|
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 |