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Sample GSM4414081 Query DataSets for GSM4414081
Status Public on May 15, 2022
Title PyMTtg;Rag1KO+CD4+ T cells rep3
Sample type SRA
 
Source name Breast tumor
Organism Mus musculus
Characteristics strain: Balb/c
group: CONTROL
sample number: 1286-51
Treatment protocol PyMTtg;Rag1KO and K14-TSLPtg;PyMTtg;Rag1KO mice were injected with CD4+ T cells at the age of 4 weeks
Growth protocol PyMT transgenic mice develop spontaneous breast tumors starting at ~4 weeks of age, these tumors are collected at endpoint (week 18-20)
Extracted molecule total RNA
Extraction protocol Tumor tissue was isolated and homogenized in RLT buffer with addition of 1% 2-mercaptoethanol. Homogenized samples were stored in TriZol reagent and total RNA extracted using the Rneasy Mini kit (QIAGEN, #74104)
RNA libraries were prepared for sequencing using standard Illumina protocols at BGI
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Analysis done at Beijing Genomics Institute (BGI) pipeline version 5.0
Filtering was done using SOAPnuke
Mapping to mm10 using Bowtie/BWA
Gene/Transcript expression was done with RSEM
Differentially expressed gene screening was done with Poisson Distribution method/Noiseq package/EB Seq package
Genome_build: mm10
 
Submission date Mar 16, 2020
Last update date May 15, 2022
Contact name Margherita Boieri
E-mail(s) mboieri@mgh.harvard.edu, margherita.boieri@gmail.com
Organization name Masachusetts General Hospital
Street address 55 Fruit Street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
 
Platform ID GPL13112
Series (1)
GSE147067 Analysis of transcriptional changes induced in PyMT breast tumor by TSLP stimulated CD4+ T cells
Relations
BioSample SAMN14384667
SRA SRX7919616

Supplementary file Size Download File type/resource
GSM4414081_1286-51.gene.FPKM.xls.gz 245.9 Kb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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