|
Status |
Public on May 29, 2018 |
Title |
DERARE KO Reserve rep3 |
Sample type |
SRA |
|
|
Source name |
Bone marrow
|
Organism |
Mus musculus |
Characteristics |
genotype: wild type reserve ko
|
Extracted molecule |
total RNA |
Extraction protocol |
LT-HSCs were sorted into 96-well plates with 7 ul lysis buffer containing RNase inhibitor (2 U/μl) from BM. First-strand cDNA synthesis and cDNA libraries were constructed using the SMARTer ultra low input RNA kit for sequencing - v3 (Clontech). RNA-seq libraries were prepared using the SMARTer ultra low input RNA kit for sequencing - v3 (Clontech Nextera)
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
wild type reserve ko
|
Data processing |
Base-calling and bcl to fastq generation was done wit CASAVA 1.8.2 from illumina. RNA-seq was aligned to genome mm10 from UCSC using tophat 2.0.10. Cufflinks was used to generate FPKM table Genome_build: mm10 Supplementary_files_format_and_content: FPKM table
|
|
|
Submission date |
Oct 03, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Madelaine Gogol |
Organization name |
Stowers Institute
|
Department |
Computational Biology Core
|
Street address |
1000 E. 50th Street
|
City |
Kansas City |
State/province |
MO |
ZIP/Postal code |
64110 |
Country |
USA |
|
|
Platform ID |
GPL17021 |
Series (2) |
GSE87556 |
DERARE RNA-seq |
GSE89492 |
A retinoid-dependent and methylation-sensitive enhancer in Hoxb cluster maintains haematopoietic stem cells and prevents leukaemogenesis |
|
Relations |
BioSample |
SAMN05859310 |
SRA |
SRX2209030 |