Embryo Fax-sorted cells TransFrags

embryo cells tiling arrays (Waterston project, Miller subgroup)

Details

Cells were isolated using FACS, sorting on GFP-fusion reporters expressing embryos. RNA was isolated, amplified, and transcripts were detected on an Affymetrix C. elegans tiling array. A smoothed density plot (log 2 transformed with a window size of 110) and transcriptionally active regions (TARs) are shown.

Series Description

Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.

Protocols

  1. Growth and isolation: RNA_isolation, Tissue isolation, Worm staging and isolation, Worm growth
  2. Sample preparation: Affy_Hybridization_and_Scanning, CDNA_amplification_for_tiling_arrays
  3. Data Analysis: Tiling_Array_Normalization_and_Smoothing, Tiling_Array_Signal_Extraction, Tiling_Array_TAR_analysis

Experimental Reagents

    Growth Conditions:
  1. Arrays: Affymetrix GeneChip C. elegans tiling 1.0R array

Sample Details

  1. Animals/Lines: BY200, Embryo, panneural, PD4251, body wall muscle, germ line precursor cells (GLP), whole organism (embryo), JR1130, intestinal cells, hypodermal cells, embryo-AVA, dopaminergic motor neurons, DM8001, coelomocytes, CZ1200, NW1229, TV1112, unc-4 expressing neurons (embryonic stage), NC1749, NC300, GABAergic cells, SS747, N2


Release Date: 2009-11-19