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Status |
Public on Oct 06, 2020 |
Title |
P08 |
Sample type |
SRA |
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Source name |
BMMC
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Organism |
Homo sapiens |
Characteristics |
cell type: BMMC tumor stage: de novo AML gender: F age: 71 disease state: acute myeloid leukemia
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Extracted molecule |
total RNA |
Extraction protocol |
Cells were isolated from bone marrow aspirates by Ficoll Hypaque Solution. Library preparations were performed according to the Microwell-seq protocol
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
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Data processing |
Base-calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. ScRNA-seq reads were aligned to the Homo_sapiens GRCh38 genome assembly using STAR version (2.5.2a) with default configurations. Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts. Genome_build: Homo_sapiens GRCh38 genome Supplementary_files_format_and_content: Tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.
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Submission date |
Oct 22, 2019 |
Last update date |
Mar 13, 2024 |
Contact name |
Junqing Wu |
E-mail(s) |
wujunqing@zju.edu.cn
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Organization name |
Zhejiang University
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Street address |
Yuhangtang Road 866
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City |
Hangzhou |
ZIP/Postal code |
310058 |
Country |
China |
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Platform ID |
GPL20795 |
Series (1) |
GSE130756 |
A single-cell survey of cellular hierarchy in acute myeloid leukemia |
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Relations |
BioSample |
SAMN13088633 |
SRA |
SRX7036735 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4135779_P08_dge.txt.gz |
5.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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