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Sample GSM661639 Query DataSets for GSM661639
Status Public on Jan 30, 2012
Title Mutant ΔMCS-P6MCS-R3-/- Murine erythroid cells mRNA-seq
Sample type SRA
Source name erythroid cells (fetal liver culture)
Organism Mus musculus
Characteristics strain: CBA/C57BL/6 mixed
genotype: delta_MCS-P6MCS-R3-/-
cell type: erythroid cells (fetal liver culture)
Growth protocol Erythroid cells were grown from fetal livers following published protocol (Dolznig et al., 2001).
Extracted molecule polyA RNA
Extraction protocol Total RNA was prepared using Trizol reagent (Sigma) and DNaseI treated (Ambion). The RNA quality was assessed using Agilent Bioanalyser. RNA with overall RIN score >9 was used for further procedures. poly(A)+ mRNA was isolated from total RNA using PolyA selection kit (Promega) according to the manufacturer’s protocol. poly(A)+ mRNA from erythroid cells was depleted of globin transcripts using GlobinClear (Ambion). The quality of obtained RNA samples was assessed using PicoChip (Agilent).
cDNA libraries were prepared from poly(A)+ mRNA from ΔMCS-P6MCS-R3-/- erythroid cells (fetal liver culture) and wild-type Ter119+ cells using the mRNA-Seq pair-end kit (Illumina) and then sequenced using massively parallel sequencing (Illumina, GAII) with 50 base paired-end reads.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
Description instrument model: Model- GAIIx Chemistry-SBS v4 cBot single generation kit with v4 flow cell SCS 2.8 RTA 1.8 Recipe v7.4
Data processing Bcl conversion to Qseq files using OLB v1.8.0 Gerald- using Eland alignment to produce sequence and export files (carried out by CASAVA 1.7.0) Reads were mapped to the mm9 mouse genome build using TopHat 1.1.1b . Transcript abundances and differential expression were tested using Cufflinks and Cuffdiff using current Ensembl transcript ID and Refseq gene annotation. Gene ontology analysis was performed using DAVID (
Submission date Jan 26, 2011
Last update date May 15, 2019
Contact name Monika S Kowalczyk
Organization name Weatherall Institute of Molecular Medicine, University of Oxford
Department MRC Molecular Haematology Unit
Lab Higgs Group
Street address Headley Way
City Oxford
State/province Oxfordshire
ZIP/Postal code OX3 9DS
Country United Kingdom
Platform ID GPL9250
Series (2)
GSE26877 Transcriptome of mouse erythroid cells (part1) poly(A)+
GSE27921 Intragenic enhancers act as alternative promoters
Reanalyzed by GSE80797
SRA SRX040567
BioSample SAMN00205410

Supplementary file Size Download File type/resource
GSM661639_RNASeq_Mutant_Ter119_Paired.sam.gz 4.8 Gb (ftp)(http) SAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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