|
| Status |
Public on Nov 30, 2019 |
| Title |
scRNA-seq [N704-N517] |
| Sample type |
SRA |
| |
|
| Source name |
colon tumor cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: ApcMin/+
age: 12 weeks
Sex: male
tissue: colon
cell type: DAPI-Cd31-Cd45-Epcam+Cd24+ cells
|
| Treatment protocol |
Male ApcMin/+ mice between 10 weeks of age were given 2% (w/v) Dextran sulfate sodium salt (DSS) (MP Biomedicals, #0216011090) in drinking water for 5 days
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
DAPI-Cd31-Cd45-Epcam+Cd24+ cells were single-cell sorted.
FACS-sorted single cells were subjected to cDNA synthesis using Bead-seq method (DOI:10.1016/j.ab.2014.10.011, DOI:10.1038/s41598-017-04616-6). The processes from the production of cDNA libraries to their amplification and first purification were carried out automatically using a Caliper Zephyr compact liquid handler (Perkin Elmer, CA, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
160120_Hiseq3B_l8_004_Dr_Okamoto_N704-N517_TCCTGAGC-GCGTAAGA_L008
|
| Data processing |
Basecalling was performed using configureBclToFastq.pl of bcl2fastq version 1.8.4 with the following arguments: --with-failed-reads --no-eamss --use-bases-mask Y*,I8,I8
Reference sequences for mapping were prepared using rsem-prepare-reference of RSEM version 1.2.31 and Bowtie2 version 2.2.9.
Reads were filtered and trimmed using prinseq-lite.pl of PRINSEQ version 0.20.4 with the following arguments: -min_len 30 -trim_tail_right 5 -trim_tail_left 5 -min_qual_mean 20 -trim_qual_right 20 -trim_qual_left 20
The processed reads were mapped to the reference sequences and TPM (Transcripts Per Million) were calculated using rsem-calculate-expression of RSEM version 1.2.31 and Bowtie2 version 2.2.9 with the default parameters.
Gene TPM values were extracted from TPM columns of RSEM gene result files.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: CSV file including TPM values; The column labels are single cell names, and the row labels are gene IDs.
|
| |
|
| Submission date |
Nov 29, 2019 |
| Last update date |
Dec 01, 2019 |
| Contact name |
Daichi Narushima |
| Organization name |
National Cancer Center Research Institute
|
| Department |
Department of Bioinformatics
|
| Street address |
5-1-1 Tsukiji, Chuo-ku
|
| City |
Tokyo |
| ZIP/Postal code |
104-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE141157 |
PROX1 mediates chemoresistance-associated recurrence via maintenance of quiescent colon cancer stem cells |
|
| Relations |
| BioSample |
SAMN13427393 |
| SRA |
SRX7241525 |
