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Sample GSM1366256 Query DataSets for GSM1366256
Status Public on May 21, 2015
Title HIP_3
Sample type SRA
 
Source name Hippocampus; Pyramidal neuron
Organism Mus musculus
Characteristics strain: C57BL/6
developmental stage: embryonic day 18
tissue: Hippocampus
cell type: Pyramidal neuron
Growth protocol Primary cultures of hippocampal and cortical neurons were plated at 100,000 per ml in neurobasal medium (Invitrogen) with B-27 supplement (Sigma) on 12-mm round German Spiegelglas coverslips (Bellco Glass) and grown for 14 days.
Extracted molecule polyA RNA
Extraction protocol We identified pyramidal neurons by cell morphology, isolated single cells by aspiration using a wide-bore pipette, deposited collected material into an eppendorf tube and froze immediately at -20C until storage at -80C. 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 TruSeq v2 system according to manufacturer instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description 49H
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 GPL17021
Series (1)
GSE56638 Deep sequencing reveals cell-type specific patterns of single cell transcriptome variation
Relations
BioSample SAMN02725852
SRA SRX515391

Supplementary file Size Download File type/resource
GSM1366256_HIP_3_counts.txt.gz 99.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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