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Sample GSM1691054 Query DataSets for GSM1691054
Status Public on Jun 09, 2016
Title DOX WiNTRLINC1 KD replicate 2
Sample type SRA
Source name DOX WiNTRLINC1 KD
Organism Homo sapiens
Characteristics tissue source: Duke's type B adenocarcinoma of the colon
cell line: LS174T
cell type: Derivatives of Ls174 colon cancer cells
genotype/variation: inducible shRNAs against the ASCL2
treated with: 1ug/ml doxycycline
Treatment protocol KD treated samples were grown for three days in conditions described above in the presence of doxycycline (final concentration of 1ug/ml). Control cells were grown as KD cells without doxycycline addition.
Growth protocol Cells were grown for three days at 37 C, 5% CO2 in DMEM standard growth medium, 10% FBS reaching a maximum confluency of 50 % before harvesting
Extracted molecule total RNA
Extraction protocol Trizol
For RNA-Seq experiments, the isolated mRNA was digested with RNaseIII, hybridized and ligated to Ion Adaptors, reverse transcribed, barcoded and amplified, using the Ion Total RNA-Seq Kit v2 (Life Technologies, Carlsbad, CA, USA). Samples were processed on an OneTouch 2 instrument and enriched on a One Touch ES station. Templating was performed using the Ion PI™ Template OT2 200 Kit (Life Technologies, Carlsbad, CA, USA) and sequencing with the Ion PI™ Sequencing 200 Kit on Ion Proton PI™ chips (Life Technologies, Carlsbad, CA, USA) according to commercially available protocols.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Description Colon epithelial adherent cells
Data processing Base calling was performed using software provided with the Ion Torrent Proton sequencer.
Sequenced reads were trimmed for adaptor sequence using cutadapt software and mapped to hg19 whole genome using tophat 2.0.9 with default settings and using additional transcript annotation data for the mm9 genome from Illumina iGenomes (
Tags overlapping the Ensembl GRCh37 human exons were counted and filtered for artifacts as follows: if an annotated gene had up to five exons, tag presence was required in at least two exons. If an annotated gene had E >5 exons, tag presence was required in at least E/5 exons. The final gene counts were calculated as the sums of their exon tags. The counts table was normalized and analyzed for differential expression using DESeq. The final list of differentially expressed genes was derived by the genes demonstrating a binomial test p-value less than 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files containing DESeq normalized counts for each Ensembl gene.
Submission date May 19, 2015
Last update date May 15, 2019
Contact name Pantelis Hatzis
Organization name Biomedical Sciences Research Center 'Alexander Fleming'
Department Molecular Biology and Genetics
Street address 34 Fleming Str
City Vari
State/province Attiki
ZIP/Postal code 16672
Country Greece
Platform ID GPL17303
Series (1)
GSE69036 A positive regulatory loop between a Wnt-regulated non-coding RNA and ASCL2 controls intestinal stem cell fate
BioSample SAMN03701686
SRA SRX1033053

Supplementary file Size Download File type/resource
GSM1691054_DOX_WNTRLINC1-KD_BR2.txt.gz 254.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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