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Sample GSM1986943 Query DataSets for GSM1986943
Status Public on Dec 30, 2015
Title α4β7+ lymphoid precursor aLP.2.115
Sample type RNA
 
Source name fetal liver
Organism Mus musculus
Characteristics cell type: alpha4-beta7+ lymphoid precursor
activation agent: NA
time: E15
Extracted molecule total RNA
Extraction protocol CellsDirectTM One-Step qRT-PCR Kit (Life Technologies)
Label SYBR Green
Label protocol PCR assays were performed using a custom panel of lymphoid development factors. Preamplified cDNA was obtained after reverse transcription (15’ at 40°C, 15’ at 50°C and 15’ at 60°C), and preamplification (22 cycles : 15’’ at 95°C, 4’ at 60°C), and diluted 1 : 5 in TE pH8 Buffer (Ambion). Sample mix was as follows : diluted cDNA (2.9 μl), Sample Loading Reagent (0.29 μl, Fluidigm), TaqmanUniversal PCR Master Mix (3.3μl, Applied Biosystem) or Solaris qPCR Low ROX Master Mix (3.3 μl, GE Dharmacon). Assay mix was as follows: Assay Loading Reagent (2.5μl, Fluidigm), Taqman (2.5μl, Applied Biosystem) or Solaris (2.5μl, GE Dharmacon). 48.48 or 96.96 dynamic array integrated fluidic circuit (IFC, Fluidigm) was primed with control line fluid, and the chip was loaded with assays (either Taqman or Solaris) and samples using an HX IFC controller (Fluidigm). The experiments were run on a BiomarkHD (Fluidigm) for amplification and detection (2’ at 50°C, 10’ for Taqman reagents or 15’ for Solaris reagents at 95°C, 40 cycles : 15’’ at 95°C, 60’’ at 60°C).
 
Hybridization protocol n/a
Scan protocol n/a
Description Lin- IL7Rα+α4β7+PLZF-CXCR5-
Data processing Normalization was performed using the average of three housekeeping genes: Actb, Gapdh, Hprt. Cells not expressing detectable levels of all three housekeeping genes were removed from further downstream analysis, along with a group of mast cell precursor contaminants. For quantification purposes, genes that were not detected were given a –ΔCt value of -30, close to the minimum value detected.
 
Submission date Dec 29, 2015
Last update date Dec 30, 2015
Contact name Herman Gudjonson
Organization name Memorial Sloan Kettering Cancer Center
Department Computational and Systems Biology Program, SKI
Lab Dana Pe'er
Street address 417 E 68th St
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL21285
Series (1)
GSE76407 Single cell analysis defines the divergence between the innate lymphoid cell and lymphoid tissue inducer lineages

Data table header descriptions
ID_REF
VALUE normalized signal (against housekeeping genes).

Data table
ID_REF VALUE
Actb 1.68560479
Adam10 -5.52253607
Aes -30
Ahr -30
Batf -30
Bcl11a -30
Bcl11b -30
Bcl2 -4.715746266
Myc -1.341662016
Cbfb -3.339748786
Ccr8 -30
Cd27 -5.08400468
Cd4 -30
Cdkn1c -1.949382316
Cxcr5 -30
Cxcr6 -30
Dtx1 -30
Ebf1 -30
Egr1 -30
Eomes -30

Total number of rows: 100

Table truncated, full table size 1 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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