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Sample GSM2789655 Query DataSets for GSM2789655
Status Public on Apr 17, 2019
Title Excitatory-1 total RNAseq
Sample type SRA
 
Source name aCaMKII-positive brain neurons
Organism Mus musculus
Characteristics tissue: brain
cell type: aCaMKII-positive brain neurons
number of cells: 100 Single cells
Growth protocol αCaMKII-Cre and vGAT-IRES-Cre transgenic mouse colonies were maintained by breeding transgenic mice to wild-type C57Bl/6J mice. Mice used for experiments were bred in the Seoul National University (SNU) Specific Pathogen Free center (LML08-404). Male mice (3-5 months) were used.
Extracted molecule total RNA
Extraction protocol Fluorescent cells were manually collected by using glass pipette. After washing in HBSS, collected cells were directly lysed with cell lysis buffer containing RNase inhibitor as follow manufacturer’s instruction of SMART-seq v4 (Ultra low input RNA kit, Clontech Laboratories, Inc.).
After generation of cDNA from homogenous cell-type samples, the construction of library was performed by using Nextera XT DNA library prep kit (Illumina, Inc., USA) according to the manufacturer’s instructions. The double-stranded library was purified by using magnetic beads to remove all reaction components. The library was amplified to add the complete adapter sequences required for cluster generation. The finished library is purified from PCR components.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample
 
Submission date Sep 21, 2017
Last update date May 15, 2019
Contact name Jung-Woong Kim
E-mail(s) jungkim@cau.ac.kr
Organization name Chung-Ang University
Department Life Science
Lab Genome Dynamics Lab
Street address 84 Heuksuk-ro Dongjak-ku
City Seoul
ZIP/Postal code 06974
Country South Korea
 
Platform ID GPL17021
Series (1)
GSE104089 Cell type-specific dysregulation of ERK signaling impairs synaptic plasticity and memory in a mouse model of Noonan syndrome
Relations
BioSample SAMN07680548
SRA SRX3203500

Supplementary file Size Download File type/resource
GSM2789655_1-lib.txt.gz 108.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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