|
| Status |
Public on Feb 23, 2022 |
| Title |
Differentiating megakaryocytes on D9, wPRE |
| Sample type |
SRA |
| |
|
| Source name |
A1ATD1 induced pluripotent stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A1ATD1
day of differentiation: 9
cell type: Differentiating megakaryocytes
transgene library: wPRE
library batch: Batch 1
|
| Treatment protocol |
Cells were methanol fixed, as per 10X protocol, and stored at -80 degrees C. They were then rehydrated as per 10X protocol and submitted for library preparation.
|
| Growth protocol |
Moreau et al., 2016. Megakaryocyte forward programming by lentiviral transduction with 3 transcription factors and two cytokine combinations.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10X library preparation.
10X VDJ protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
D9.wPRE
Single cell RNA-Seq
cDNA
counts.mtx
|
| Data processing |
Quality of fastq files was assessed with Fastqc v0.11.3 and summarised with MultiQC v1.8.
Alignment and protein-coding gene quantification were performed using 10x cellranger v3.1.0.
To maintain consistency between sequencing runs, alignment was performed by using only R2 strands, trimmed to 91 nt.
Cells with fewer than 200 unique features and cells with more than 25% of counts from mitochondrial genes were discarded from count matrix.
The processing was performed with regard to the regular gene expression library (GSE160604).
Genome_build: GRCh38
Supplementary_files_format_and_content: counts.mtx: MatrixMarket of raw expression levels for cells.
Supplementary_files_format_and_content: meta.csv: Comma-separated metadata for cells.
|
| |
|
| Submission date |
Feb 12, 2021 |
| Last update date |
Feb 23, 2022 |
| Contact name |
Irina Mohorianu |
| E-mail(s) |
data-submissions@stemcells.cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
Wellcome-MRC Cambridge Stem Cell Institute
|
| Street address |
Puddicombe Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0AW |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE166723 |
Identifying novel surface markers for megakaryocyte progenitor cells [timecourse transgene] |
| GSE168291 |
Identifying novel surface markers for megakaryocyte progenitor cells |
|
| Relations |
| BioSample |
SAMN17904055 |
| SRA |
SRX10092681 |
