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Sample GSM5694068 Query DataSets for GSM5694068
Status Public on Jul 01, 2024
Title mitfa_24hpf_rep1
Sample type RNA
 
Source name zebrafish mitfa:GFP positive cells
Organism Danio rerio
Characteristics cell type: mitfa:GFP pigment lineage cells
developmental stage: 24hpf
Treatment protocol No treatment
Growth protocol Zebrafish were bred, raised and maintained at 28.5 °C according to standard protocols (Westerfield M, 2000) and were housed at the CSIR-Institute of Genomics and Integrative Biology (IGIB), Mathura Road New Delhi, India. Embryos were staged both using timing (hours post fertilization (hpf); days post fertilization (dpf)) and morphological features according to (Kimmel, 1995)
Extracted molecule total RNA
Extraction protocol RNA was isolated from each of these sorted populations according to manufacturer’s protocols (Nucleospin RNA XS kit; MachereyNagel)
Label Cy3
Label protocol The microarray hybridization and scanning were performed at the Agilent certified microarray facility of Genotypic Technology, Bengaluru, India. The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000
 
Hybridization protocol Labeled cRNA sample were fragmented at 60oC and hybridized on to Agilent Zebrafish Gene Expression Microarray 8X60K. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65o C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)
Scan protocol The hybridized slides were scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D). Raw data extraction from Images was obtained using Agilent Feature Extraction software
Data processing Images were quantified using Feature Extraction Software (Version-11.5 Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift (Percentile shift normalization is a global normalization, where the locations of all the spot intensities in an array are adjusted. [This normalization takes each column in an experiment independently, and computes the percentile of the expression values for this array, across all spots (where n has a range from 0-100 and n=75 is the median). It subtracts this value from the expression value of each entity.
 
Submission date Nov 17, 2021
Last update date Jul 01, 2024
Contact name Vivek T Natarajan
E-mail(s) tnvivek@igib.in
Organization name CSIR-IGIB
Lab Pigment Cell Biology Lab
Street address Mathura Road
City Delhi
State/province Delhi
ZIP/Postal code 110025
Country India
 
Platform ID GPL26813
Series (1)
GSE189059 Time-course gene expression analysis of melanocyte development

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GT_EA826_Xhyb_XM_005173130.1_374895 1925.6553
GT_EA826_Spec_XM_001340647.4_347975 106.083
GT_EA826_Spec_NM_213302.1_232925 33839.176
GT_EA826_Spec_NM_001042775.1_120086 83.25867
GT_EA826_Xhyb_XM_001923680.4_408335 63.031544
GT_EA826_Xhyb_NM_200976.2_62691 25540.213
GT_EA826_Xhyb_NM_001077328.1_222255 387.20746
GT_EA826_Xhyb_NM_001100033.1_128336 58.2708
GT_EA826_Xhyb_XM_005172003.1_135936 6.768738
GT_EA826_Xhyb_XM_005162816.1_426665 4777.5474
GT_EA826_Spec_XM_005162256.1_157006 11.464022
GT_EA826_Spec_XM_005170028.1_16741 397.5164
GT_EA826_Xhyb_NM_001282089.1_161336 1779.1921
GT_EA826_Xhyb_XM_005162815.1_426685 4823.092
GT_EA826_Xhyb_XM_003201366.2_78311 9200.446
GT_EA826_Spec_NM_001076606.1_6571 1538.7635
GT_EA826_Spec_XM_005171901.1_382535 1.575844
GT_EA826_Xhyb_XM_005162814.1_426635 4876.405
GT_EA826_Xhyb_XM_005167693.1_63941 581.69464
GT_EA826_Spec_NM_001102571.1_117803 124.603

Total number of rows: 44280

Table truncated, full table size 1932 Kbytes.




Supplementary file Size Download File type/resource
GSM5694068_SG13134300_257419110001_S001_GE1_1105_Oct12_1_3.txt.gz 10.6 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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