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Sample GSM1370411 Query DataSets for GSM1370411
Status Public on Mar 31, 2016
Title WT-control (KD) rep2
Sample type SRA
 
Source name EML Cell Line
Organism Mus musculus
Characteristics cell line: EML
treatment: knockdown control
tissue: Bone marrow
cell type: Basophil
strain: BDF1
Growth protocol EML cells were maintained in medium containing stem cell factor (SCF). EML cells were grown in IMDM containing 20% FBS and SCF (200 ng/ml, PeproTech).
Extracted molecule total RNA
Extraction protocol RNA was extracted from TRIZOL (Invitrogen) or RNeasy RNA isolation kit (Qiagen).
Sequencing libraries were manually generated for high-throughput sequencing. Either end of DNA strands was filled using the Epicentre DNA END-Repair kit (Epicentre Biotechnologies, Madison, WI). Adenine was added at 3’ ends by Taq DNA polymerase (New England Biolabs, Beverly, MA) under dATP conditions. Illumina’s adaptor oligomers was ligated at both ends using Quick Ligation kit (Qiagen). After purified twice, DNA libraries are amplified using Solexa primers (Illumina, San Diego, CA) and Pusion PCR master mix (Thermo Scientific, Hudson, NH).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome using Tophat-2.0.9 with parameters --bowtie1 --segment-length 21
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by Cufflinks with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
 
Submission date Apr 17, 2014
Last update date May 15, 2019
Contact name Tae-Young Roh
Organization name Ewha Womans University
Department Life Sciences
Lab Sysgem Genomics
Street address 52 Ewhayeodae-gil, Seodaemun-gu
City Seoul
State/province --- Select One ---
ZIP/Postal code 03760
Country South Korea
 
Platform ID GPL11002
Series (1)
GSE56867 Functional analysis of KAI1
Relations
BioSample SAMN02729213
SRA SRX519917

Supplementary file Size Download File type/resource
GSM1370411_WT-KD_rep2.txt.gz 383.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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