|
| Status |
Public on Apr 05, 2021 |
| Title |
Blood_Neutrophil_Treated_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Mus musculus |
| Characteristics |
strain: NOD.C3C4
tissue: Blood
cell type: Neutrophils
treatment: PDC166-NP
|
| Treatment protocol |
Treated sample come from NOD.c3c4 mice treated intravenously with 10 doses of PDC166-coated NPs. Some samples come from mice treated additionally with blocking antibodies against several cytokines.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA purification using Rneasy Mini kit (QIAGEN)
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit v2 according to the manufacturer's protocol (Illumina, San Diego, CA)
Bulk RNAseq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Blood Neutrophils from Treated mice
Neu_B3_26681
Partek_DEseq2_Blood_Treated_Untreated.xlsx
Partek_DEseq2_Treated_Liver_Blood_Treated.xlsx
Raw_counts_Liver_Blood.xlsx
|
| Data processing |
Contaminant rRNA filtering with Bowtie2 (2.2.5)
Alignment with STAR 2.5.3a to the GENCODE release 16 of the Mus musculus genome (mm10 assembly)
Raw count of reads per gene was obtained with Partek “Quantify to annotation model (Partek E/M)” tool
Counts were normalized by CPM
Differential expression analysis was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheets (xlsx) containint differential expression analysis
|
| |
|
| Submission date |
Feb 08, 2021 |
| Last update date |
Apr 05, 2021 |
| Contact name |
Pere Santamaria |
| E-mail(s) |
pesantam@clinic.cat
|
| Organization name |
IDIBAPS
|
| Street address |
C/Rosselló 149-153
|
| City |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE166361 |
Regulatory neutrophil transcriptional profiling |
|
| Relations |
| BioSample |
SAMN17833959 |
| SRA |
SRX10048764 |
