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Sample GSM2652208 Query DataSets for GSM2652208
Status Public on Jun 08, 2017
Title WT-AST
Sample type SRA
 
Source name Astrocytes
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Cortex
age: 10 weeks
genotype/variation: wild type
Growth protocol Astrocytes were cultured with DMEM plus 10%FBS, and identified by GFAP immunofluorescence staining;NSC were cultured as neurospheres with DMEM/F12 plus N2 supplements, and identified by sox2/nestin immunofluorescence staining.
Extracted molecule total RNA
Extraction protocol Cultured medium was removed, cells were washed twice with PBS, and RNA was harvested using Trizol reagent. RNA library prep kit for Illumina (NEB.Cat#E7530S) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: ftp://www.icugi.org/pub/genome/cucumber/Chinese_long/v2/cucumber_ChineseLong_v2_genome.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
 
Submission date Jun 07, 2017
Last update date May 15, 2019
Contact name Bo Jing
E-mail(s) scenery126@gmail.com
Phone +8613122776193
Organization name 同济大学医学院
Street address 同济大学医学院713
City 上海
State/province 上海
ZIP/Postal code 200092
Country China
 
Platform ID GPL21273
Series (1)
GSE99784 Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Nrl-/- Retinal Transcriptomes
Relations
BioSample SAMN07203243
SRA SRX2893626

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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