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Sample GSM1563048 Query DataSets for GSM1563048
Status Public on Dec 08, 2016
Title glp-4(bn2); let-7(mn112)_3
Sample type RNA
 
Source name staged L4 worms
Organism Caenorhabditis elegans
Characteristics strain: glp-4(bn2); let-7(mn112)
Treatment protocol whole worms were harvested in M9 and transferred to TRI Reagent (MRC)
Growth protocol Worms were grown until the late L4 stage (glp-4(bn2); let-7(wild-type): 33h 25°C; glp-4(bn2); let-7(mn112): 34h 25°C)
Extracted molecule total RNA
Extraction protocol RNA was extracted using TRI Reagent (MRC)
Label biotin
Label protocol RNA was processed according to the Affymetrix GeneChip WT Amplified Double Stranded cDNA Synthesis Kit, fragmented with the Affymetrix GeneChip WT Double-Stranded DNA Terminal Labeling Kit and Biotin labeled using the GeneChip WT Genechip WT Terminal Labeling Kit
 
Hybridization protocol hybridization was performed overnight for 16 h in a GeneChip hybridization oven (Affymetrix)
Scan protocol Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader
Data processing All tiling arrays were processed in R using bioconductor and the packages tilingArray and preprocessCore. The arrays were RMA background corrected and log2 transformed on the oligo level using the following command: expr <- log2(rma.background.correct(exprs(readCel2eSet(filenames,rotated=TRUE)))). We mapped the oligos from the tiling array (bpmap file from www.affymetrix.com) to the c.elegans genome assembly ce6 (www.genome.ucsc.edu) using bowtie allowing no error and unique mappig position. Expressions for individual transcripts were calculated by intersecting the genomic positions of the oligos with transcript annotation (WormBase WS190) and averaging the intensity of the respective oligos.
probe group file: probeId_to_tr_min10probes.tab
 
Submission date Dec 09, 2014
Last update date Dec 08, 2016
Contact name Dimos Gaidatzis
E-mail(s) d.gaidatzis@fmi.ch
Organization name Friedrich Miescher Institute
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platform ID GPL5634
Series (1)
GSE64024 mRNA expression analysis in glp-4(bn2); let-7(wild-type) and glp-4(bn2); let-7(mn112) animals

Supplementary file Size Download File type/resource
GSM1563048_hg20130423cet1r_08_glp-4_bn2_let-7_mn112_45_5h_794_Ce25b_MR_v02_.CEL.gz 23.0 Mb (ftp)(http) CEL
Processed data are available on Series record

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