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Sample GSM718983 Query DataSets for GSM718983
Status Public on Dec 06, 2011
Title Rio-Zero total RNA fetal head
Sample type SRA
Source name 14.5dpc fetal head
Organism Mus musculus
Characteristics strain: FVB/N
tissue type: fetal head dissected from 14.5dpc mouse embryo
fragmentation method: RNA hydrolysis
rrna depletion: 1 round
sequencing facility: CeMM, Vienna
Growth protocol CCE feeder-independent ES cells were grown under standard conditions, and differentiation was induced by withdrawal of LIF and addition of 0.266µM retinoic acid (RA). Mouse fetal heads were dissected at 14.5 days postcoitum.
Extracted molecule total RNA
Extraction protocol DNase I treated 5µg of high quality total RNA from cells or tissues was subjected to ribosomal RNA depletion by using the Ribo-Zero rRNA removal Kit (Human/Mouse/Rat) according to the manufacturer’s protocol. The quality of the purified RNA was checked on Agilent 2100 Bioanalyzer with Agilent RNA 6000 Pico Kit according to the manufacturer’s protocol. The purified Ribo-Zero RNA fraction (100ng) was subsequently fragmented by addition of 5× fragmentation buffer (200mM Tris pH8.2, 500mM KAc and 150mM MgAc2) and heating at 94°C for 4min in a total volume of 100µl. The reaction was stopped by putting the sample on ice. The fragmented RNA was purified by RNeasy Mini Kit according to the manufacturer protocol, and subsequently ethanol precipitated and dissolved in 10µl nuclease-free ddH2O.The fragmented RNA was used as template for cDNA synthesis using 5µg random hexamers in a total volume of 20µl according to the Superscript II Reverse Transcriptase standard protocol. Second-strand synthesis was performed by adding 91.8µl water, 30µl 5× Second strand buffer, 3µl 10mM dNTP, 4µl DNA polymerase I, 1µl E. coli DNA ligase and 0.2µl RNase H, followed by incubation at 16°C for 2hour. T4 DNA Polymerase (1µl) was added followed by an additional 10 min at 16 °C. The ds-cDNA was purified by using the MinElute Reaction Cleanup Kit according to the manufacturer’s protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description Ribo-Zero total RNA, Trizol isolated
Data processing Alignment: Sequence reads were obtained using the Illumina HiSeq 2000 Pipeline and mapped to the mouse genome (mm9, July 2007) using Bowtie. All reads mapping with three or fewer mismatches were retained.
Submission date May 02, 2011
Last update date May 15, 2019
Contact name Florian M Pauler
Phone +43 2243 9000-7434
Organization name IST Austria
Lab Simon Hippenmeyer
Street address Am Campus 1
City Klosterneuburg
ZIP/Postal code 3400
Country Austria
Platform ID GPL13112
Series (1)
GSE22959 Sequencing of the non-ribosomal transcriptome allows the simultaneous identification of protein-coding and non-protein-coding RNAs
Reanalyzed by GSM1955408
SRA SRX060244
BioSample SAMN00262830

Supplementary file Size Download File type/resource
GSM718983_FH_RZ.bed.gz 599.6 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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