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Status |
Public on Sep 20, 2013 |
Title |
LSC with BRD7116 for 6h_2 |
Sample type |
RNA |
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Source name |
LSC with BRD7116 for 6h
|
Organism |
Mus musculus |
Characteristics |
cell type: leukemia stem cell perturbagen: small molecule type: treatment name: BRD7116 concentration: 5µM in 0.2% DMSO vehicle: DMSO duration: 6 h
|
Growth protocol |
See citation; Freshly isolated LSCe cells were treated with either 5 µM BRD7116 or DMSO vehicle control for 6 hours in suspension in Iscove's Modified Dulbecco's Medium, 10% FBS, 1% Pen-Strep at 37˚C/ 5% CO2 (250,000 cells in 150µL per 96-well, then drug was added in 20µL media
|
Extracted molecule |
total RNA |
Extraction protocol |
See citation; Total RNA was extracted from the cells (RNeasy kit 74104, Qiagen)
|
Label |
biotin
|
Label protocol |
See citation; In vitro transcription synthesized aRNA and incorporated a biotin-conjugated nucleotide.
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|
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Hybridization protocol |
See citation; Labeled cRNA was normalized to 150 ng/ µl and hybridized to Illumina's MouseRef-8 v2.0 Expression BeadChip. The labeled RNA strand was hybridized to the bead on the BeadChip containing the complementary gene-specific sequence. After a 16 hour hybridization, the beadchips were washed and stained using a Cy3 streptavidin conjugate.
|
Scan protocol |
See citation; Illumina’s BeadArray Reader was used to measure the fluorescence intensity at each addressed bead location according to manufacturer's instruction.
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Description |
PrimLeuk_BRD7116_2 n5719882018_E replicate 2
|
Data processing |
Raw data were normalized by cubic spline method implemented in Illumina Normalizer module of GenePattern analysis tool kit
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Submission date |
Sep 20, 2013 |
Last update date |
Sep 20, 2013 |
Contact name |
Kimberly Hartwell |
E-mail(s) |
hartwell@broadinstitute.org
|
Organization name |
Broad Institute
|
Department |
Cancer Program
|
Street address |
7 Cambridge Center
|
City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02142 |
Country |
USA |
|
|
Platform ID |
GPL6885 |
Series (1) |
GSE51033 |
Niche-based screening identifies small-molecule inhibitors of leukemia stem cells |
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