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| Status |
Public on Nov 21, 2023 |
| Title |
ECs, DB_7_152 |
| Sample type |
SRA |
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| Source name |
sciatic nerve
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| Organism |
Mus musculus |
| Characteristics |
genotype: Plxnd1 WT
reporter: Chd5CreER/R26-TdTomato
batch: 1292
tissue: sciatic nerve
cell type: FACS-isolated peripheral nerve ECs
condition: intact
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Sciatic nerves were freshly harvested in F12medium, pooled, finely chopped and incubated in dissociation buffer (Trypsin 0.2mg/ml, Collegenase Type II 50ul/ml, Hyaluyronidase 1:50, PronaseE 1:10, DNAse 2.5μg/ml) in DMEM and incubated on rotor at 37 C with intermittent mixing for 30 min. Enzymes were inactivated with 5% FBS+ 2mM EDTA in PBS w/o Ca2+, Mg2+. Cell suspension was passed through cell strainer, stained (CD45-APC) and resuspended in 2% BSA PBS w/o Ca2+, Mg2+. Tdtomato+ or Cherry+ (negative for CD45+ myeloid population) were purified by FACS.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Intact nerve
Raw_counts_Tomato.tsv.gz
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| Data processing |
FASTQ files were demultiplexed from the raw base call (BCL) files using 10x Genomics 'cellranger demux' (CellRanger v3.0.2).
Single end reads were trimmed with trimmomatic (v0.39) to remove adapters and exclude low-quality reads from the analysis and aligned to the mm10 reference genome using STAR aligner (v2.5.3a).
FeatureCounts (v1.6.4) was used to compute reads mapping on exons as annotated in GENCODE Mus musculus basic gene annotation (version M16) and obtain transcript quantification summarized at the gene level, excluding multimapping reads.
Assembly: mm10, GRCm38, GENCODE Mus musculus basic gene annotation (version M16)
Supplementary files format and content: 1292_all.counts.tsv.gz and 1133_all.counts.tsv.gz: Tab separated files of raw counts.
Supplementary files format and content: counts_Cherry_ComBat-seq.tsv.gz: Only genes with at least 1 CPM (Counts per million) in at least 3 samples were retained. Batch effect correction was performed on counts matrix with SVA’s R package ComBat-seq (v3.35.2).
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| Submission date |
May 24, 2023 |
| Last update date |
Nov 21, 2023 |
| Contact name |
Aurora Maurizio |
| E-mail(s) |
maurizio.aurora@hsr.it, auroramaurizio1@gmail.com
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| Organization name |
IRCCS Ospedale San Raffaele
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| Department |
Center for Omics Sciences (COSR)
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| Street address |
Via Olgettina, 60
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| City |
Milano MI |
| State/province |
Italy |
| ZIP/Postal code |
20132 |
| Country |
Italy |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE233355 |
Structured wound angiogenesis instructs mesenchymal barrier compartments in the regenerating nerve [bulkRNASeq] |
| GSE233360 |
Structured wound angiogenesis instructs mesenchymal barrier compartments in the regenerating nerve |
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| Relations |
| BioSample |
SAMN35355043 |
| SRA |
SRX20509392 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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