|
Status |
Public on Aug 17, 2018 |
Title |
human cord blood CD34+ sample2 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 |
SAMN08163116 |
SRA |
SRX3463150 |