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Sample GSM2333733 Query DataSets for GSM2333733
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

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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