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Sample GSM1024394 Query DataSets for GSM1024394
Status Public on Jun 26, 2013
Title Vector 1 RNA-Seq
Sample type SRA
Source name 4T1 vector transduced
Organism Mus musculus
Characteristics genotype/variation: Control
strain: BALB/cfC3H
cell line: 4T1
Growth protocol Vector control and Wnt5a expressing 4T1 cells were grown to 70% confluency under conditions recommended by ATCC.
Extracted molecule total RNA
Extraction protocol RNA was isolated using Trizol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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 Illumina Genome Analyzer IIx
Data processing CASAVA version 1.8.0 was used to convert the *.bcl files to *.fastq files.
TopHat version 2.0.0 was used to align the *.fastq files to the UCSC mm9 reference genome using the default settings and parameter -r 150.
Cufflinks version 1.3.0 was used with default settings to calculate transcript abundances from the TopHat alignment files (*.bam) and also calculate differential expression.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited *.txt file of the isoform transcript list containing columns for nearest reference ID, gene name, locus, status and FPKM value which were derived from the Cufflinks suite of tools, Cuffdiff.
Submission date Oct 23, 2012
Last update date May 15, 2019
Contact name Rosa Serra
Phone 205-934-0842
Organization name University of Alabama at Birmingham
Department Cell Biology
Lab Serra
Street address 1918 University Blvd. 660 MCLM
City Birmingham
State/province AL
ZIP/Postal code 35294-0005
Country USA
Platform ID GPL11002
Series (2)
GSE41792 Differential expression in Wn5a and vector transduced 4T1 cells. [RNA-Seq]
GSE41793 Differential expression in Wn5a and vector transduced 4T1 cells.
SRA SRX200683
BioSample SAMN01779644

Supplementary file Size Download File type/resource
GSM1024394_Vector.txt.gz 570.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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