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Sample GSM3029225 Query DataSets for GSM3029225
Status Public on Jan 14, 2019
Title HCT116_Ctrl_1
Sample type SRA
Source name HCT116
Organism Homo sapiens
Characteristics cells: control cells
passages: 8-15
pull down: Pull down with Pan-AGO peptide (Hauptmann et al., 2015 PNAS
Treatment protocol cells were treated where indicated with Doxorubicin (doxo) for 20h, 40h or 80h
Growth protocol HeyA8 cells are cultured in RPMI1640 medium supplemented with 10% FBS and 1% L-Glutamine. HCT116 cell lines were cultured in McCoy's 5A medium, supplemented with 10% FBS and 1% L-Glutamine.
Extracted molecule total RNA
Extraction protocol AGO1-4 were pulled down from whole cell lysate (Hauptmann et al., 2015 PNAS). The RNA was isolated using Trizol.
Preadenylated, barcoded 3┬┤adapter oligonucleotide was ligated followed by ligation of a 5┬┤adapter. Ligation products were reverse transcribed and amplified by PCR.
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 3000
Description miRNAseq_in_HeyA8_and_HCT116.xlsx
Data processing Illumina HiSeq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the hg19 genome using TopHat
The miRNA normalized counts was generated as in Farazi et al., Cancer research 2011 (GEO accession number GSE28884)
Genome_build: hg19
Supplementary_files_format_and_content: format: xlsx content: Normalized counts
Submission date Mar 02, 2018
Last update date Jan 14, 2019
Contact name Markus Hafner
Phone 3014026956
Organization name NIH
Department NIAMS
Lab Markus Hafner
Street address 50 South Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platform ID GPL21290
Series (1)
GSE111363 Induction of DISE by tumor suppressive microRNAs
BioSample SAMN08631222
SRA SRX3758350

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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