|
| Status |
Public on Aug 17, 2018 |
| Title |
human cord blood CD34+ sample1 m6A |
| Sample type |
SRA |
| |
|
| Source name |
human umbilical cord blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary umbilical cord blood CD34+ cells
rip antibody: EpiMark N6-Methyladenosine Enrichment Kit (NEB E1610S)
sample type: IP
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from freshly isolated human UCB CD34+ cells and chemically fragmented. m6A marked RNAs were isolated with a specific antibody.
RNA libraries were prepared for sequencing using Clontech/Nextera non-stranded protocol. Libraries were sequenced on two NextSeq flowcells in high-output mode with 76 base single-end reads.
|
| |
|
| 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 human genome hg19 from UCSC using Tophat 2.1.1 with --no-coverage-search.
Genome_build: hg19
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 |
GPL18573 |
| Series (2) |
| GSE107954 |
m6A-seq mapping of human umbilical cord blood hematopoietic stem/progenitor cells |
| GSE107957 |
Hematopoietic stem cell expansion through suppression of YTHDF2-mediated m6A-marked mRNA decay |
|
| Relations |
| BioSample |
SAMN08163118 |
| SRA |
SRX3463148 |
