|
| Status |
Public on Aug 25, 2020 |
| Title |
human K562 rescued ETO2 full length without TAF110 (D1)-2 |
| Sample type |
SRA |
| |
|
| Source name |
human K562 cells
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: ETO2+/+ without domain TAF110
|
| Growth protocol |
Human K562 cells were cultured in RPMI 1640 medium containing 10 % fetal bovine serum. Control C57BL/6J and Eto2 KO mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Fetal livers isolated from E14.5 control and knockout mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy Mini Kit (human K562 cells) and PicoPure RNA isolation kit (fetal liver cells)
RNA sequencing libraries were generating from 1 ug (K562 cells and total fetal liver cells) or 10 ng (FACS sorted fetal liver cells) of RNA using Illumina TruSeq mRNA Library Preparation kit following manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 and mm10 whole genome using hisat2 v2.1.0 with default parameters respectively. Multimappnig reads were filtered using samtoools 1.9, uniquely aligned reads were then mapped to gene features using Subread featureCounts v1.6.4
Differential expression between groups of samples was tested using R version 3.5.1 with DESeq2 1.22.1
Genome_build: hg38 , mm10
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample
|
| |
|
| Submission date |
Dec 17, 2019 |
| Last update date |
Aug 25, 2020 |
| Contact name |
Xiang Guo |
| E-mail(s) |
xguoellen@gmail.com
|
| Phone |
2402052897
|
| Organization name |
NIH
|
| Department |
NIDDK
|
| Lab |
LCDB
|
| Street address |
50 south drive, blg50
|
| City |
bethesda |
| State/province |
MD |
| ZIP/Postal code |
20814 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE142226 |
Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin accessibility and looping (RNA-Seq) |
| GSE142228 |
Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin accessibility and looping |
|
| Relations |
| BioSample |
SAMN13616063 |
| SRA |
SRX7398229 |
