|
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
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|
|
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 |