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Sample GSM1097464 Query DataSets for GSM1097464
Status Public on Sep 02, 2014
Title IGFBP7_LD3_WT
Sample type SRA
 
Source name Mammary gland
Organism Mus musculus
Characteristics genetic background: C57BL/6
tissue: Mammary gland
Stage: lactation day 3
genotype: wild type
Extracted molecule total RNA
Extraction protocol Breast epithelial cells were isolated from the lactating (day 3) inguinal mammary glands of the WT or Igfbp7-/- (KO) mice and lineage positive (Lin-, CD45+,CD35+, and Ter119+) cells were removed through magnetic cell separation strategy (StemCell Technologies, EasySep negative selection kit).
Total RNA was extracted from the Lin- breast cells using the TRIzol Reagent. Two rounds of Poly(A) RNA selection were carried out by using the MicroPoly(A) Purist kit.
RNA libraries were prepared for sequencing using SOLiD Total RNA-seq Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model AB 5500xl Genetic Analyzer
 
Data processing Barcoded libraries are loaded into 6 individual flowchip lanes. 5500 Series Genetic Analyzers ICS v1.2.1 software used for color space calling.
.xsq files were converted to .csfasta and .qual files using XSQ_Tools
Paired .csfasta and .qual files were converted to fastq format to be compatible with the aligner bowtie. 
Genesifter v4.0 software with Bowtie WTS PE pipeline was used for the data mapping.
Reads within the fastq file were trimmed of any adaptor/primer sequence and then aligned to the mouse genome reference, mm9, using bowtie (bowtie-0.12.3/bowtie - (colorspace reads and index, allowing up to 2 mismatches)).  Following alignment of reads with bowtie, nucleotide variants were called with SamTools (samtools (0.1.15) pileup and varFilter, defaults setting except –D = 100000). 
To identify differentially expressed genes, normalized expression values were calculated per gene by a Reads Per Million mapped reads (RPM) and a Reads Per Kilobase of exon per Million mapped read(RPKM)method.
Genome_build: Mus musculus B37.2
Supplementary_files_format_and_content: wig file and xlsx file include RPM and RPKM value for individual genes
 
Submission date Mar 12, 2013
Last update date May 15, 2019
Contact name Yutaka Amemiya
E-mail(s) yamemiya@sri.utoronto.ca
Organization name Sunnybrook Research Institute
Lab Genomics Core Facility
Street address 2075 Bayview Ave.
City Toronto
State/province ON
ZIP/Postal code M4N3M5
Country Canada
 
Platform ID GPL15907
Series (1)
GSE45118 mRNA Expression Comparison Between Igfbp7-null and wild type mice at Lactation Day 3
Relations
SRA SRX248087
BioSample SAMN01943713

Supplementary file Size Download File type/resource
GSM1097464_IGFBP7_WT_LD3_RPM_RPKM.txt.gz 585.9 Kb (ftp)(http) TXT
GSM1097464_wt_chr1.wig.gz 2.4 Mb (ftp)(http) WIG
GSM1097464_wt_chr10.wig.gz 1.8 Mb (ftp)(http) WIG
GSM1097464_wt_chr11.wig.gz 2.6 Mb (ftp)(http) WIG
GSM1097464_wt_chr12.wig.gz 1.4 Mb (ftp)(http) WIG
GSM1097464_wt_chr13.wig.gz 1.4 Mb (ftp)(http) WIG
GSM1097464_wt_chr14.wig.gz 1.3 Mb (ftp)(http) WIG
GSM1097464_wt_chr15.wig.gz 1.4 Mb (ftp)(http) WIG
GSM1097464_wt_chr16.wig.gz 1.3 Mb (ftp)(http) WIG
GSM1097464_wt_chr17.wig.gz 1.4 Mb (ftp)(http) WIG
GSM1097464_wt_chr18.wig.gz 1.1 Mb (ftp)(http) WIG
GSM1097464_wt_chr19.wig.gz 1.2 Mb (ftp)(http) WIG
GSM1097464_wt_chr2.wig.gz 2.7 Mb (ftp)(http) WIG
GSM1097464_wt_chr3.wig.gz 1.8 Mb (ftp)(http) WIG
GSM1097464_wt_chr4.wig.gz 2.1 Mb (ftp)(http) WIG
GSM1097464_wt_chr5.wig.gz 2.2 Mb (ftp)(http) WIG
GSM1097464_wt_chr6.wig.gz 1.8 Mb (ftp)(http) WIG
GSM1097464_wt_chr7.wig.gz 2.0 Mb (ftp)(http) WIG
GSM1097464_wt_chr8.wig.gz 1.7 Mb (ftp)(http) WIG
GSM1097464_wt_chr9.wig.gz 1.9 Mb (ftp)(http) WIG
GSM1097464_wt_chrMT.wig.gz 39.0 Kb (ftp)(http) WIG
GSM1097464_wt_chrX.wig.gz 1.0 Mb (ftp)(http) WIG
GSM1097464_wt_chrY.wig.gz 2.4 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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