|
| Status |
Public on Jul 04, 2016 |
| Title |
Haematopoietic progenitor cell Prog_Rep_839 |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Haematopoietic progenitor cell
strain: C57BL/6
age: 8-12 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bone marrow cells were isolated from the femurs, tibiae and iliac crest of 20 8-12 week old C57BL/6 mice.
The cells were lineage depleted and stained with antibodies to separate individual populations by FACS.
Single-cell sorting was done using a FACS Influx5 (BD Biosciences) using unstained cells and single-stained cells are gate-settng controls.
Cells were sorted directly into individual wells of a 96-well PCR plate containing lysis buffer.
Single-cell RNA-seq analysis was performed as described previously (Picelli et al., 2014).
Pooled libraries were run on the Illumina Hi-Seq 2500.
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 |
single cell RNA-Seq
|
| 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: HT-Seq counts / gene counts (.txt)
|
| |
|
| Submission date |
May 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Evangelia Diamanti |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE81682 |
The transcriptional landscape of mouse blood stem/progenitor cell transitions at single cell resolution |
|
| Relations |
| BioSample |
SAMN05157041 |
| SRA |
SRX1786816 |
