|
| Status |
Public on Jul 26, 2020 |
| Title |
WT undiff rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
erythroid progenitor cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: umbilical cord derived erythroid progenitor cells
cell line: HUDEP-2
genotype/variation: WT
Stage: undifferentiated
|
| Treatment protocol |
WT-HUDEP-2 and HBBko cells were cultured and differentiated in triplicates.
|
| Growth protocol |
WT-HUDEP-2 and HBBko cells were cultured and differentiated in triplicates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested and RNA was extracted using the RNeasy Mini kit 74104, Rnase-Free DnaseI Kit 79254 and Qiashredder 79654. RNA concentrations were quantified using Qubit™ RNA BR Assay (ThermoFisher) and 500ng were used for library preparation.
RNA-seq library was made using Illumina TruSeq RNA Library Prep Kit v2 and following manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Paired-end 150bp reads were generated on a HiSeq4000.
Reads for all eighteen samples (three replicates of HBBko and three WT HUDEP-2 samples at three time-points) were quantified using kallisto (Bray et al., 2016) and the hg38 index to assign reads to transcripts.
Differential analysis of transcript abundance and consolidation of individual transcripts to gene-level abundance was calculated using sleuth (Pimentel et al., 2017)
Genome_build: hg38
Supplementary_files_format_and_content: .txt format of log2 fold change comparing WT and HBBko at different time points
|
| |
|
| Submission date |
Jul 03, 2020 |
| Last update date |
Jul 26, 2020 |
| Contact name |
Jacob Corn Lab |
| Organization name |
ETH Zurich
|
| Street address |
Otto-Stern-Weg 7
|
| City |
ZURICH |
| State/province |
zURICH |
| ZIP/Postal code |
8093 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE153764 |
ATF4 regulates MYB to increase g-globin in response to loss of β-globin [RNA-seq] |
| GSE153768 |
ATF4 regulates MYB to increase g-globin in response to loss of β-globin |
|
| Relations |
| BioSample |
SAMN15438747 |
| SRA |
SRX8664897 |
