|
Status |
Public on May 29, 2018 |
Title |
intermediate-term hematopoietic stem cell rep 1 |
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_1
|
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 |
SAMN05972099 |
SRA |
SRX2323931 |