|
Status |
Public on May 26, 2015 |
Title |
haematopoietic stem cell [HSC1_64] |
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_64
|
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 |
SAMN03073642 |
SRA |
SRX704222 |