|
| Status |
Public on Jul 15, 2016 |
| Title |
Marginal-H3K4me1-R3 |
| Sample type |
SRA |
| |
|
| Source name |
Marginal Zone B cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6JNimr
tissue: Spleen
age: 7-9 weeks
Sex: Female
immunization: None
flow strategy: B220+AA4.1-Cd23-IgMhigh
chip antibody: H3K4me1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Female mouse C57BL/6 B cell populations were sorted on BD FACSAriaII, BD Influx or Beckman Coulter MoFlo XDP cell sorters; collected cells were centrifuged and cross-linked with 1% formaldehyde and sonicated to shear the chromatin to ~500bp fragments; DNA was isolated with antibodies and purified by phenol-chloroform extraction
Libraries were prepared with Illumina's DNA Sample prep kit according to the manufacturer's instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Marginal-H3K4me1.narrowpeak
|
| Data processing |
fastq files were created with CASAVA 1.8.1
ChIP-seq reads were trimmed to a common length (40bp) and aligned to the mm10 genome assembly using BWA version 0.7.8 with the following configurations: -l 28 -k 2 -n 4
Aligned input samples were pooled and peaks were called at a p value threshold of 0.005 using macs2 version 2.0.10 with default parameters.
An optimal peak set was generated for each cell type using the ENCODE Irreproducibility Discovery Rate (IDR) pipeline using a pooled consistency threshold of q < 0.005.
Genome_build: mm10
Supplementary_files_format_and_content: ENCODE narrowPeak
|
| |
|
| Submission date |
Aug 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jethro Johnson |
| E-mail(s) |
jethro.johnson@jax.org
|
| Organization name |
Jackson Laboratory for Genomic Medicine
|
| Lab |
Weinstock Lab
|
| Street address |
10 Discovery Drive
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06032 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE72017 |
Long non-coding RNAs in B cells (ChIP-Seq) |
| GSE72019 |
Long non-coding RNAs in B cells |
|
| Relations |
| BioSample |
SAMN03983937 |
| SRA |
SRX1143940 |
