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Sample GSM818955 Query DataSets for GSM818955
Status Public on Nov 01, 2011
Title RNA-Seq Universal siRNA control in neural progenitor cells, after 48h
Sample type SRA
Source name Neural progenitor cells
Organism Mus musculus
Characteristics cell type: ES-cell derived neural progenitor cells
differentiation: 4 days of differentiation
modification: Universal siRNA (Invitrogen) transfected, 48h
Treatment protocol siRNA transfection was done by Lipofectamine treatment. Magnetic beads was used for PSA NCAM sorting.
Growth protocol Mouse ES-cells were differentiated with B27 and N2 supplement (GIBCO) as monolayers on gelatinized cellbinding surface (Corning) with 0.5uM retinoic acid (all-trans, Sigma) at day 0 and day 2.
Extracted molecule total RNA
Extraction protocol Libraries were constructed from total RNA. Libraries were prepared according to Illumina's instructions accompanying the mRNA-Seq sample preparation kit (Part # 1004898 Rev.D). Briefly, the mRNA was purified from total RNA by PolyA selection. The mRNA was subjected to fragmentation using divalent cations under elevated temperature. cDNA synthesis was performed with fragmented RNA, and cDNA was end-repaired with a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3? to 5? exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3? end. After adapter ligation, size selection was achieved by excising a band of 200±25 bp from an agarose gel to remove excess adapters. The gel purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Description Control transfected
library selection: Poly(A)-selection
Data processing Reads were aligned by Bowtie, with options -n 2 -m 1, against genome build mm9.
Expression values (FPKM) were calculated by ( with options -mRNAnorm -fulltranscript and RefSeq gene annotation downloaded from UCSC genome browser 1 July 2010.
Submission date Oct 18, 2011
Last update date May 15, 2019
Contact name Rickard Sandberg
Organization name Karolinska Institutet
Department Department of Cell and Molecular Biology
Street address Berzelius vag 35
City Stockholm
ZIP/Postal code 17177
Country Sweden
Platform ID GPL11002
Series (2)
GSE33024 Sequentially acting Sox transcription factors in neural lineage development
GSE33060 Sequentially acting Sox transcription factors in neural lineage development [RNA-seq]
SRA SRX101768
BioSample SAMN00740006

Supplementary file Size Download File type/resource
GSM818955_s4_NPC_48h_siRNA_ctrl_rnaseq.bed.gz 110.4 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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