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Sample GSM2884214 Query DataSets for GSM2884214
Status Public on Aug 17, 2018
Title human UCB CD34+ wild type 3
Sample type SRA
 
Source name human UCB CD34+ HSPCs
Organism Homo sapiens
Characteristics cell type: UCB CD34+ HSPCs
genotype: wild type
Growth protocol human UCB cells were cultured with StemSpan medium (StemCell Technologies) supplemented with growth factors interleukin 6(IL-6; 20ng/ml, Peprotech), stem cell factor (SCF; 100ng/ml, Peprotech), Flt3 ligand (FLT3-L; 100ng/ml, Peprotech) and thrombopoietin (TPO; 20ng/ml, Peprotech).
Extracted molecule total RNA
Extraction protocol CD34+ GFP+ cells were sorted into Trizol.
RNA libraries were prepared for sequencing using Clontech/Nextera non-stranded protocol. Libraries were sequenced on a NextSeq in high output mode with 76 base single-end reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Fastq files were generated with bcl2fastq2 (2.18.0.12).
Reads were aligned to the human genome hg38 from UCSC using Tophat 2.0.13 with default parameters. Annotations were from Ensembl 87. Counts of reads on genes were from HTSeq-count with -m intersection-nonempty.
Reads were also aligned to ERCC control sequences and counts tabulated. A scaling factor was calculated based on the median of the ERCC counts for each sample and used for normalization.
Differentially expressed genes were found using the edgeR package (3.18.1) in R (3.4.1). Differentially expressed genes were required to have a BH-adjusted p-value < .05 and a 2-fold change in expression.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file with counts normalized using median ERCC counts for each sample. IDs are ensembl gene ids from Ensembl 87.
 
Submission date Dec 12, 2017
Last update date May 15, 2019
Contact name Madelaine Gogol
Organization name Stowers Institute
Department Computational Biology Core
Street address 1000 E. 50th Street
City Kansas City
State/province MO
ZIP/Postal code 64110
Country USA
 
Platform ID GPL18573
Series (2)
GSE107956 Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and YTHDF2 KD human umbilical cord blood CD34+ cell Transcriptomes
GSE107957 Hematopoietic stem cell expansion through suppression of YTHDF2-mediated m6A-marked mRNA decay
Relations
BioSample SAMN08163099
SRA SRX3463208

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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