|
| Status |
Public on May 26, 2020 |
| Title |
20170926_MM1_XZ4704-1_S10 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow neutrophil
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
cell type: MM neutrophils
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from those populations using QIAGEN RNeasy Mini Kit. RNA quality was evaluated spectrophotometrically, and the quality was assessed with the Agilent 2100 Bioanalyzer.
RNA-sequencing libraries were prepared using KAPA mRNA HyperPrep Kit (Illumina Platforms). Once prepared, indexed cDNA libraries were pooled in equimolar amounts and were sequenced with paired-end on an Illumina HiSeq2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file: 2019Granulocyte_bulk_matrix.csv
|
| Data processing |
QC were performed using MultiQC. Adaptor sequences and low quality score bases were trimmed using trimmomatic/0.36.
The resulting reads were then mapped to the mouse genome references sequence (GRCm38/mm10 Ensemble release 81) and counted using alignment software STAR2.5.2b.
Gene differential expression analysis were using EdgeR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: 2019Granulocyte_bulk_matrix.csv: Comma-separated text file.
|
| |
|
| Submission date |
Sep 16, 2019 |
| Last update date |
May 26, 2020 |
| Contact name |
Xuemei Xie |
| E-mail(s) |
xiexuemei.fiona@gmail.com
|
| Organization name |
Boston Children's Hospital
|
| Department |
Transfusion Medicine
|
| Lab |
Luo's Lab
|
| Street address |
811 Enders Building, 320 Longwood Ave.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE137538 |
RNA sequencing of different neutrophil subpopulations from bone marrow |
| GSE137540 |
Single-cell transcriptome profiling reveals neutrophil heterogeneity in homeostasis and infection |
|
| Relations |
| BioSample |
SAMN12768997 |
| SRA |
SRX6855611 |
