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Sample GSM1366235 Query DataSets for GSM1366235
Status Public on May 21, 2015
Title DR_4
Sample type SRA
Source name Dorsal Raphe; 5-HT neuron
Organism Mus musculus
Characteristics strain: e-PET-YFP
developmental stage: post natal day 60
tissue: Dorsal Raphe
cell type: 5-HT neuron
Extracted molecule polyA RNA
Extraction protocol Serotonergic neurons, identified with YFP expression, were isolated by pipette directly from acute slices of the dorsal raphe. Collected samples were individually amplified using three rounds of a linear in vitro-transcription-based method.
Samples were prepared for multiplexed paired-end sequencing using the Illumina mRNA-Seq system according to manufacturer instructions.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description Sample_9-8_1
Data processing genome_build: mm9
genome_build: rn5
Illumina Casava 1.8.1 and 1.8.2 software used for basecalling.
We trimmed reads for adapter and poly-A contamination using in-house software before aligning to the mouse genome and transcriptome using RNA-Seq Unified Mapper (versions 2.0.2_06 and 2.0.3_04) and mouse genome build mm9 (mouse) or to the rat genome using STAR and rat genome build rn5. We required three or less mismatches per 100 bases.
Using uniquely aligned reads to RefSeq annotations downloaded from UCSC genome browser, we assigned read counts to genes using HTSeq and htseq-count. Only exonic reads were counted, with overlap assigned using the intersection non-empty method.
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each gene
Submission date Apr 09, 2014
Last update date May 15, 2019
Contact name Junhyong Kim
Organization name University of Pennsylvania
Department Biology
Lab Junhyong Kim
Street address 433 S University Avenue
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platform ID GPL13112
Series (1)
GSE56638 Deep sequencing reveals cell-type specific patterns of single cell transcriptome variation
BioSample SAMN02725956
SRA SRX515370

Supplementary file Size Download File type/resource
GSM1366235_DR_4_counts.txt.gz 88.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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