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Sample GSM836269 Query DataSets for GSM836269
Status Public on Dec 31, 2013
Title Fetal liver sample for RNA-seq 4
Sample type SRA
Source name hnRNP L KO mouse
Organism Mus musculus
Characteristics genotype/variation: hnRNP L -/-
Growth protocol C57BL/6, LckCre transgenic, Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo and CD45.1 mice were purchased from Jackson Laboratories or were maintained at the Institut de recherches cliniques de Montreal. All animals were housed under specific pathogen-free environment at the Institut de recherches cliniques de Montreal, and all experiments were done conformed to ethical principles and guidelines approved by the institutional animal care committee.
Extracted molecule total RNA
Extraction protocol RNA was extracted from fetal liver cells using Tri Reagent (Molecular Research Center) followed by a purification using Rneasy Mini kit and Rnase-free Dnase on column (Qiagen) for 15 min at room temperature both following manufacturer’s instructions. RNA integrity and quality have been confirmed using a bioanalyzer (Agilent). rRNA from each biological sample was depleted from total RNA using a RiboMinus kit (Invitrogen) and the treated RNA was then fragmented using RNase III. Ligation of the adaptor mix A and reverse transcription were performed following the manufacturer’s protocol. Libraries were size selected for fragments between 150 and 300 bp, amplified for 12 cycles of polymerase chain reaction (PCR), and purified using PureLink PCR micro kit (Invitrogen). Barcoded library concentrations were determined by quantitative PCR using a standard curve of template at known concentrations (DH10B), and approximately 0.25 ng of each library was used for each full emulsion PCR (emPCR) reaction (4 emPCR/sample). Approximately 200 millions of beads from each two samples were deposited on single full slides (2 slides for 4 samples in total) and sequenced using the Opti Fragment Library Sequencing kit-Master Mix 50.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model AB SOLiD System 3.0
Data processing _junc.txt - Generated by Bioscope transcriptome analysis (ver 1.3) using default parameters
Fetal_liver_XXXXX_wt/ko.txt - Generated by Bioscope transcriptome analysis (ver 1.3) using default parameters
BAM file - Generated by Bioscope transcriptome analysis (ver 1.3) using default parameters
Submission date Nov 18, 2011
Last update date May 15, 2019
Contact name Brian Wilhelm
Organization name University of Montreal
Street address 2950 Chemin Polytechnique
City Montreal
ZIP/Postal code H1J 3R4
Country Canada
Platform ID GPL9318
Series (1)
GSE33815 Analysis of Fetal liver cells from hnRNP L KO mice
SRA SRX107325
BioSample SAMN00760416

Supplementary file Size Download File type/resource
GSM836269_Fetal_Liver_34836_KO.txt.gz 892.0 Kb (ftp)(http) TXT
GSM836269_Fetal_Liver_34836_KO_junc.txt.gz 29.2 Mb (ftp)(http) TXT
GSM836269_ko2_slide1.bam 4.5 Gb (ftp)(http) BAM
GSM836269_ko2_slide2.bam 4.4 Gb (ftp)(http) BAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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