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Sample GSM3588001 Query DataSets for GSM3588001
Status Public on Feb 28, 2019
Title BM4-anno
Sample type SRA
 
Source name Bone marrow aspirate from healthy donor
Organism Homo sapiens
Characteristics gender: M
age: 23
Treatment protocol Not applicable, material from human subjects
Growth protocol Not applicable, material from human subjects
Extracted molecule polyA RNA
Extraction protocol Bone marrow aspirates were viably frozen after using density gradient centrifugation to isolate mononuclear cells.
Single-cell transcriptome analysis was performed using the Seq-Well method.
Bone marrow aspirates were viably frozen after using density gradient centrifugation to isolate mononuclear cells.
Single-cell transcriptome analysis was performed using the Seq-Well method.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description single-cell genotyping by targeted PCR.
Single cell annotations for BM4
Data processing Data procesing was performed in three main steps:
1) Cell barcodes were extracted from sequencing reads prior to alignment.
2) Reads were aligned to the human genome using STAR guided by RefSeq gene annoations, producing both genome and pseudo-transcriptome alignments.
3) For each cell barcode, reads mapping uniquely to a gene were collapsed by their unique molecular identifier (UMI).
4) For each gene and cell barcode the number of UMIs was used to generate a digital expression matrix (DEM).
Single-cell genotyping analysis was performed by assigning reads to the expected mutant or wild-type allele, and collapsing reads by their UMI and cell barcode.
Genome_build: Hg38
Supplementary_files_format_and_content: Processed data is provided as tab-delimited text files. There are two files per sample. The first file contains a number of annotations (columns) for each cell (rows). The second file contains a digital expression matrix containing the number of UMIs for each gene (rows) and cell (columns).
 
Submission date Feb 01, 2019
Last update date Mar 02, 2019
Contact name Peter van Galen
E-mail(s) petervangalen@gmail.com
Organization name MGH / Broad Institute
Department Pathology
Lab Dr. Bradley Bernstein
Street address 185 Cambridge Street
City Boston
State/province Massachusetts
ZIP/Postal code 02114
Country USA
 
Platform ID GPL18573
Series (1)
GSE116256 Single-cell RNA-seq reveals AML hierarchies relevant to disease progression and immunity
Relations
BioSample SAMN10861663
SRA SRX5324573

Supplementary file Size Download File type/resource
GSM3588001_BM4.anno.txt.gz 183.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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