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| Status |
Public on Jul 22, 2020 |
| Title |
TRN251 |
| Sample type |
SRA |
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| Source name |
TRN
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| Organism |
Mus musculus |
| Characteristics |
sample type: sNuc-seq
used for patch-seq: No
facs sorting signal: Violet+
plate type: TRN adjacent
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| Extracted molecule |
total RNA |
| Extraction protocol |
Sucrose gradient nuclei isolation followed by FACS sorting for Violet+, Violet+ GFP+ or Violet+ NeuN+ nuclei
Modified SMARTseq2 single nuclei RNA-Seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
nuclear RNA
TPM.TRN.tsv
X012116_GPEp24_E8_S248
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| Data processing |
RSEM v1.2.87 was run on raw fastq fileswith default parameters on alignments created by Bowtie on UCSC gene annotation
TPM estimates were tranformed to log space by taking log TPM +1
TopHat2 v2.0.10 was used to map fastq files to mm10 reference
RNASeq-QC was run on the TopHat2 bamfiles to get QC metrics
For TRN and patch-seq samples, cells were removed if they had less than 40% genome mapping rate or or less than 1500 detected genes
Clustering and DE analysis of TRN samples was perfomed with biSNE software (https://github.com/yinqingl/nucseq_analysis), including normalizing the log TPM data to a normalized log TPM
For non-TRN samples, nuclei expressing <1500 genes were removed
Seurat v2.2.0 was used for clustering of the non-TRN samples
Genome_build: mm10
Supplementary_files_format_and_content: Formatted expression matrix (tab deliminated text file) with cells as columns, genes as rows, and TPM values as entries
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| Submission date |
Feb 13, 2020 |
| Last update date |
Jul 22, 2020 |
| Contact name |
Joshua Levin |
| E-mail(s) |
jlevin@broadinstitute.org
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| Organization name |
Broad Institute
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| Department |
Stanley Center
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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 (1) |
| GSE145273 |
Integrated single-cell analysis reveals coupled molecular gradient and functional subnetworks in the thalamic reticular nucleus |
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| Relations |
| BioSample |
SAMN14097343 |
| SRA |
SRX7722288 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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