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| Status |
Public on May 22, 2024 |
| Title |
CAMs, 2 months, rep1 |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
Sex: male
tissue: Brain
cell type: CAMs
age: 2 months
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| Treatment protocol |
We FACS sorted (FACSAria, BD Biosciences) CD3-CD11b+CD45+CD206+ CAMs from brains of C57BL/6 mice (Janvier Labs) aged 2 months (young) and 18 months (old)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from FACS sorted mouse brain macrophages stabilized in RNAprotect buffer according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Plus Micro Kit (QIAGEN, Hilden, Germany).
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from approximately 500 pg total-RNA. Double stranded cDNA was amplified by LD PCR (13 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA).
Equimolar amounts of each library were sequenced on an Illumina NextSeq 2000 instrument controlled by the NextSeq 2000 Control Software (NCS) v1.2.0.36376, using two 100 cycles P2 Flow Cell with the dual index, single-read (SR) run parameters
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Data processing |
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.7.17.
The resulting .cbcl files were converted into .fastq.gz files with the bcl2fastq v2.20 software.
Quality of raw data was evaluated with FastQC.
Poor quality sequences were trimmed or removed with fastp tool, with default parameters, to retain only good quality paired reads.
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used for mapping on mm10 reference genome and quantification with gencode vM25 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
The GSEA analysis was started on the Gene sets derived from the GO Biological Process ontology (BP) database using the ClusterProfiler package, gseGO function. Then the Simplify function was used via GOSemSim to eliminate the redundant GO terms
Assembly: mm10
Supplementary files format and content: Format TSV: gene counts in each sample
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| Submission date |
May 15, 2024 |
| Last update date |
May 22, 2024 |
| Contact name |
Damien Levard |
| E-mail(s) |
levard@cyceron.fr
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| Organization name |
Inserm U1237 PhIND
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| Lab |
Institut Blood and Brain @ Caen Normandie
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| Street address |
Bd Henri Becquerel
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| City |
Caen |
| ZIP/Postal code |
14074 |
| Country |
France |
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| Platform ID |
GPL30172 |
| Series (1) |
| GSE267623 |
Central nervous system-associated macrophages modulate the immune response following stroke in aged mice |
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| Relations |
| BioSample |
SAMN41413697 |
| SRA |
SRX24571564 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8270976_S434-01-P1.quant.genes.sf.gz |
428.6 Kb |
(ftp)(http) |
SF |
SRA Run Selector |
| Raw data are available in SRA |
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