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| Status |
Public on Aug 15, 2018 |
| Title |
mRNA sequencing of MCF-7 cells treated with 100nM TCDD, replicate 1 |
| Sample type |
SRA |
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| Source name |
MCF-7 breast cancer cells
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| Organism |
Homo sapiens |
| Characteristics |
treatment: TCDD
concentration: 100nM
cell line: MCF-7
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| Treatment protocol |
6hrs treatment withTCDD
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| Growth protocol |
250,000 MCF-7 cells were seeded in 35 mm plates in DMEM supplemented with 10 % FBS for 24 hr, followed by overnight serum-starvation in phenol red-free DMEM
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA purification kits from Qiagen (Valencia, CA) were used according to manufacturers instructions
Libraries were prepared from 1 µg of total RNA using a TruSeq RNA Prep Kit (Illumina Inc., San Diego, CA)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
Alignment to hg19 using TopHat 2.0.7 with BowTie 0.12.9 and SamTools 0.1.18
Counts by gene calculated using R/Bioconductor packages GenomicFeatures and GenomicRanges, with Ensembl gene annotations
Normalized counts calculated using DESeq
Differential Gene expression calculated using DESeq (version 1) with treatment as the single variable
Genome_build: hg19
Supplementary_files_format_and_content: raw_counts_100nM_TCDD.txt is a tab-delimited text file containing raw read counts per gene. Samples DMSO-1, DMSO-2, DMSO-3, and DMSO-4 refer to GSM2028919, GSM2028920, GSM202821, and GSM2028922, respectively.
Supplementary_files_format_and_content: normalized_counts_100nM_TCDD.txt is a tab-delimited text file containing counts per gene after normalization by the estimateSizeFactors function in the Bioconductor package DESeq. Samples DMSO-1, DMSO-2, DMSO-3, and DMSO-4 refer to GSM2028919, GSM2028920, GSM202821, and GSM2028922, respectively.
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| Submission date |
May 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
James Denvir |
| E-mail(s) |
denvir@marshall.edu
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| Organization name |
Marshall University School of Medicine
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| Department |
Biochemistry and Microbiology
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| Lab |
Genomics and Bioinformatics Core Facility
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| Street address |
One John Marshall Drive
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| City |
Huntington |
| State/province |
WV |
| ZIP/Postal code |
25755 |
| Country |
USA |
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| Platform ID |
GPL18460 |
| Series (2) |
| GSE98514 |
Expression profiling of four replicates of MCF-7 cells treated with 100nM TCDD |
| GSE98515 |
Expression profiling of MCF-7 cells with treatment of TCDD |
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| Relations |
| BioSample |
SAMN06887158 |
| SRA |
SRX2781385 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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