Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Nfix

Cell type

Cell type Class
Neural
Cell type
Cerebellum neural progenitors
NA
NA

Attributes by original data submitter

Sample

source_name
Cerebellum neural progenitor cells
cell type
Cerebellum granule neuron progenitor cells
age
Postnatal Day 7
strain
CD1
chip antibody
NfiX (Sigma Aldrich, SAB1401263)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarifed from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were constructed using the standard protocol for the NEBNext Ultra II DNA Library Prep kit from Illumina (Part#E6240). Briefly, DNA was end-repaired and the blunt, phosphorylated ends were then treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adaptors which have a single 'T' base overhang at the 3' end. AMPure XP beads were used for size selection of the dA-tailed DNA and then the DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~275bp were purified using the AMPure XP beads. Libraries were sequenced on the Illumina HiSeq2000 according to the manufacturer's instructions. Paired-end sequencing was not used.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
23437417
Reads aligned (%)
74.6
Duplicates removed (%)
14.2
Number of peaks
6243 (qval < 1E-05)

mm9

Number of total reads
23437417
Reads aligned (%)
74.5
Duplicates removed (%)
14.4
Number of peaks
6217 (qval < 1E-05)

Base call quality data from DBCLS SRA