|
| Status |
Public on Jan 11, 2022 |
| Title |
T5-5 |
| Sample type |
SRA |
| |
|
| Source name |
Human prostate cancer cell xenograft in mouse
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
sh-rna transfection: FGFRL1 sh-RNA
cells: PC3M
|
| Growth protocol |
Cells were collected at the log growth phase and subcutaneously injected into mice (1 x 106 cells in 100 µl of PBS). Mice were housed under controlled conditions (12 h light/12 h dark cycles, temperature 21 ± 3 ℃) and fed standard chew food and tap water ad libitum. Tumors were grown for 45 days, and the tumor sizes and body weights of mice were measured every five days. After sacrificing the mice with CO2 asphyxiation followed by cervical dislocation, tumors were excised and divided into two parts: one for fixation with 10 % neutral-buffered formalin, and another for protein analysis and RNA sequencing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumors were snapfrozen in liquid nitrogen. The total RNA was isolated using Qiagen RNeasy mini kit according to manufacturer's instructions.
NEB #E7760S/L
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
xenografts_norm_counts_disambiguated.txt
|
| Data processing |
Image analysis, base calling, and quality check were performed with the Illumina data analysis pipeline RTA3.4.4 and the program Bcl2fastq v2.20
trimming of adapter sequences using the ‘ILLUMINACLIP’ step from ‘Trimmomatic’ version 0.36
Alignment of reads with TopHat v2.0.14
disambiguation of human/mouse reads performed with Disambiguate 1.0
gene level raw counts calculation using ‘HTSeq’ version 0.9.1 and GRCh37.75/ GRCm38.p4 annotation files (.gtf) for human and mouse reads respectively
gene and transcripts level FPKM calculation using cufflinks-2.2.1 and GRCh37.75/GRCm38.p4 gtfs for human and mouse reads respectively
Genome_build: GRCh37.75 and GRCm38.p4
Supplementary_files_format_and_content: Matrix txt-table with disambiguated and normalized counts for every gene and every sample
|
| |
|
| Submission date |
May 12, 2021 |
| Last update date |
Jan 11, 2022 |
| Contact name |
Pirkko Härkönen |
| E-mail(s) |
harkonen@utu.fi
|
| Phone |
+358407343520
|
| Organization name |
University of Turku
|
| Department |
Institute of Biomedicine
|
| Street address |
Medisiina D, 5th floor, Kiinamyllynkatu 10
|
| City |
Turku |
| State/province |
Finland |
| ZIP/Postal code |
20520 |
| Country |
Finland |
| |
|
| Platform ID |
GPL25526 |
| Series (1) |
| GSE174361 |
Gene expression profile in prostate cancer xenograft tumors after FGFRL1 knockdown |
|
| Relations |
| BioSample |
SAMN19131422 |
| SRA |
SRX10859349 |
