Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
Cerebellum
MeSH Description
The part of brain that lies behind the BRAIN STEM in the posterior base of skull (CRANIAL FOSSA, POSTERIOR). It is also known as the "little brain" with convolutions similar to those of CEREBRAL CORTEX, inner white matter, and deep cerebellar nuclei. Its function is to coordinate voluntary movements, maintain balance, and learn motor skills.

Attributes by original data submitter

Sample

source_name
mouse 4 month cerebellum, Mll4 WT, input
strain/background
C57BL/6
genotype/variation
Mll4 WT
tissue
cerebellum
age
4 months
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP assays were performed as a modification of the previously described methods (Dhar et al., 2016; Dhar et al., 2012). In brief, cerebellar (4-month-old) tissues were isolated. DNA was purified from chromatin immunoprecipitates for MLL4 or IgG using the phenol/chloroform extraction. IgG was used as a negative control for ChIP. Then, DNA was amplified by quantitative PCR and normalized to input. To compare H3K4me1, H3K27ac, and H3K4me3 levels between Mll4f/f and Mll4 BSKO cerebellum, ChIP with reference exogenous genome (ChIP-Rx) was carried out as previously described (Li et al., 2016; Orlando et al., 2014). In brief, two biological replicates for Mll4f/f and Mll4 BSKO cerebellum were used for ChIP-Rx experiments. Drosophila melanogaster chromatin and Drosophila-specific H2Av antibody were added to each ChIP assay as a minor fraction. The following components for ChIP-Rx were purchased from Active Motif: the spike-in chromatin (53083), Drosophila-specific H2Av antibody (61686), spike-in ChIP positive control primer set (71037), and negative control primer set (71028). The immunoprecipitated DNAs were sequenced by Next-Generation Sequencing (NGS) (UCI GHTF). ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
11808369
Reads aligned (%)
93.9
Duplicates removed (%)
38.9
Number of peaks
284 (qval < 1E-05)

mm9

Number of total reads
11808369
Reads aligned (%)
93.2
Duplicates removed (%)
39.0
Number of peaks
292 (qval < 1E-05)

Base call quality data from DBCLS SRA