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Sample GSM1507608 Query DataSets for GSM1507608
Status Public on May 26, 2015
Title haematopoietic stem cell [HSC1_46]
Sample type SRA
 
Source name Bone marrow
Organism Mus musculus
Characteristics strain: C57BL/6
age: 9-12 weeks old
cell type: haematopoietic stem cell
Extracted molecule total RNA
Extraction protocol Bone marrow cells were isolated from the bones (femurs and tibiae) of 9–12-week-old C57BL/6 mice. Cells were stained with antibodies to permit the separation of the individual populations. A FACS Influx (BD Biosciences) was used for all single-cell sorting, unstained populations and single-stains were used as gate-setting controls. Single cells were sorted by FACS directly into individual wells of a 96-well plate containing lysis buffer. Single cell RNA-Seq analysis was performed as described previously (Picelli et al., 2014). Pooled libraries were then run on the Illumina Hi-Seq 2500.
single cell RNA libraries were prepared for sequencing using the Illumina Nextera XT DNA preparation kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description HSC1_46
Data processing RNA-seq reads aligned to mm10 using STAR (version 2.3.0) with parameters --outFilterMultimapScoreRange 1 --outSAMstrandField intronMotif --genomeLoad NoSharedMemory --outStd SAM.
SAM files converted to BAM format and then sorted using samtools (version 0.1.18).
Read counts for features were calculated using HTSeq (version 0.6.1).
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq counts/spreadsheet.
 
Submission date Sep 18, 2014
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 GPL17021
Series (1)
GSE61533 Molecular signatures of heterogeneous stem cell populations are resolved by linking single cell functional assays to single cell gene expression
Relations
BioSample SAMN03073609
SRA SRX704204

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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