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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 19, 2017 |
| Title |
LepR-cre, rep2 |
| Sample type |
SRA |
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| Source name |
bone marrow cell
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| Organism |
Mus musculus |
| Characteristics |
developmental stage: adult
cell type: bone marrow stromal cell
cell population: CD45-TER119-CD31-Myh11-creER/TdTomato+
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from sorted cells was extracted using the RNAeasy Plus Micro kit (Qiagen).
Complementary DNA was generated using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories) from 1ng of total RNA. Nextera XT DNA Sample preparation Kit (Illumina) was used for preparation of DNA libraries.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
RNA-Seq data generated from Illumina HiSeq 2500 were processed following a recently developed reproducible pipeline (Wang Z and Ma’ayan A, F1000Res. Vol.5. 2016). Briefly, paired-end sequencing reads were aligned to mouse genome mm10 using Spliced Transcripts Alignment to a (STAR) (Dobin A, et al., Bioinformatics, 29(1), 2013).
We next used featureCount (Liao Y et al., Bioinformatics, 30(7), 2014) to assign aligned reads to genes.
Genome_build: mm10
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| Submission date |
Nov 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Paul S Frenette |
| Organization name |
Albert Einstein College of Medicine
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| Department |
Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research
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| Street address |
1301 Morris Park Avenue , Room 101
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| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE89811 |
RNA-seq analysis of bone marrow peri-vascular stromal cells |
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| Relations |
| BioSample |
SAMN06014625 |
| SRA |
SRX2345265 |
| 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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