|
| Status |
Public on Jan 28, 2014 |
| Title |
WT E14.5 FL SLAM LSK 4h DMSO Rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Fetal liver hematopoeitic stem cell (SLAM LSK)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6J
tissue: fetal liver
cell type: HSC
age: E14.5
treatment: DMSO
time: 4h
|
| Treatment protocol |
FL cells were cultured on OP9-DL1 cells for 4 or 10 hrs in the presence of DMS0 Gamma Secretase ihibitor (1uM)
|
| Growth protocol |
Livers wer dissected from WT (C57B/6) embryos at E14.5 and cultured on OP9-DL1 cells. SLAM-LSK HSCs were FACs sorted after the indicated culture time
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted into Arcturus Pico pure extraction buffer and RNA prepared per instructions on the Arcturus Pico Pure RNA isolation kit
|
| Label |
biotin
|
| Label protocol |
ssDNA was fragmented and biotinylated by terminal transferase end labeling
|
| |
|
| Hybridization protocol |
ssDNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to Mouse Gene 2.0st GeneChips
|
| Scan protocol |
A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.
|
| Description |
DMSO_L1_a_4815
|
| Data processing |
Affymetrix.cel files (containing probe intensities) were exported from Command Console software and imported into Partek Genomics Suite (v6.6, Partek Inc., St. Louis, MO) where RMA was applied yielding normalized, log2 transformed signal intensities. Transcript IDs were filtered to exclude technical controls, leaving 34,365 IDs for differential expression analysis. To find differentially expressed genes, SAM (Significance Analysis for Microarrays, samr v2.0, Stanford University) was applied using a two-class (GSI vs DMSO) paired (by litter pool) design.
probe group file: MoGene-2_0-st.pgf
meta-probeset file: MoGene-2_0-st.mps
|
| |
|
| Submission date |
Dec 30, 2013 |
| Last update date |
Jan 28, 2014 |
| Contact name |
dawson gerhardt |
| E-mail(s) |
dawsonm@upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Street address |
BRB2/3 421 Curie Blvd.
|
| City |
Philadelphia |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL16570 |
| Series (1) |
| GSE53713 |
Expression data from mouse E14.5 fetal liver SLAM LSKs |
|
