|
| Status |
Public on Feb 16, 2017 |
| Title |
patient 2 [SLX-8969.N709_N508] |
| Sample type |
SRA |
| |
|
| Source name |
patient 2 single cell RNA-Seq
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: patient 2
disease state: myeloprolifertive disease
cell type: hameatopoietic stemand progenitor cells
protocol: Smart-Seq2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD90+, CD34+, CD38-, CD45RA- cells were flow sorted and subjected to Smart-Seq 2
Smart-Seq2 and Nextera XP
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: patient2.txt
|
| Data processing |
Illumina basecalling
Sequenced reads were trimmed for Nextera Transposase Sequence,
Trimmed reads were mapped to Human GRCh38-77 reference genome from ENSEMBL plus ERCC92 spike-in controls with tophat 2.0.13 and bowtie 2.2.3
Quality control of the cells were performed by looking at the number of detected genes. Cells expressing low counts were removed for the following step
Gene expression count matrix were calculated with seqmonk
Genome_build: GRCh38-77
Supplementary_files_format_and_content: Space separated raw counts. Rows are genes, columns are cells.
|
| |
|
| Submission date |
Mar 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Anthony Green |
| Organization name |
University of Cambridge
|
| Department |
Department of heamatology
|
| Lab |
Green's Lab
|
| Street address |
Hills Road
|
| City |
Cambridge |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB2 0XY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE79102 |
SC3-consensus clustering of single cell RNA-Seq data |
|
| Relations |
| BioSample |
SAMN04545930 |
| SRA |
SRX1626536 |
