|
| Status |
Public on Feb 29, 2024 |
| Title |
2 wk MPP4 biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
age: 2 weeks
Sex: pooled male and female
cell type: LinnegcKitposSca1posFlk2posCD150negCD48pos
genotype: C57Bl/6 wild-type
treatment: steady state isolation
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated from 5000 - 20,000 HSPCs using the RNeasy Plus Micro Kit (Qiagen, 74034). RNA integrity number (RIN) was determined by Bioanalyzer (Agilent Technologies) and RNA samples with RIN > 9.0 were further processed. RNA samples were processed over multiple experimental “sort days” and stored at -80°C in RNA isolation buffer until library preparation. A total of 3biological replicates were sequenced for each population. RNA was quantified and QC using an Agilent Bioanalyzer. Illumina sequencing libraries were prepared and sequenced at the NYU Genome Technology Center (New York, NY).
The NuGen Ovation Trio low input RNA-seq library preparation kit was used for library preparation.
All libraries were prepared at the same time in order to minimize batch effects. Libraries were sequenced using an Illumina NovaSEQ 6000 instrument with paired end 50 base pair sequencing to a target depth of 40 million unique reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing QC was performed using FastQC and MultiQC.
Paired-end reads were mapped to the mouse reference genome (GRCm38 ver104) using STAR and quantified with Feature Counts
Assembly: GRCm38 ver104
Supplementary files format and content: tab-delimited text files contain raw counts for each sample
|
| |
|
| Submission date |
Aug 15, 2023 |
| Last update date |
Feb 29, 2024 |
| Contact name |
Melissa Proven |
| E-mail(s) |
map2337@columbia.edu
|
| Organization name |
Columbia Unversity
|
| Lab |
Passegue
|
| Street address |
650 W 168 ST
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE240912 |
Maternal IL-10 restricts fetal emergency myelopoiesis [Bulk RNA-seq] |
| GSE240915 |
Maternal IL-10 restricts fetal emergency myelopoiesis |
|
| Relations |
| BioSample |
SAMN36996109 |
| SRA |
SRX21375315 |
