|
| Status |
Public on May 15, 2022 |
| Title |
K14-TSLP +/tg, TSLPR -/- + Ly5.1 CD4+ Non-draining LN 3252-43, 1213-46, 3295-38, 3296-39 |
| Sample type |
SRA |
| |
|
| Source name |
Non-draining LN
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
group: TEST
sample number: 3252-43, 1213-46, 3295-38, 3296-39
|
| Treatment protocol |
K14-TSLP +/tg, TSLPR -/- mice were injected with PyMT tumors and Ly5.1 CD4+ T cells. TSLPR -/- mice were injected with PyMT tumors and TSLPRKO CD4+ T cells. MMTV-PyMT mice spontaneously develop breast tumor, and Rag1KO mice were injected with CD4+ T cells at 4 weeks of age. In all samples CD4+ T cells were sorted when the mouse had terminal tumors, stimulated in vitro with aCD3, aCD28, IL-2 and TSLP fror 5 hours.
|
| Growth protocol |
CD4+ T cells are sorted from lymph nodes of mice with terminal tumors
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Stimulated CD4+ T cells were resuspended in RLT buffer with addition of 1% 2-mercaptoethanol and total RNA extracted using the Rneasy Mini kit (QIAGEN, #74104)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
K14-TSLP +/tg, TSLPR -/- + Ly5.1 CD4+
Sample 2
|
| 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
Supplementary_files_format_and_content: FPKM
|
| |
|
| Submission date |
Mar 17, 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) |
| GSE147106 |
Analysis of transcriptional changes induced in TSLP in CD4+ T cells |
|
| Relations |
| BioSample |
SAMN14390954 |
| SRA |
SRX7924975 |
