|
| Status |
Public on Nov 11, 2013 |
| Title |
RNA-seq of PolyA minus from Mouse Ter119+ erythroid cells |
| Sample type |
SRA |
| |
|
| Source name |
RNA-seq of PolyA minus from Mouse Ter119+ erythroid cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57bl\6
rna subtype: PolyAMinus RNA
cell type: Ter119+ erythroid cells
|
| Growth 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 |
RNA was isolated with Tri-Reagent (Sigma). The RNA quality was assessed using Agilent Bioanalyser. Only RNA with overall RIN score >9 was used for further procedures. Subsequently, RNA was treated with DNAseI (DNA-free, Ambion) according to the manufacturer’s protocol kit according to the protocol. Good quality and DNA-free RNA was subjected to polyA fractionation using PolyA selection kit (Promega) using the standard kit protocol. The RNA fraction was precipitated overnight and resuspended with water. The quality of obtained RNA samples was assessed using PicoChip (Agilent). A Paired sequencing library was generated using the standard Illumina prtocol.
For RNA-Seq libraries, total RNA was split into poly(A)+ and poly(A)- RNA using the PolyATract mRNA isolation system (Promega). Poly(A)- RNA libraries were generated using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre), after depletion of ribosomal transcripts with RiboMi- nus Eukaryote Kit for RNA sequencing (Invitrogen and sequenced on Illumina GA-IIx.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Reads were mapped to the mm9 mouse genome build using TopHat 1.1.4b
Read coverage was calculated genome-wide to produce a UCSC Wig file
Genome_build: mm9
Supplementary_files_format_and_content: wig file of read densities from tophat coverage output.
|
| |
|
| Submission date |
Aug 01, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jim Hughes |
| E-mail(s) |
jim.hughes@imm.ox.ac.uk
|
| Phone |
1865222113
|
| Organization name |
University of Oxford
|
| Department |
MHU
|
| Lab |
Genome Biology Group
|
| Street address |
Weatherall Institute Of Molecular Me
|
| City |
oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE49456 |
Transcriptome analysis of Mouse Ter119+ erythroid cells [PolyA-] |
| GSE49460 |
Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs |
|
| Relations |
| BioSample |
SAMN02299335 |
| SRA |
SRX330846 |
