|
| Status |
Public on Sep 11, 2019 |
| Title |
CFUE_RNA_3 |
| Sample type |
SRA |
| |
|
| Source name |
Cultured human umbilical cord derived CD34+ human hematopoietic stem and progenitor cells (HSPCs)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Cultured human umbilical cord derived CD34+ human hematopoietic stem and progenitor cells (HSPCs)
Stage: CFUE
surface markers to isolate cells by facs-based methods: IL-3R−CD34−CD36+
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Progenitor cells at each stage were sorted by a combination of cell surface markers for IL-3R, CD34 and CD36. Total RNAs were extracted by RNeasy Plus Mini Kit (Cat# 74134, QIAGEN).
Illumina TruSeq RNA Sample Prep Kit (Part # 15008136) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava 1.8.2 software was used for basecalling.
FASTQ format sequencing reads were aligned to the hg19 genome using TopHat Version 1.3.3 software with default parameters
Reads in every gene were counted using the Rsubread featureCounts function. Genes with less than 3 samples with >1 read counts/million (cpm) were called not expressed and were not used in further analysis. The read count data was normalized using the TMM method. Differentially expressed genes were identified using the edgeR exact test.
Genome_build: hg19
Supplementary_files_format_and_content: Counts per gene and RPKM Reads per KB per Million Reads
|
| |
|
| Submission date |
Mar 13, 2019 |
| Last update date |
Sep 11, 2019 |
| Contact name |
Vince Schulz |
| E-mail(s) |
[email protected]
|
| Organization name |
Yale University
|
| Department |
Department of Pediatrics
|
| Lab |
Gallagher
|
| Street address |
333 Cedar St. LMP 4085
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06519 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE128268 |
A Unique Epigenomic Landscape Defines Human Erythropoiesis (RNA-seq) |
| GSE128269 |
A Unique Epigenomic Landscape Defines Human Erythropoiesis |
|
| Relations |
| BioSample |
SAMN11119926 |
| SRA |
SRX5517000 |
