NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4289690 Query DataSets for GSM4289690
Status Public on Sep 21, 2020
Title Ectoderm sample 4 from stage HH22 chick
Sample type RNA
 
Source name Frontonasal ectodermal zone ectoderm
Organism Gallus gallus
Characteristics tissue: Frontonasal ectodermal zone ectoderm
treatment: Normal stage HH22 (72hr)
Treatment protocol Inhibition of neural SHH signaling was achieved by injecting hybridoma cells expressing either immuno‐neutralizing anti‐SHH antibody (5E1) or anti‐β‐galactosidase antibody control cells (40-1A) into the neural tube at Stage 10 (HH10). SHH-N treatment was performed using affi-Gel Blue beads (50 – 100 mesh, 200 – 250 diameter) soaked in recombinant SHH-N protein (400 ng/ml in PBS with 0.1% bovine serum albumin (BSA)) or 0.1% BSA (control) at 37° C for one hour. Forty-eight hours after SHH signal inhibition, SHH-soaked beads were placed between the facial ectoderm and the forebrain neuroectoderm. Embryos were collected at HH22 for genomic analysis.
Growth protocol Fertilized chicken eggs (Gallus gallus, Rhode Island Red, Petaluma Farms, CA) were incubated at 39° C in humidified conditions and prepared for surgical manipulation.
Extracted molecule total RNA
Extraction protocol Agilent manufacturer's instruction.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned on the Agilent scanner immediately after washing.
Data processing The scanned images were analyzed with Feature Extraction Software 10.1 (Agilent) using default parameters)
 
Submission date Jan 29, 2020
Last update date Sep 21, 2020
Contact name Andrea J Barczak
Organization name UCSF Sandler Center Functional Genomics Core Facility
Street address 1550 4th St Rock Hall 545
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platform ID GPL28095
Series (1)
GSE144499 miR-199 Family Regulates Sonic Hedgehog Expression During Craniofacial Development

Data table header descriptions
ID_REF
VALUE Log2 Normalized signal intensity

Data table
ID_REF VALUE
4 5.319
5 5.356
6 5.435
7 5.285
9 5.356
10 5.473
11 5.356
12 5.356
13 5.285
14 5.473
15 5.435
16 5.319
17 5.319
18 5.319
19 5.285
20 5.319
21 5.435
22 5.356
23 10.979
24 5.356

Total number of rows: 14352

Table truncated, full table size 158 Kbytes.




Supplementary file Size Download File type/resource
GSM4289690_miRNA_252154210003_S01_miRNA-v1_95_May07_1_2.txt.gz 1.9 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap