|
| Status |
Public on May 27, 2020 |
| Title |
THP-1 A5-KD 4.5hrs rep2 |
| Sample type |
SRA |
| |
|
| Source name |
THP-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP-1
genotype/variation: A5-KD
|
| Growth protocol |
The human acute leukemia cell lines THP1 were maintained in Roswell Park Memorial Institute 1640 medium (RPMI-1640) with 10% FBS, 100 IU ml−1 penicillin and 100μg ml−1 streptomycin.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
polyA RNA
Cells was labeled with 100μM 4sU (Sigma) for 1h and then washed twice with 1×PBS and incubated with standard medium supplemented with 10mM uridine (Sigma). Cell collected at indicated time points was extraction using TRIzol. NEBNext RNA Library Prep Kit (NEB, #E7760) was used for library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
slam_count.csv
|
| Data processing |
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole transcriptome using hisat v2.1.0 with default parameters
T>C conversion was calculated following slamdunk pipeline
Genome_build: hg38
Supplementary_files_format_and_content: .csv file was generated following slamdunk pipeline
|
| |
|
| Submission date |
Mar 12, 2020 |
| Last update date |
May 27, 2020 |
| Contact name |
Jiazhen Wang |
| E-mail(s) |
jiazhen_wang@hactcm.edu.cn
|
| Organization name |
Henan University of Chinese Medicine
|
| Street address |
156 Jinshui East Road
|
| City |
Zhengzhou |
| ZIP/Postal code |
450046 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE128575 |
Chromatin state maintains human myeloid leukemia by regulating m6A demethylase ALKBH5 expression |
| GSE146874 |
Chromatin state maintains human myeloid leukemia by regulating m6A demethylase ALKBH5 expression [Slam-seq] |
|
| Relations |
| BioSample |
SAMN14365333 |
| SRA |
SRX7900138 |
