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Sample GSM4310601 Query DataSets for GSM4310601
Status Public on Jul 22, 2020
Title TRN212
Sample type SRA
 
Source name TRN
Organism Mus musculus
Characteristics sample type: sNuc-seq
used for patch-seq: No
facs sorting signal: Violet+
plate type: TRN adjacent
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description nuclear RNA
TPM.TRN.tsv
no processed data
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
 
Submission date Feb 13, 2020
Last update date Jul 22, 2020
Contact name Joshua Levin
E-mail(s) jlevin@broadinstitute.org
Organization name Broad Institute
Department Stanley Center
Street address 75 Ames St
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL19057
Series (1)
GSE145273 Integrated single-cell analysis reveals coupled molecular gradient and functional subnetworks in the thalamic reticular nucleus
Relations
BioSample SAMN14097646
SRA SRX7723051

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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