|
| Status |
Public on Jan 01, 2020 |
| Title |
MLL total RNA RIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
293T cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
cell type: human embryonic kidney cells
cell line source gender: male
cell line source tissue: embryonic kidney
cell line source age: fetus
rip antibody: customized antibody recognizing the MLLC180(aa2829-2883) [PMID 17908926]
|
| Treatment protocol |
no treatment
|
| Growth protocol |
HEK293T cell line was cultured in Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 10% fetal bovine serum and 1% 100×Pen Strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
using RIPA lysis buffer to extract RNAs
standard illumina protocols
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
clean reads were obtained by removing reads containing adapter and filtering reads containg low quality base
Index of the hg38 was built using Bowtie2 and single-end reads were aligned to the reference genome by Hisat
FPKM and TPM of each gene and sRNA was calculated based on the length of the gene and reads count mapped to the gene by using RSEM
Genome_build: ftp://ftp.ensembl.org/pub/release-92/fasta/homo_sapiens/dna/
Supplementary_files_format_and_content: tab-delimited excel files include FPKM or TPM values for each sample
|
| |
|
| Submission date |
Jun 15, 2018 |
| Last update date |
Jan 02, 2020 |
| Contact name |
rui heng wang |
| E-mail(s) |
chishiba0520@163.com
|
| Phone |
1858057173
|
| Organization name |
shanghaijiaotong university
|
| Department |
insitute of hematology
|
| Lab |
lh708
|
| Street address |
ruijin two street
|
| City |
shanghai |
| State/province |
shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN09429328 |
| SRA |
SRX4220729 |
