|
| Status |
Public on Feb 15, 2021 |
| Title |
MaeaCsf1r-Cre HSC rep3 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
age: adult
tissue: bone marrow
cell type: Haematopoietic stem cells
genotype: MaeaCsf1r-Cre
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from ~2000 sorted HSCs was extracted using the RNAeasy Plus Micro kit (Qiagen), and assessed for integrity and purity using an Aligent 2100 Bioanalyzer (Agilent Technologies).
Complementary DNA libraries were then generated using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories) and the Nextera XT DNA Sample preparation Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
J699_AHW2L5BGXY_TAGGCATG-ATAGAGAG_HSC6
|
| Data processing |
Library adaptor sequences were trimmed using trim galore ( https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ )
Then reads were aligned to the mouse genome (mm10) using Spliced Transcripts Alignment to a Reference (STAR 2.5.3a)
Aligned reads were then quantified to transcriptome (mm10 - Ensembl Transcripts release 83), normalized and differentially expressed genes were identified using Partek Flow
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file contains gene counts for individual samples generated by Partek Flow
|
| |
|
| Submission date |
Jun 27, 2019 |
| Last update date |
Feb 15, 2021 |
| Contact name |
Paul Frenette |
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research
|
| Street address |
1301 Morris Park Avenue , Room 101
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE133431 |
MAEA is an E3 ubiquitin ligase promoting autophagy and maintenance of haematopoietic stem cells |
|
| Relations |
| BioSample |
SAMN12148220 |
| SRA |
SRX6371802 |
