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Status |
Public on Mar 21, 2022 |
Title |
CD34+ differentiation Day8-KD1, RNA-seq |
Sample type |
SRA |
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Source name |
human CD34+ cells
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Organism |
Homo sapiens |
Characteristics |
genotype: KD time: differentiation Day8 cell type: CD34+ cells
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Growth protocol |
Primary CD34+ umbilical cord cells (Lonza, cat. 2C-101) were cultured as described (Wilber et al., 2010). HUDEP2 cells was cultured in SFEM medium and induced in DMEM medium as described (Vinjamur and Bauer, 2018). K562 cells were cultured in RPMI 1640 medium containing 10 % fetal bovine serum.Hemogen WT and KO mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Fetal livers isolated from E14.5 control and knockout mice.
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated using RNeasy Plus Micro Kit RNA sequencing libraries were generating from 100ng-1 ug of RNA using Illumina TruSeq Stranded mRNA Library Preparation kit (20020594) following manufacturer’s protocol.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Data processing |
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 and mm10 whole genome using hisat2 v2.1.0 with default parameters respectively. Multimappnig reads were filtered using samtoools 1.9, uniquely aligned reads were then mapped to gene features using Subread featureCounts v1.6.4 Differential expression between groups of samples was tested using R version 3.5.1 with DESeq2 1.20.0 Genome_build: hg38 , mm10 Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample ...
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Submission date |
Sep 21, 2021 |
Last update date |
Mar 21, 2022 |
Contact name |
Xiang Guo |
E-mail(s) |
xguoellen@gmail.com
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Phone |
2402052897
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Organization name |
NIH
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Department |
NIDDK
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Lab |
LCDB
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Street address |
50 south drive, blg50
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City |
bethesda |
State/province |
MD |
ZIP/Postal code |
20814 |
Country |
USA |
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Platform ID |
GPL20301 |
Series (2) |
GSE184558 |
Hemogen /BRG1 cooperativity modulates promoter and enhancer activation during erythropoiesis [RNA-seq] |
GSE184606 |
Hemogen /BRG1 cooperativity modulates promoter and enhancer activation during erythropoiesis |
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Relations |
BioSample |
SAMN21541035 |
SRA |
SRX12286520 |
Supplementary file |
Size |
Download |
File type/resource |
GSM5592541_CD34D8KDRep1.cutadapt.bam.featurecounts.s2.txt.gz |
4.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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