|
| Status |
Public on May 15, 2022 |
| Title |
PyMTtg;Rag1KO+CD4+ T cells rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Breast tumor
|
| Organism |
Mus musculus |
| Characteristics |
strain: Balb/c
group: CONTROL
sample number: 2100-95
|
| 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 |
SAMN14384669 |
| SRA |
SRX7919615 |
