|
| Status |
Public on Feb 22, 2016 |
| Title |
KO-Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HSPCs
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: HSPCs
genotype/variation: KO
|
| Growth protocol |
HSPCs were sorted fy flow cytometry and cultured for 24 hours . Total RNA was isolated with a QIAGEN Rnase kit.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Rnase kit
Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
FastQC (V 0.10.1) was used to check the data quality. The first 10 bases and last 20 bases were trimmed based on FastQC results.
Tophat (V 2.0.12) was used for the alignment with default parameters.
Cuffdiff from Cufflinks (V 2.2.1) was used to call the differentially expressed genes, with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: The DEGs file was generated using cuffdiff. It followed the standard gene_exp.diff format of cuffdiff outputs.
|
| |
|
| Submission date |
Jul 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexandros Tzatsos |
| E-mail(s) |
atzatsos@gwu.edu
|
| Phone |
2029949104
|
| Organization name |
George Washington University
|
| Department |
GW Cancer Center
|
| Lab |
Cancer Epigenetics Laboratory
|
| Street address |
800 22nd St NW SEH 8850
|
| City |
Washington |
| State/province |
DC |
| ZIP/Postal code |
20052 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE70728 |
Role of the histone demethylase KDM2B in hematopoietic homeostasis and malignancies [RNA-seq] |
| GSE70729 |
Role of the histone demethylase KDM2B in hematopoietic homeostasis and malignancies |
|
| Relations |
| BioSample |
SAMN03853776 |
| SRA |
SRX1091433 |
