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| Status |
Public on Apr 12, 2021 |
| Title |
Non-IRR anti-NRP1 3 |
| Sample type |
SRA |
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| Source name |
bone marrow endothelial cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
radiation dose: 0 Gy
iv treatment: 10 ug anti-NRP1
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| Treatment protocol |
Mice were irradiated and treated daily for 2 days with with intravenous IgG control or anti-NRP1 antibody. At 72 hours, mice were euthanized and bone marrow endothelial cells were FACs sorted for ve-cadherin+cd45- cells.
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| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was isolated using the Qiagen microRNeasy kit
Libraries for RNA-Seq were constructed with Clontech Kit to generate strand-specific RNA-seq libraries. The workflow consists of poly(A) RNA selection, RNA fragmentation and double-stranded cDNA generation using a mixture of random and oligo(dT) priming, followed by end repair to generate blunt ends, adaptor ligation, strand selection, and PCR amplification to produce the final libraries
Amplified libraries were quantified by Qubit dsDNA HS (High Sensitivity) Assay Kit, and quality-checked by the Agilent 4200 TapeStation System. Different index adaptors were used for multiplexing samples in one sequencing lane. Sequencing was performed with NextSeq500 High Output sequencer to produce 75 base-pair single-end reads (1 x 75 bp).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
B3
Normalized_Gene_counts.txt
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| Data processing |
Reads per gene were quantified using STAR - 2.7.2a [3] and mm10 (Ensembl GRCm38.97). After obtaining gene counts, the counts were normalized by CPM. The Principal Component Analysis (PCA) was applied to the transcript counts. The differential gene expressions were examined by GSA. For all results of differential gene expression analysis, statistical filter were applied, which was p<0.05, FDR<0.05, and Fold Change |FC|>2.
Partek® Flow® software, version 7.0 Copyright ©; 2019 Partek Inc., St. Louis, MO, USA.
STAR: ultrafast universal RNA-seq aligner, A Dobin, CA Davis, F Schlesinger, J Drenkow, C Zaleski, S Jha, P Batut, Bioinformatics 29 (1), 15-21Fast gapped-read alignment with Bowtie 2. Langmead B, Salzberg SL. Nat Methods. (2012)
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| Submission date |
May 03, 2020 |
| Last update date |
Apr 12, 2021 |
| Contact name |
John P Chute |
| E-mail(s) |
John.Chute@cshs.org
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| Organization name |
University of California, Los Angeles (UCLA)
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| Street address |
615 Charles E Young Drive South OHRC 545
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE149776 |
Bone Marrow Endothelial Cell Response to anti-NRP1 infusion |
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| Relations |
| BioSample |
SAMN14823968 |
| SRA |
SRX8244490 |
| 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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