|
| Status |
Public on Sep 05, 2018 |
| Title |
NoDox_3 |
| Sample type |
SRA |
| |
|
| Source name |
Subcutaneous tumor grown from KCip53-1_NoDox
|
| Organism |
Mus musculus |
| Characteristics |
host strain: Immunocompromised (NSG) mouse
cell line used for tumor growth: KCip53-1 mouse pancreatic cancer cell line
tissue: Subcutaneous tumor grown from KCip53-1 cell line
doxycycline treatment time (days): 0
doxycycline removal time (days): N/A
doxycycline concentration (g/l): N/A
|
| Treatment protocol |
Doxycycline was administered in the drinking water (0.2g/L in a 5% sucrose solution) and changed every 3-4 days.
|
| Growth protocol |
Immunocompromised (NSG) animals 8-10 weeks of age were used for all subcutaneous or orthotopic tumor growth experiments. For subcutaneous tumors, 500,000 cells were injected in a 200uL solution of 50% Matrigel and 50% RPMI media. Each mouse was implanted subcutaneously with two tumors, and tumor growth was recorded at least 3X weekly until tumors reached a 1.5cm diameter.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tissue from subcutaneous tumors was collected in lysis buffer for RNA extraction. RNA was isolated using the Qiagen AllPrep DNA/RNA/miRNA Universal kit according to the manufacturer’s instructions.
PolyA+, non strand specific libraries were prepared by the University of Michigan Sequencing Core, and all samples were sequenced on an Illumina HiSeq 4000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
id_63644_sample_NoDox_3
|
| Data processing |
Illumina Casava v1.8.2 software used for basecalling.
Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using Bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1
Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score (placeholder); (6) strand; (7) gene span; (8) number of introns and exons; (9) length (sum of feature lengths, e.g. introns and exons); (10) read count (sense strand); (11) density (RPK) – count/length; (12) RPKM - count/(length/1E3)/(mapped read count/1E6)
|
| |
|
| Submission date |
Nov 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Mats Ljungman |
| E-mail(s) |
[email protected], [email protected], [email protected]
|
| Organization name |
University of Michigan
|
| Street address |
NCRC, B520 Room 1346 2800 Plymouth Rd.
|
| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48109-2800 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE106853 |
Mutant p53R270H drives altered metabolism and increased invasion in pancreatic ductal adenocarcinoma |
|
| Relations |
| BioSample |
SAMN08022090 |
| SRA |
SRX3388088 |
