|
| Status |
Public on Sep 23, 2021 |
| Title |
DBA3 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: EB purified from thawed bone marrow
diagnosis: DBA
genotype: RPL11
treatment for anemia: Transfusions
Sex: F
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Bone marrow mononuclear cells were thawed then 1000 to 80 000 CD71+GYPA+ EB were FACS-isolated from each sample. Total RNA was extracted and mRNA isolated by the NEBNext Poly (A) mRNA Magnetic Isolation Module, followed by first and second strand cDNA synthesis (NEBNext Directional RNA First and Second Strand Synthesis Modules), per the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequencing data was demultiplexed and 100 bp reads aligned to the GRCh38 3.0.0 using “STAR 2.5.3a”
Post-alignment QC was performed using Picard and Sequence Alignment/Map (SAM) tools
Raw counts at the gene level were obtained using the “Rsubread” Bioconductor package
Data normalization and differential expression analysis across different groups were performed using the “DESeq2” Bioconductor package
Genome_build: CRCh38 3.0.0
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample
|
| |
|
| Submission date |
Aug 24, 2021 |
| Last update date |
Sep 23, 2021 |
| Contact name |
Deena Iskander |
| E-mail(s) |
d.iskander@imperial.ac.uk
|
| Organization name |
Imperial College
|
| Street address |
Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE181830 |
Single-cell profiling of human bone marrow progenitors reveals mechanisms of failing erythropoiesis in Diamond-Blackfan anemia |
|
| Relations |
| BioSample |
SAMN20958574 |
| SRA |
SRX11891693 |
