|
| Status |
Public on Sep 11, 2019 |
| Title |
CFUE_ERRBS_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 |
genomic DNA |
| Extraction protocol |
Progenitor cells at each stage were sorted by a combination of cell surface markers for IL-3R, CD34 and CD36. Erythroblasts at each stage of terminal erythroid differentiation were sorted by a combination of cell surface markers for glycophorin A, band 3, and α4 integrin. Genomic DNA was isolated using a Qiagen Gentra Puregene kit.
Enhanced Reduced Representation Bisulfite sequencing (ERRBS) was performed at the Weill Cornell Genomics Core.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Fastq format reads were trimmed using Trim Galore v0.4.0 in rrbs mode
Trimmed reads were mapped to the hg19 genome using Bismark_v0.14.3.
Quantitation of methylation was performed using bismark_methylation_extractor.
Differential methylation was identified using methylKit v1.2.4
Genome_build: hg19
Supplementary_files_format_and_content: Text file containing cytosine methylation positions and quantitation.
|
| |
|
| Submission date |
Mar 13, 2019 |
| Last update date |
Sep 12, 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 |
GPL11154 |
| Series (2) |
| GSE128267 |
A Unique Epigenomic Landscape Defines Human Erythropoiesis (ERRBS) |
| GSE128269 |
A Unique Epigenomic Landscape Defines Human Erythropoiesis |
|
| Relations |
| BioSample |
SAMN11119947 |
| SRA |
SRX5516975 |
