|
| Status |
Public on Aug 17, 2018 |
| Title |
ST-HSC m6A 1 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Wild type
cell type: ST-HSC
rip antibody: ANTI-m6A rabbit polyclonal antibody from Synaptic Systems (catalog # 202003)
sample type: IP
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from sorted 100K LT-, ST-HSCs and MPPs and chemically fragmented. m6A marked RNAs were isolated with specific antibody.
RNA libraries were prepared for sequencing using Clontech/Nextera non-stranded protocol. Libraries were sequenced on two lanes of a NextSeq 500 in high output mode to length 51, single-end.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Fastq files were generated with bcl2fastq2 (2.18.0.12).
Reads were aligned to the mouse genome mm10 from UCSC using tophat 2.1.1 with -T (transcriptome only alignment, report in genomic coordinates) and a transcriptome of refseq genes (refgene) from UCSC mm10.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files normalized by reads per million mapped reads from tophat transcriptome alignment.
|
| |
|
| Submission date |
Dec 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Madelaine Gogol |
| Organization name |
Stowers Institute
|
| Department |
Computational Biology Core
|
| Street address |
1000 E. 50th Street
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE107955 |
m6A-seq mapping of mouse hematopoietic stem/progenitor cells |
| GSE107957 |
Hematopoietic stem cell expansion through suppression of YTHDF2-mediated m6A-marked mRNA decay |
|
| Relations |
| BioSample |
SAMN08163108 |
| SRA |
SRX3463140 |
