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| Status |
Public on Nov 26, 2017 |
| Title |
HFF_6 mg/mL_3 |
| Sample type |
SRA |
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| Source name |
3D collagen cultured human foreskin fibroblast
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HFF
culture condition: 6 mg/mL collagen matrix
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| Treatment protocol |
No treatment
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| Growth protocol |
Cells embedded in 3D collagen matrices were prepared by mixing cells suspended in culture medium and 10X reconstitution buffer, 1:1 (v/v), with soluble rat tail type I collagen in acetic acid (Corning, Corning, NY) to achieve the desired final concentration10,22,23. 1 M NaOH was used to normalize pH in a volume proportional to collagen required at each tested concentration (pH 7.0, 10-20 μl 1 M NaOH), and the mixture was placed in 48 well culture plates and let polymerize at 37C. Final gel volumes were 200 uL.
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| Extracted molecule |
total RNA |
| Extraction protocol |
3D collagen I gels were seeded in three independent experiments and harvested after 24 hours of culture for RNA extraction and directly homogenized in Trizol reagent (Thermofisher, Waltham, MA). Total RNA was isolated following manufacturer’s instructions. Isolated RNA was further purified using High Pure RNA Isolation Kit (ROCHE, Branford, CT). RNA integrity was verified using RNA Analysis ScreenTape (Agilent Technologies, La Jolla , CA) before sequencing.
TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Alignment was performed using Bowtie2 and quantification using eXpress pipe line. Reads aligned to the reference human genome Hg19
Genome_build: Hg19
Supplementary_files_format_and_content: eXpress pipeline outputs (fpkm)
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| Submission date |
Jul 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Ortiz |
| E-mail(s) |
daortizv@ucsd.edu
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| Phone |
8583668053
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| Organization name |
University of California San Diego
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| Department |
Bioengineering
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| Lab |
Stephanie Fraley
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| Street address |
9500 Gilman Dr
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| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL15520 |
| Series (1) |
| GSE101209 |
Gene expression changes associated with high density collagen microenviroment in cancer cells |
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| Relations |
| BioSample |
SAMN07343055 |
| SRA |
SRX2996245 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2700351_HFF_6mg_3_output.txt.gz |
6.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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