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| Status |
Public on Aug 16, 2016 |
| Title |
Nucleus from Hippocampus brain region A1-P2-DG_S209_L001_R1 |
| Sample type |
SRA |
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| Source name |
Mouse Hippocampus region
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| Organism |
Mus musculus |
| Characteristics |
age: 12 weeks
strain: C57BL/6
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| Extracted molecule |
nuclear RNA |
| Extraction protocol |
nuclei isolation by gradient centrifugation and FACS sorting
SMART-Seq2 protocol, with MAXIMA -h RT enzyme, applied on single nuclei sorted 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 |
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S209_L001_R1_001
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| Data processing |
sNUc-Seq libraries were aligned using Bowtie2 to the mouse transcriptome (RefSeq mm10 and Ensemble GRCm38 merged using Cufflink). RSEM v1.27 was used to estimate gene expression, in transcript per million (TPM) values, and TPM estimates were transformed to log-space by taking log(TPM+1). A library was filtered out if it had less than 2,000 detected genes or more than 8,000 detected genes. All libraries were normalized using a normalization procedure based on Bland-Altman (MA) plot and density estimation. For a pair of cells, we normalize one cell with respect to another so that genes are not differentially expressed on average, but using only a small set of highly expressed and lowly variable genes, which provides robustness against typical noise in single cells RNA-seq data.
Genome_build: RefSeq mm10 and Ensembl GRCm38
Supplementary_files_format_and_content: tab delimited matrix with RSEM computed log(TPM+1) values after normalization
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| Submission date |
Aug 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Naomi Habib |
| Organization name |
Broad Institute
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| Department |
Zhang
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| Lab |
Zhang
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| Street address |
75 Ames st
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE84371 |
Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons |
| GSE85721 |
Single nuclei RNA-seq from adult mouse Hippocampus |
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| Relations |
| BioSample |
SAMN05582150 |
| SRA |
SRX2031567 |
| 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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