|
Status |
Public on Apr 28, 2023 |
Title |
2515874_DOE16_14 |
Sample type |
SRA |
|
|
Source name |
2515874_DOE16_14
|
Organism |
Homo sapiens |
Characteristics |
cell line: CD34 donor: #1 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 |
SAMN34062790 |
SRA |
SRX19859694 |