|
| Status |
Public on Nov 10, 2022 |
| Title |
B5: WT mice+WT B16-PBS rep1 |
| Sample type |
SRA |
| |
|
| Source name |
WT mice+WT B16-PBS
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tumor genotype: WT tumor
condition: WT mice+WT B16-PBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Qiagen Rneasy Mini kit. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WT mice+WT B16-PBS rep1
|
| Data processing |
The samples were sequenced using Illumina NovaSeq6000 sequencer with paired-end 50 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the GRCm38 human reference genome by STAR (Version2.5.2).
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized abundance measurements(FPKM) at gene level for each samples
|
| |
|
| Submission date |
Nov 09, 2021 |
| Last update date |
Nov 10, 2022 |
| Contact name |
Ning Yang |
| E-mail(s) |
yangn@mskcc.org
|
| Organization name |
MSKCC
|
| Street address |
430 E 67th St, RRL853
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE188496 |
Next Generation Sequencing Analysis of mouse tumors treated with rMVA |
|
| Relations |
| BioSample |
SAMN23010673 |
| SRA |
SRX13085531 |
