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| Status |
Public on Sep 24, 2016 |
| Title |
10T2M |
| Sample type |
SRA |
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| Source name |
MCF10A cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: breast epithelium
treatment: vehicle control, 72h
culture medium: DMEMF12, 5% Horse Serum, 20 ng/mL EGF, 0.5 mg/mL Hydrocortisone, 100 ng/mL Cholera Toxin, 10 mg/ml Insulin, Pen/Strep
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| Treatment protocol |
Cells were treated with 5 ng/mL of TGF-b or vehicle control for 72 hours.
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| Growth protocol |
see characteristics: Culture Medium above
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells lysed in 10 mM Tris-Cl, pH 7.4, 5 mM MgCl2, 100 mM KCl, 1% (v/v) Triton X-100, 0.5% (w/v) deoxycholate, 1000 U/ml RNasin, 2mM DTT and 100 µg/ml Cycloheximide. Total RNA and RNA from polysomal fractions were isolated with Trizol LS as per manufacturer's instructions. Poly(A) RNA was isolated using Dynabeads mRNA DIRECT Micro Kit (Life Technologies) according to manufacturer’s instructions.
Ion Total RNA-Seq Kit v2 (Life Technologies) was used according to manufacturer’s recommendations to prepare libraries. the Ion PI Template OT2 200 Kit v2 (Life Technologies) was used as per manufacturer’s instructions to generate template Ion PI Ion Sphere particles using the Ion OneTouch 2 System. Ion PI Chip preparation was done using the Ion PI Sequencing 200 Kit v2 (Life Technologies) and sequenced on the Ion Proton Sequencer platform.
Single-read RNA-seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| Description |
total mRNA
10TM_biological replicate
10_quant_gene_reads_normalized.txt; 10gsa_result_filter120.xlsx
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| Data processing |
Running and Basecalls Performed on an Ion Proton Sequencer using Torrent Suite v3.6
Fastq files extracted from Torrent Suite output and fed into Partek Flow Suite
Within Partek Flow Suite, align to hg19 using Tophat2 and Bowtie2, normalize and analye for differential relative representation using Partek Gene Specific Analysis Feature
Partek GSA outputs imported to Excel, filtered to require 120 total observed reads across all conditions for a given cell type (ave 10/library), and compound enrichments calculated
Genome_build: hg19
Supplementary_files_format_and_content: .txt files - Partek GSA raw output. .xlsx files - import of Partek GSA raw output, compound enrichment calculation.
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| Submission date |
May 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Arindam Chaudhury |
| E-mail(s) |
achaudhu@bcm.edu
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| Phone |
7137988884
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| Organization name |
Baylor College of Medicine
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| Department |
Molecular Physiology and Biophysics
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| Lab |
Neilson Lab
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| Street address |
One Baylor Plaza / MS BCM335
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL17303 |
| Series (1) |
| GSE81955 |
Analysis of polysomal enrichment and depletion of mRNA in untreated and TGF-beta treated MCF-10A and MCF7 cells |
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| Relations |
| BioSample |
SAMN05180018 |
| SRA |
SRX1802061 |
| 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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