|
| Status |
Public on Nov 15, 2017 |
| Title |
P12_m6A_WT_IP rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
testes
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: P12
strain: C57BL/6
genotype: Wild Type
fraction: RNA fraction of m6A IP
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TriZol.
Total RNA was subjected to two rounds of poly(A) RNA selection, using the MicroPoly(A) Purist kit, (Life Technologies) according to the manufacturer's protocol. RNA was fragmented by incubating for 45 second with pre-warmed Zinc chloride buffer (10 mM ZnCl2, 10mM Tris-HCl, ph 7.0), to fragment the RNA to ~100 nucleotide long fragments. The reaction was stopped with 0.2M EDTA and immediately placed on ice. A fraction of teh RNA was subjected to immunoprecipitation with a anti-m6A antibody. A strand specific protocol was used to generate cDNA from input and anti-m6A immunoprecipitated samples.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Libraries were separated by barcode, matching reads were collapsed and barcodes removed. Single-end RNA-Seq reads were mapped to the mouse genome (mm9 assembly) using STAR.
Reads for each transcript were extracted using HTSeq. Differential gene expression was calculated with DESeq2. To determine sites of m6A modification RPKM and winscore of each 100bp sliding window along the transcriptome is calculated using in house generated script.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include fold change and p-value calculated by DESeq2 (DGE_P12 and DGE_P14). tab-delimited text file (m6A_peaks_winscore.txt) include windscore for 100bp windows enriched after m6A immuprecipitation.
|
| |
|
| Submission date |
Jan 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Pedro J Batista |
| E-mail(s) |
pedro.batista@nih.gov
|
| Phone |
3014356294
|
| Organization name |
National Institutes of Health
|
| Department |
National Cancer Institute
|
| Lab |
Cell Biology
|
| Street address |
37 Convent Street Bldg 37
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE93566 |
Regulation of the transition from mitosis to meiosis by the conserved RNA-helicase YTHDC2/BGCN [RNA-Seq] |
| GSE93567 |
Regulation of the transition from mitosis to meiosis by the conserved RNA-helicase YTHDC2/BGCN |
|
| Relations |
| BioSample |
SAMN06220576 |
| SRA |
SRX2487000 |
