|
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 |