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Status |
Public on Jul 22, 2020 |
Title |
TRN53 |
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 no Neun selection
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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 no processed data
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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 |
SAMN14097211 |
SRA |
SRX7723596 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data not provided for this record |
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