|
| Status |
Public on Apr 25, 2012 |
| Title |
Mouse_Liver_IP |
| Sample type |
SRA |
| |
|
| Source name |
Mouse liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Normal mouse liver
antibody: anti-m6A
vendor: Synaptic Systems
catalog#: 202-003
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was purified from whole mouse liver using 5PRIME PerfectPure RNA Cultured Cell kit (cat#2302340). PolyA RNA was selected by one round of Sigma GenElute mRNA Miniprep Kit (cat#MRN70-1KT). Total RNA of normal human brain was purchased from Biochain, CA, USA. RNA was fragmented chemically to ~100 nt long fragments and subjected to IP using anti-m6A antibodies. 1st strand cDNA was synthesized using Illumina random primers and Invitrogen SuperScript II Reverse Transcriptase (Cat# 18044-014) then 2strand cDNA was synthesized by Illumina's mRNA Sample preparation Kit (Part# 1004814). DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation ~200 bp DNA fragments (insert plus adaptor and PCR primer sequences) were isolated from 2% agarose gel. Purified DNA fragments were PCR amplified with Illumina primers for 15 cycles and 10pM DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Supplementary_files_format_and_content: Supplementary data human brain' and 'Supplementary data mouse liver' files are provided in .txt format. They contain a dataset of all identified m6A peaks in normal human brain and nornal mouse liver, respectively. Corresponding legends are: id – KnownCanonical identification; chr – chromosome; txStart – transcription start position on chromosome; txEnd – Transcription end position on chromosome; strand - +/- chromosome strand; geneSymbol – official symbol of gene; desc – description; Factor_iscoding– either coding or noncoding, depending on the annotation of the gene in the UCSC table; Meanexpquant – expression quantile of the gene based on reads in input experiment; Peaksnum – number of peaks identified in gene; Peakspos – position of peaks relative to beginning of transcript (after removing introns); Peaksexonnum – ordinal number of exons in which the peaks were identified; Peaksexlengths – lengths of the exons in which the peaks were found; Peakscores – the peakscore of the identified peaks; Annotpeakpos – segment along the gene in which the peaks.
|
| |
|
| Submission date |
Apr 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Sharon Moshitch-Moshkovitz |
| E-mail(s) |
sharon.moshkovitz@sheba.health.gov.il
|
| Organization name |
Sheba Medical Center
|
| Department |
Cancer Research Center
|
| Street address |
Laboratory wing
|
| City |
Tel-Hashomer |
| ZIP/Postal code |
52621 |
| Country |
Israel |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE37004 |
m6A mapping in mouse RNA (mouse liver and human brain) |
| GSE37005 |
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq |
|
| Relations |
| Reanalyzed by |
GSE80797 |
| SRA |
SRX136680 |
| BioSample |
SAMN00849872 |
