|
| 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 (http://david.abcc.ncifcrf.gov/content.jsp?file=functional_annotation.html#intro).
|
| |
|
| Submission date |
Jan 26, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Monika S Kowalczyk |
| E-mail(s) |
monika.kowalczyk@imm.ox.ac.uk
|
| URL |
http://www.imm.ox.ac.uk/wimm-research/molhaem/doug-higgs
|
| 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 |
|
| Relations |
| Reanalyzed by |
GSE80797 |
| SRA |
SRX040567 |
| BioSample |
SAMN00205410 |
