|
| Status |
Public on Jul 09, 2023 |
| Title |
4T1_BF10-3 |
| Sample type |
SRA |
| |
|
| Source name |
Orthotopic breast tumor tissue
|
| Organism |
Mus musculus |
| Characteristics |
treatment: IL10/CSF1R (BF10) fusion protein
tissue: Orthotopic breast tumor tissue
cell type: brest cancer
|
| Treatment protocol |
The treatment of IL10/CSF1R fusion protein (twice per week) for totoal 6 doses when tumor size reach 100 mm3. Tumor tissues isolated (~100 mm3) isolated and total RNA were extracted by Trizol, followed by cDNA were sequenced by Illumina NextSeq 550.
|
| Growth protocol |
1*105 of 4T1 cancer cells were orthotopic injection in Balb/c mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol protocol for tissue RNA extraction. Extracted RNA were quantificated by using Qubit fluorometer with Quant-iT RNA BR assay kit.
Libraries were prepared using Illumina TruSeq Stranded mRNA Sample Prep Kit + limited cycles of PCR by KAPA HiFi Polymerase following the directions of the manufacturer. RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
For BulkRNA sequencing, libraries were sequenced on Illumina NextSeq 550, with 75bp from read 1, and at a depth of 33-40 million reads per sample.
Reads were trimmed, clean and quality checked using Fastp v0.20.1
High-quality reads were then imported into STAR v2.7.5a for alignment into BAM files.
BAM files were imported into the RSEM v1.3.3 for expected counts, FPKM and TPM estimation.
Expected counts table was imported into the DESeq2 v1.28.0 for DEG analysis.
Genome_build: The mouse genome mm10 (GRCm38.101)
Supplementary_files_format_and_content: FPKM of sequencing reads in .txt file.
Supplementary_files_format_and_content: DESeq2 for differential expression gene analysis .csv files.
|
| |
|
| Submission date |
Jan 04, 2022 |
| Last update date |
Jul 09, 2023 |
| Contact name |
JuPei Chen |
| E-mail(s) |
pei03231987@nycu.edu.tw
|
| Organization name |
National Yang Ming Chiao Tung University
|
| Street address |
No. 155, Sec. 2, Linong St. Beitou Dist.
|
| City |
Taipei |
| ZIP/Postal code |
112 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL21626 |
| Series (1) |
| GSE193045 |
Interleukin-10/CSF1R fusion protein rejuvenates the exhausted T cells for executing antitumor activity II |
|
| Relations |
| BioSample |
SAMN24614337 |
| SRA |
SRX13602731 |
