|
| Status |
Public on May 26, 2015 |
| Title |
haematopoietic stem cell [HSC1_29] |
| 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_29
|
| 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 |
SAMN03073682 |
| SRA |
SRX704187 |
