|
| Status |
Public on Mar 01, 2023 |
| Title |
BMI g1_CD34+ cells, Donor #3911 |
| Sample type |
SRA |
| |
|
| Source name |
CD34+ HSPCs, Donor #3911
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CD34+ HSPCs, Donor #3911
cell type: adult erythroid cells
genotype: Cas9 BMI1 g#1 RNP
treatment: Erythorid differentiation
time: Day 8 Diff
|
| Treatment protocol |
For induction of erythroid differentiation, HUDEP2 cells were grown in IMDM supplemented with 50 ng/ml hSCF, 3 IU/ml erythropoietin, 2.5% fetal bovine serum, 250 µg/ml holo-transferrin, 10 ng/ml heparin, 10 µg/ml insulin, 1 µg/ml doxycycline, and 1% pen-step for the first 3 days then followed by another 3 or 4 days of culture with fresh media of the same recipe without hSCF
|
| Growth protocol |
cells were grown in StemSpanTM serum-free medium (SFEM) supplemented with 50 ng/ml human stem cell factor (hSCF), 10 µM dexamethasone, 1 µg/ml doxycycline, 3 IU/ml erythropoietin, and 1% pen-strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared from 0.5-2 million HUDEP2 cells (day 6 or 7 of differentiation) or primary progenies of CD34+ HSPCs (day 8 or 13 of culture) using RNeasy® Mini Kit following the manufacturer's instruction
Libraries were prepared using TruSeq Stranded Total RNA kit following the manufacturer's instruction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Sequencing reads were processed using the ENCODE3 long RNA-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/)
Assembly: hg38
Supplementary files format and content: TSV files include RPKM and expected count values for each Sample
|
| |
|
| Submission date |
Nov 17, 2022 |
| Last update date |
Mar 01, 2023 |
| Contact name |
KUNHUA QIN |
| E-mail(s) |
qink@chop.edu, kunhua.qin@gmail.com
|
| Phone |
2153603146
|
| Organization name |
Children's Hospital of Philadelphia
|
| Lab |
Gerd A Blobel
|
| Street address |
3615 Civic Center Blvd, 315H
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE218232 |
Molecular Dissection of Polycomb Group Protein-mediated Fetal Hemoglobin Repression [RNA-seq] |
| GSE218233 |
Molecular Dissection of Polycomb Group Protein-mediated Fetal Hemoglobin Repression |
|
| Relations |
| BioSample |
SAMN31774975 |
| SRA |
SRX18298019 |
