|
| Status |
Public on May 29, 2018 |
| Title |
intermediate-term hematopoietic stem cell rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Hematopoietic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 8-12 weeks old
cell type: intermediate-term hematopoietic stem cell
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from sorted HSPCs using the QIAamp DNA blood mini kit (QIAGEN).
Libraries were constructed using the Pico Methyl-Seq™ library prep kit (Zymo Research), and each library was subjected to 50 bp single-end sequencing on a single lane of a HiSeq 2500 device (Illumina).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
cd49bhi_2
|
| Data processing |
Base-calling and bcl to fastq generation was done with CASAVA 1.8.2 from illumina.
Reads were trimmed with trim_galore (0.4.0) with default options. Adapter sequence AGATCGGAAGAGC was trimmed.
Ran bismark (0.14.3) with option --non_directional. Ran bismark methylation extractor with --report --ignore 10 --ignore_3prime 1 --bedGraph --counts --buffer_size 10G --cytosine_report.
Used R (3.2.2) with bsseq package (1.6.0) to smooth methylation data and find differentially methylated regions.
bigWig tracks were generated in R 3.2.2 by dividing by the total number of alignments and multiplying by 1e6 (rpm).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig tracks with rpm-normalized coverages.
|
| |
|
| Submission date |
Nov 03, 2016 |
| 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 |
GPL17021 |
| Series (2) |
| GSE89490 |
WGBS assessment of global methylation alterations in hematopoietic stem and progenitor cells [methyl-seq] |
| GSE89492 |
A retinoid-dependent and methylation-sensitive enhancer in Hoxb cluster maintains haematopoietic stem cells and prevents leukaemogenesis |
|
| Relations |
| BioSample |
SAMN05972098 |
| SRA |
SRX2323932 |
