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Sample GSM6968279 Query DataSets for GSM6968279
Status Public on May 29, 2024
Title STAT5ab F/F Cre+/- (Stat5-/-) 24363 N335
Sample type SRA
 
Source name bone marrow
Organism Mus musculus
Characteristics tissue: bone marrow
age: 3 months
cell type: Lin-cKit+
genotype: Stat5 KO
index library: SIGAB2
Extracted molecule total RNA
Extraction protocol The femora, tibiae, and ilia of C57BL/6 mice of WT and STAT5ab mice were crushed and the bone marrow cells were released and the red blood cells were lysed with ammonium chloride solution (STEMCELL Technologies). The cells were stained with the fluorophore-conjugated monoclonal antibodies, and sorted using an Influx cell sorter (BD Biosciences) equipped with five lasers. The cells were sorted into 1.5 ml tubes containing PBS + 2% FCS. Sorted cells were harvested, resuspended in 0.04% BSA (Thermo Fisher) and counted. Cells were processed using the 10x Chromiumâ„¢ Single Cell 3' kit (v2), following manufacturers instructions.
Libraries were prepared using 10x Chromiumâ„¢ Single Cell 3' kit (v2), following manufacturers instructions. Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A mRNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled cell barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriate size fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction P5, P7, a sample index, and an Ilumina Read 2 are added (via End Repair, A-tailing, Adaptor Ligation, and PCR). The resulting libraries contain the P5 and P7 primer sequences required for Illumina sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
Data processing The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v2.1.1 ( https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: h5 compressed file with filtered UMI counts
 
Submission date Jan 24, 2023
Last update date May 29, 2024
Contact name Hugo P. Bastos
E-mail(s) hpb29@cam.ac.uk
Organization name Wellcome - MRC Cambridge Stem Cell Institute
Department Haematology
Street address Jeffrey Cheah Biomedical Centre, Puddicombe Way
City Cambridge
ZIP/Postal code CB2 0AW
Country United Kingdom
 
Platform ID GPL24247
Series (1)
GSE223632 Maintenance of haematopoietic stem cells by tyrosine-unphosphorylated STAT5 and JAK inhibition - STAT5 deficient HSPCs (LK)
Relations
BioSample SAMN32895731
SRA SRX19157777

Supplementary file Size Download File type/resource
GSM6968279_RBG25823_filtered_gene_bc_matrices_h5.h5 21.3 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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