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Sample GSM1651908 Query DataSets for GSM1651908
Status Public on Jul 27, 2015
Title Mut1_total_RNA
Sample type SRA
Source name Mut1_total_RNA
Organism Mus musculus
Characteristics genotype: Runx1 deficient
tissue: Bone Marrow
strain: C57BL/6J
Growth protocol Mice were treated according to the University of Pennsylvania’s Animal Resources Center and IACUC protocols.
Extracted molecule total RNA
Extraction protocol 24,000 Flt3- LSK cells were sorted into Trizol and RNA was purified (Qiagen). Spike-in RNA (ERCC RNA Spike-In Mix, Life Technologies) was added following the manufacturer’s instructions.
Two types of sequencing libraries were prepared; one from polyA-selected RNA to analyze mRNAs, and one from total RNA to compare rRNA levels. mRNA was isolated from total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, NEB). PolyA-selected mRNA was fragmented to average size of 300 nt, reverse transcribed to generate double-stranded cDNA, and converted to a paired end library using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530, NEB) according to manufacturer's instructions including the optional double size selection procedure using Agencourt AMPure XP beads. Prepared libraries were quantified with dsDNA HS Kit (Q32851) for Qubit and the size distribution was assessed using High Sensitivity DNA Kit (5067-462) for Bioanalyzer
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Sequenced reads mapped to the combination reference of mouse genome (release mm9), ERCC transcripts and rDNA region through Tophat
Gene level read counts estimated by FeatureCounts for combination of Ensembl genes(release 66), ERCC transcripts and rRNA genes
Differentially expressed genes were called by edgeR
Genome_build: mm9 + ERCC + rDNA
Supplementary_files_format_and_content: text file, gene level read counts matrix
Submission date Apr 06, 2015
Last update date May 15, 2019
Contact name Long Gao
Phone 267-425-0053
Organization name The Children’s Hospital of Philadelphia
Lab Tan Lab
Street address 4002 Colket Translational Research Building (CTRB) 3501 Civic Center Boulevard
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platform ID GPL17021
Series (1)
GSE67609 Runx1 deficiency decreases ribosome biogenesis and confers stress resistance to hematopoietic stem and progenitor cells
BioSample SAMN03462061
SRA SRX978925

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

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