|
| Status |
Public on Jan 30, 2012 |
| Title |
non-polyA_RNASeq |
| Sample type |
SRA |
| |
|
| Source name |
sorted erythroid cells (Ter119+)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: erythroid cells
strain: C57BL/6/CBA
|
| Treatment protocol |
Mouse primary erythroid cells were sorted from the spleens of acetylphenylhydrazine-treated mice based on the expression of Ter119 (Spivak et al., 1973; Vernimmen et al., 2009).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using Trizol reagent (Sigma) and DNaseI treated (Ambion). The total RNA quality was assessed using Agilent Bioanalyser. RNA with overall RIN score >9 was used for further procedures. poly(A)- fraction was separated from mRNA (or poly(A)+) using PolyA selection kit (Promega) according to the manufacturer's protocol with the modification of keeping the poly(A)- fraction. poly(A)- fraction was depleted of ribosomal transcripts by using RiboMinus Eukaryote Kit for RNA-sequencing (Invitrogen) according to the manufacturer's protocol followed by RNA purification on RiboMinus Concentration Module (Invitrogen). The quality of obtained RNA samples was assessed using PicoChip (Agilent). The library was prepared according to DGE Small RNA Sample Prep kit (Illumina). Size selection 100-350bp
Model- GAIIx Chemistry-SBS v4 cBot single generation kit with v4 flow cell SCS 2.8 RTA 1.8 Recipe v7.4
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
wild type
|
| Data processing |
The reads were aligned to the mm9 mouse genome build using bowtie (version 0.12.3) with indices on m2 (map twice to the genome). Before downstream analysis duplicate reads of the same chromosome and start position were collapsed to a single representative read to exclude overrepresented PCR products. The sam file was split into forward and reverse strand based on the sam biwise FLAG. All aligned reads starts were summed in sliding windows of 600 bp (increment of movement 60 bp) to create summary windows.
|
| |
|
| Submission date |
Mar 12, 2011 |
| Last update date |
Jun 11, 2013 |
| 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) |
| GSE27920 |
Transcriptiome of mouse erythroid cells (part2) poly(A)- |
| GSE27921 |
Intragenic enhancers act as alternative promoters |
|
| Relations |
| BioSample |
SAMN02196932 |
