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| Status |
Public on Oct 02, 2012 |
| Title |
vehicle_replicate1_PE |
| Sample type |
SRA |
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| Source name |
vehicle_replicate1_PE
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| Organism |
Mus musculus |
| Characteristics |
grafting: A549-luc-C8
strain: SCID-beige
gender: female
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| Treatment protocol |
Animals were weighed and engrafted (day 0). Treatment was conducted on days 0,2,4,7,9. Injections of 120 nmol Py-Im polyamide in 200 uL PBS/DMSO (4:1) were performed subcutaneously. Animals were weighed again on day 6, typically not exhibiting weight loss of more then 10 %, imaged on day 10, sacrificed and tumors harvested.
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| Growth protocol |
RPMI medium supplemented with 10%FBS and Pen-Strep
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| Extracted molecule |
total RNA |
| Extraction protocol |
Experiments were performed in female SCID-beige mice (Charles River) between 8 and 12 weeks of age. Cells were injected into the left flank area of the animals as suspensions of 25 x 106 mL-1 in RPMI, 200 µL per injection. Treatment and tumor proliferation monitoring. Mice were treated following the schedule delineated in Supporting Information (Table S1). Tumor proliferation was monitored using the XENOGEN imaging device. The animals were anesthetized with 2 5 % isoflurane and subsequently transferred to the imaging chamber, whereupon the isoflurane levels were reduced to 1-2.5 %. The floor of the imager was heated to +37 ºC to avoid hypothermia. Breathing frequency was monitored and not allowed to drop below 1 s-1, adjusting the isoflurane levels accordingly at all times. Endpoint criteria and euthanasia. Animal endpoint criteria encompassed weight loss of over 15 %, restriction of motor function by the engrafted tumor, dehydration of over 10 % and moribund behavior. Where appropriate, the animals were euthanized by asphyxiation in a CO2 chamber. Tumor tissue harvest. Animals were resected and tumors excised using standard forceps, scissors and surgical blades. The tumors were combined into one sample per condition and mechanically sheared in TRIZOL, employing a specialized device (tissue tearer, model 985370). Total RNA workup was performed following the standard TRIZOL procedure, followed by a DNAse digest, double poly-A select; libraries prepared using standard Illumina reagents and protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
A549-luc-C8
processed_DESeq
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| Data processing |
Bowtie mapping to hg19+mm9 transcriptome, then eXpress, then DESeq
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| Submission date |
Aug 20, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Jevgenij A. Raskatov |
| E-mail(s) |
raskatov@caltech.edu
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| Phone |
6263956084
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| Organization name |
CalTech
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| Department |
CCE
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| Lab |
Dervan
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| Street address |
1200 EAST CALIFORNIA BOULEVARD
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| City |
PASADENA |
| State/province |
California |
| ZIP/Postal code |
91125 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE40218 |
Gene Expression Changes in a Tumor Xenograft by a Py-Im Polyamide |
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| Relations |
| SRA |
SRX179415 |
| BioSample |
SAMN01121004 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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