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Sample GSM1079784 Query DataSets for GSM1079784
Status Public on Apr 10, 2013
Title Dicer_Null_2
Sample type SRA
Source name Dicer -/- murine MSC cell line
Organism Mus musculus
Characteristics cell type: murine MSC cell line
genotype: Dicer -/-
strain: C57BL/6
rna: small RNA
Treatment protocol Monoclonal immortalized Dicer WT and KO MSCs were cultured to near-confluence under normal growth conditions and then harvested for RNA isolation.
Growth protocol Monoclonal immortalized MSCs were cultured in Alpha-MEM supplemented with pen/strep and 10% fetal bovine serum.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Qiazol reagent according to manufacturer's instructions. 15-50 nt small RNAs were selected from a 15% polyacrylamide TBE-urea gel.
Libraries were cloned and sequenced using the Illumina small RNA-sequencing protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer II
Description Small RNAs (15-50 nts in length) from immortalized monoclonal lines of Dicer-/- (Dicer KO) mesenchymal stem cells (MSCs), a fibroblast cell type present in adult bone marrow, were analyzed.
Data processing Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Raw reads were processed to remove traces of 3' linker (CTGTAGGCACCATCAAT) and summarized by sequence identity (observations).
Genome_build: mm9
Supplementary_files_format_and_content: Text file with sequence and count
Submission date Feb 07, 2013
Last update date May 15, 2019
Contact name A Bhutkar
Organization name MIT
Street address 77 Massachusetts Avenue
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
Platform ID GPL9250
Series (2)
GSE44156 Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts [small_RNA-Seq]
GSE44163 Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts
SRA SRX228546
BioSample SAMN01915276

Supplementary file Size Download File type/resource
GSM1079784_Dicer_Null_seq_obs.txt.gz 7.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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