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Sample GSM2468338 Query DataSets for GSM2468338
Status Public on Jan 25, 2019
Title KO Marrow-2
Sample type SRA
 
Source name Lin-Sca1+cKIT+CD48-CD150+
Organism Mus musculus
Characteristics strain: C57/Bl6
tissue: Bone marrow - Marrow fraction
genotype: Gfra2 KO
Treatment protocol no treatment
Extracted molecule total RNA
Extraction protocol Bone & marrow fraction were separated from tibia, femur and humeri of WT and Gfra2KO mice. After RBC lysis, mature hematopoietic cells were depleted using the EasyStep Mouse Hematopoietic Progenitor Cell Isolation Cocktail (Stem cell Technologies, 19756) according to the manufacturer’s protocol. The depleted cell population was stained for 20 minutes in PBS with 2 % FCS for LSK CD48-CD150+ markers. After dead cell exclusion using DAPI, pools of 30 viable LSK CD48-CD150+ cells were sorted using BD Influx™ cell sorter into 4 µl lysis buffer (0.5 U/µl SUPERase In RNase Inhibitor in 0.2 % (v/v) Triton-X-100) containing 12.5 mM DTT and 2.5 mM dNTP. RNAseq was performed following Smart-seq2 protocol (Picelli 2014)
Pooled libraries of 4 replicates per sample were prepared using the Illumina Nextera XT DNA preparation kit & sequencing was performed on the Illumina HiSeq 4000
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq counts (.txt)
 
Submission date Jan 25, 2017
Last update date May 15, 2019
Contact name Evangelia Diamanti
E-mail(s) ed347@cam.ac.uk
Phone 01223 62317
Organization name University of Cambridge
Department Haematology
Lab Gottgens
Street address Wellcome Trust / MRC Building, Hills Road
City Cambridge
ZIP/Postal code CB2 0XY
Country United Kingdom
 
Platform ID GPL21103
Series (1)
GSE94078 Gene expression profiling of LSKSLAM cells in mice deficient for cholinergic fibers
Relations
BioSample SAMN06271525
SRA SRX2517800

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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