|
| Status |
Public on Jun 20, 2024 |
| Title |
FoxM1 DD/DD_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
FoxM1 DD/DD; MMTV-PyMT +
|
| Organism |
Mus musculus |
| Characteristics |
tissue: mammary tumors
tumor stage: end point tumor
strain: female wild-type C57BL6
genotype: FoxM1 DD/DD
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Spontaneous tumor growth driven by MMTV-PyMT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumors were harvested and dissociated into single-cell suspension. Shortly, tumors were mechanically chopped and digested with 0.1% Collagenase IV and 0.01% DNase in DMEM at 37C for 30 min. Cells were washed twice with PBS followed by lysis of RBCs with ACK Lysing Buffer (Gibco). After two washes, cells were filtered using 40 microm sterile cell strainers and trypan blue staining was performed to asses for the viability of the cells. Drop-seq was performed on the single cell suspension. Libraries were made and sequenced. The DNA sequences for both Cre and PYMT elements were added to the mouse mm10 genome as chromosomes.
Nextera XT tagmentation using Illumina cat# FC-131-1096 (Drop-seq protocol)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Single cell RNA-seq was performed using Drop-seq platform
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Illumina paired end raw FastQ file were processed for read alignment and gene expression. Drop-seq single-cell data was analyzed using the data anlysis protocol described in Drop-seq cook-book (Macosko et al. 2015)(http://mccarrolllab.com/dropseq/) and used the Drop-seq_tools-1.13. We used STAR aligner to align the reads against Mus musculus GRCm38 genome version Ensm38_90 (From Ensembl) and corresponding gene modle is extracted from Ensembl version 90.
Quality of read and mapping were checked using the program FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Digital Gene Expression (DGE) data obtained from an aligned library is done using the Dropseq program DigitalExpression (integrated in Drop-seq_tools-1.13). Number of cells that were extracted from aligned BAM file is based on knee plot which extracts the number of reads per cell, then plot the cumulative distribution of reads and select the “knee” of the distribution.
Genome_build: GRCm38.p5 (Ensembl 90: Aug 2017).
Supplementary_files_format_and_content: Tab-delimited text file. Gene expression (as count) of each gene for each extracted cell
|
| |
|
| Submission date |
Jun 21, 2021 |
| Last update date |
Jun 20, 2024 |
| Contact name |
Maria Paula Zappia |
| E-mail(s) |
mpzappia@uic.edu
|
| Organization name |
University of Illinos at Chicago
|
| Department |
Biochemistry and Molecular Genetics
|
| Lab |
Frolov - 2356
|
| Street address |
900 S Ashland Ave
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60607 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE178612 |
FoxM1-Retinoblastoma Interaction Induces Tumor Microenvironment That Drives Metastasis |
|
| Relations |
| BioSample |
SAMN19798904 |
| SRA |
SRX11189884 |
