|
| Status |
Public on Apr 03, 2019 |
| Title |
CML1_CMLSC23 |
| Sample type |
SRA |
| |
|
| Source name |
CML1_CMLSCs
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: Chronic Myelogenous Leukemia (CML) patient
subject id: CML1
leukemia stage: Chronic Phase (Newly diagnosed)
bcr-abl status: PRESENCE
tissue: bone marrow
cell type: CML stem cells (CMLSCs)
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Primary CML cells were subjected directly to flow sorting
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cells were directly collected into lysis buffer and converted to cDNA.
Library was prepared using Nextera XT DNA sample preparation following Smart-seq2 protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
CML1_S40
|
| Data processing |
Illumina Casava software used for basecalling.
The reads qualities were assessed using fastqc (version 0.10.1) ;
Aligned the reads to hg19 using tophat (version 2.0.14), with default setting except set parameter read-mismatches to 2
HTseq-count (version 0.6.1p1) was used to generate gene count table.
Genome_build: hg19
Supplementary_files_format_and_content: htseq.counts.txt: tab-delimited text file includes the raw counts for each sample generated by htseq-count.
Supplementary_files_format_and_content: TPMs.txt: tab-delimited text file includes the TPM (Transcript Per Million) values generated by RSEM (version 1.3.0). The annotation of the genes are also provided in the file.
|
| |
|
| Submission date |
May 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael R. Green |
| E-mail(s) |
michael.green@umassmed.edu
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Molecular, Cell and Cancer Biology
|
| Lab |
Michael R. Green
|
| Street address |
364 Plantation Street
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE81730 |
Single cell gene expression profiling in normal HSCs and CML stem cells |
|
| Relations |
| BioSample |
SAMN05163019 |
| SRA |
SRX1792164 |
