|
| Status |
Public on Apr 28, 2023 |
| Title |
2515882_DOE16_22 |
| Sample type |
SRA |
| |
|
| Source name |
2515882_DOE16_22
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CD34
donor: #3
time: day 6_EP ctrl
|
| Treatment protocol |
NA
|
| Growth protocol |
Healthy donor CD34+ HSPCs were cultured at a density of 0.5-1.0x10e6/mL in X-VIVO 10 (Lonza, BEBP02-055Q) medium supplemented with 100 ng/µL recombinant human SCF (R&D systems, 255-SC/CF), 100 ng/µL recombinant human TPO (R&D systems, 288-TP/CF), and 100 ng/µL recombinant Flt-3 ligand (R&D systems, 308-FK/CF).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
One million cells from each treatment condition were collected and the RNA was extracted using a Qiagen RNeasy Plus Mini kit (# 74136).
Libraries were prepared using standard reagents from New England BioLabs for Illumina sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
RNA-seq
|
| Data processing |
Reads were mapped to hg19 using STAR --twopassMode Basic
Bam files were processed using https://github.com/BioinfoUNIBA/REDItools
gene expression was quantified using kallisto based on cDNA ensembl v94
Assembly: hg19
Supplementary files format and content: tpm
|
| |
|
| Submission date |
Apr 03, 2023 |
| Last update date |
Apr 28, 2023 |
| Contact name |
Jonanthan Yen |
| E-mail(s) |
thiyagarajibms@gmail.com
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Hematology
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE228821 |
Transcriptome-wide deamination analysis |
| GSE228822 |
Potent and uniform fetal hemoglobin induction via base editing |
|
| Relations |
| BioSample |
SAMN34062782 |
| SRA |
SRX19859702 |
