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| Status |
Public on Sep 16, 2011 |
| Title |
HMEC-mRNA-Seq |
| Sample type |
SRA |
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| Source name |
mammary epithelial cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HMEC
cell type: primary human mammary epithelial cells
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from 2 million cells was extracted with TRIZOL (Invitrogen, Carlsbad, CA) using manufacturer's instructions, followed by mRNA purification with Dynabeads Oligo (dT)25 (Invitrogen, Carlsbad, CA). First strand synthesis was performed with SuperScript® III First-Strand Synthesis System (Invitrogen, Carlsbad, CA), followed by purification with Sephadex G50 beads (medium) (GE Healthcare, UK) and second strand synthesis with dUNTPs. cDNA was sonicated with a Bioruptor (Diagenode, Woburn, MA) followed by end repair, addition of a 3' base, and ligation of adaptors. Fragments were purified on a 2% agarose gel and the second strand was degraded with AmpErase UNG (Applied Biosystems, Foster City, CA). Samples were amplified with between 7 and 10 cycles of PCR, followed by gel purification.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
polyA-selected RNA
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| Data processing |
mRNA-Seq reads were mapped with the TopHat program with default parameters.
Genome build: hg18
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| Submission date |
May 06, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Gary Chung Hon |
| Organization name |
UT Southwestern
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| Department |
OB/GYN
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| Street address |
5323 Harry Hines Blvd.
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| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
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| Platform ID |
GPL10999 |
| Series (2) |
| GSE29069 |
Global DNA Hypomethylation Coupled to Repressive Chromatin Domain Formation and Gene Silencing in Breast Cancer |
| GSE29119 |
Gene expression analysis of breast cancer (HCC1954) and normal breast cells (HMEC) |
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| Relations |
| SRA |
SRX061998 |
| BioSample |
SAMN00264835 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM721141_HMEC.RNA-Seq.bam |
965.3 Mb |
(ftp)(http) |
BAM |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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