|
| Status |
Public on Oct 13, 2017 |
| Title |
P2_cell_246 |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow
|
| Organism |
Homo sapiens |
| Characteristics |
markers: CD3-14-19-CD34+CD38+
Sex: Male
age: 59
subject: P2
disease: patients with bone marrow failure and cytogenetic abnormalities
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The C1 Single-cell Auto Prep System (Fluidigm) was employed to perform SMARTer (Clontech) WTA on up to 96 individual cells, according to the manufacturer’s protocols (full details available at www.fluidigm.com). WTA products were converted to Illumina sequencing libraries using Nextera XT (Illumina). Samples with single cell and bulk controls were sequenced on an Illumina HiSeq 2500 or 3000 Systems using a 75-bp paired-end sequencing strategy
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
P2_cell_246
|
| Data processing |
Paired-end reads were mapped to the hg19 genome with RSubread, featureCounts function within the Rsubread package was applied to summarize data to integer-based, gene-level read counts with annotation of ENSEMBL.
log(TPM+1) was calculated and used to represent gene expression, then expression of each gene was normlazation cross cells.
Genome_build: hg19
Supplementary_files_format_and_content: comma separated file containing normalized, centered transcripts per million (log(tpm+1)) values for filtered cells from healthy donors and patients.
|
| |
|
| Submission date |
May 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Shouguo Gao |
| E-mail(s) |
gaos2@nih.gov
|
| Phone |
3014029014
|
| Organization name |
National Institutes of Health
|
| Department |
NHLBI
|
| Lab |
Hematology Branch
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE99095 |
Single-cell RNA-seq reveals differentiation hierarchy of normal human bone marrow and a distinct transcriptome signature of aneuploid cells |
|
| Relations |
| BioSample |
SAMN07145640 |
| SRA |
SRX2835626 |
