 and to generate the multidimensional scaling (MDS) plot.
The analysis was performed in genes expressed at >1 count per million (CPM) in two or more samples, and generalized linear models were used to compare gene expression data.
Genome_build: mm9
Supplementary_files_format_and_content: Reads on each gene were counted with featureCounts (v1.5.3) from Subread package, and edgeR package in R was used.
|
| |
|
| Submission date |
May 21, 2019 |
| Last update date |
Apr 07, 2020 |
| Contact name |
Yotaro Ochi |
| Organization name |
Kyoto Univiersity
|
| Department |
Department of Pathology and Tumor Biology
|
| Street address |
Yoshida-Konoe-cho
|
| City |
Kyoto |
| ZIP/Postal code |
606-8501 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE131581 |
Combined Cohesin-Runx1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes [RNA-seq] |
| GSE131583 |
Combined Cohesin-Runx1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes |
|
| Relations |
| BioSample |
SAMN11808125 |
| SRA |
SRX5877949 |
