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Status |
Public on Jul 26, 2020 |
Title |
WT undiff rep 1 |
Sample type |
SRA |
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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.
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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
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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 |
SAMN15438749 |
SRA |
SRX8664895 |