|
| Status |
Public on Dec 31, 2020 |
| Title |
Clone-WT-3 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
HUDEP-2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HUDEP-2
cell type: erythroblast cells
tissue: Umbilical Cord blood derived
genotype: wild type
|
| Growth protocol |
Cells were expanded in StemSpan serum-free expansion medium (SFEM; Stem Cell Technologies) supplemented with 1 µM dexamethasone, 1 µg/mL doxycycline, 50 ng/mL human stem cell factor (SCF), 3 units/mL erythropoietin (EPO), and 1% penicillin–streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
HUDEP-2 cells' RNA was harvested using RLT reagent (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RNA.count.all.txt.gz
Clone_WT_3
|
| Data processing |
Illumina Casava software used for basecalling.
Sequenced reads were aligned and counted by RNA-seq pipeline(WARDEN) at https://www.stjude.cloud/tools.html
Briefly, paired-end reads were aligned to hg19 by STAR and counted by HTSEQ.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for each gene for each sample
|
| |
|
| Submission date |
May 30, 2019 |
| Last update date |
Dec 31, 2020 |
| Contact name |
Mitch Weiss |
| E-mail(s) |
mitch.weiss@stjude.org
|
| Phone |
9015953760
|
| Organization name |
st jude children's research hospital
|
| Department |
Hematology
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE115357 |
FBXO11-Mediated Proteolysis of BAHD1 Relieves PRC2-dependent Transcriptional Repression in Erythropoiesis |
|
| Relations |
| BioSample |
SAMN11891779 |
| SRA |
SRX5931573 |
