|
| Status |
Public on Apr 15, 2024 |
| Title |
IκBα KO, E14.5 LT-HSC Fetal liver, replicate 1, 10x scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Fetal Liver
|
| Organism |
Mus musculus |
| Characteristics |
cell type: LSK
tissue: Fetal Liver
strain: CD1
age: E14.5
genotype: I{kappa}B{alpha} KO
|
| Extracted molecule |
total RNA |
| Extraction protocol |
E14.5 fetal livers were lineage depleted and FACS sorted for the LSK population from pools of Ikba 2 WT and 3 KO.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs 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 RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
10x Genomic scRNA-seq
|
| |
|
| 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, gene counting and aggregation were made using the Cell Ranger software v6.0.0 from 10xGenomics
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Oct 03, 2022 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Anna Bigas |
| E-mail(s) |
abigas@imim.es
|
| Phone |
+34933160440
|
| Organization name |
Institut Hospital del Mar d'Investigacions Mèdiques
|
| Department |
Cancer Research
|
| Lab |
Stem Cells and Cancer
|
| Street address |
Dr. Aiguader 88
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE188525 |
A critical requirement for IκBα in controlling dormancy in Hematopoietic stem cells via retinoic acid during embryonic development |
| GSE214699 |
A critical requirement for IκBα in controlling dormancy in Hematopoietic stem cells via retinoic acid during embryonic development [scRNA-seq_10x] |
|
| Relations |
| BioSample |
SAMN31138965 |
| SRA |
SRX17781954 |
