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Sample GSM7110561 Query DataSets for GSM7110561
Status Public on Jun 13, 2023
Title Donor 4978, Relapse
Sample type SRA
 
Source name Bone marrow aspirate
Organism Homo sapiens
Characteristics tissue: Bone marrow aspirate
subject id: Donor 4978
time point: Relapse
Extracted molecule polyA RNA
Extraction protocol Bone marrow aspirates were obtained from The Finnish Haematology Registry and Clinical Biobank. The mononuclear cell fraction was isolated using Ficoll density gradient separation.
Cell counting and viability assessments were conducted using To-Pro-3 viability dye. Thereafter, GEM generation & barcoding, reverse transcription, cDNA amplification and 3’ gene expression library generation steps were all performed according to the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Single Index) User Guide (10x Genomics CG000204 Rev D) with all stipulated 10x Genomics reagents.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10X Genomics
4978_R
Data processing Reads were aligned and quantified using CellRanger v6.0.0. Cell type annotations were predicted using the dataset from Granja et. al. (GSE139369) as a reference.
Assembly: hg38
Supplementary files format and content: Processed data is provided as tab-delimited text files. For each sample there are two files: a cell (rows) x gene (columns) count matrix and a metadata file with cell type annotations for each cell.
 
Submission date Mar 21, 2023
Last update date Jun 13, 2023
Contact name Eva Szegezdi
E-mail(s) eva.szegezdi@universityofgalway.ie
Organization name University of Galway
Street address University Road
City Galway
ZIP/Postal code H91 TK33
Country Ireland
 
Platform ID GPL24676
Series (1)
GSE227903 Cell-cell interactome of the hematopoietic niche and its changes in acute myeloid leukemia
Relations
BioSample SAMN33847010
SRA SRX19744042

Supplementary file Size Download File type/resource
GSM7110561_4978_R_count_mat.txt.gz 14.6 Mb (ftp)(http) TXT
GSM7110561_4978_R_meta.txt.gz 14.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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