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| Status |
Public on Jan 18, 2020 |
| Title |
MCF7_IL1A_3 |
| Sample type |
SRA |
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| Source name |
MCF7
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast
genotype: cell line
time: 5 days
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| Treatment protocol |
MCF7 cells were treated with vehicle control (0.1% BSA in 1xPBS), 25 ng/ml IL-1 alpha (Gold Biotechnology, 1110-01A-10), or 25 ng/ml IL-1 beta (Gold Biotechnology, 1110-01B-10). MDA-MB-231 cells were treated with vehicle control (0.1% BSA in 1xPBS). At Day 5, total RNA was extracted for RNA-sequencing.
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| Growth protocol |
MCF7 and MDA-MB-231 cells were grown in a 37°C, 5.0% (vol/vol) CO2 incubator in Dulbecco Modified Eagle Medium (DMEM; Gibco, Waltham, MA; 1185‐076) supplemented with 10% FB Essence (Seradigm, Radnor, PA; 3100‐500), 0.4mM of L‐glutamine (L‐glut; Gibco/Invitrogen, Waltham, MA; 25030081), and 10U/mL of penicillin G sodium and 10 mg/mL of streptomycin sulfate (pen‐strep; Gibco/Invitrogen; 15140122).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using GeneJET RNA Purification Kit according to the manufacturer’s instructions (Thermo Scientific; K0732), RNA quantitiy and quality was then verified useng Biotek plate reader Gen 5 software, microspots protocol.
One microgram of total DNAse-treated RNA was prepared with DNAse 1, RNase-free(Thermo, #EN0521)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
MCF7 cells were treated with vehicle control (0.1% BSA in 1xPBS), 25 ng/ml IL-1 alpha (Gold Biotechnology, 1110-01A-10), or 25 ng/ml IL-1 beta (Gold Biotechnology, 1110-01B-10). At Day 5, total RNA was extracted for RNA-sequencing.
25 ng/ml IL-1a, 3
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| Data processing |
Single-end 76 bp read length Fastq files were checked for quality using fastqc/v0.11.2 and fastq_screen/v0.4.4
Reads were quality trimmed using fastq-mcf (ea-utils/v1.1.2-806).
Trimmed fastq files were mapped to hg19 (UCSC version from igenomes)
Duplicates were marked using picard-tools/v1.127
Read counts were generated using featureCounts (subread/v1.4.6).
Normalized read counts and differentially expressed genes found using edgeR/v3.2.4
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited txt files that includes raw read counts for each sample per gene
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| Submission date |
Aug 27, 2019 |
| Last update date |
Jan 18, 2020 |
| Contact name |
Nikki Delk |
| E-mail(s) |
[email protected]
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| Phone |
9728832581
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| Organization name |
University of Texas at Dallas
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| Department |
Biological Sciences
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| Street address |
800 West Campbell Road
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| City |
Richardson |
| ZIP/Postal code |
75080 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE136420 |
IL-1-conferred gene expression pattern in ERa+ BCa and AR+ PCa cells is intrinsic to ERa- BCa and AR- PCa cells and promotes cell survival |
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| Relations |
| BioSample |
SAMN12642657 |
| SRA |
SRX6762302 |
| 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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