Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
Hypothalamus
MeSH Description
Ventral part of the DIENCEPHALON extending from the region of the OPTIC CHIASM to the caudal border of the MAMMILLARY BODIES and forming the inferior and lateral walls of the THIRD VENTRICLE.

Attributes by original data submitter

Sample

source_name
Hypothalumus
background strain
B6/FVB
genotype
Sim1 +/-
sgrna
Promoter
Sex
female
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA-seq - RNeasy Mini Kit (Qiagen), ChIP-seq - Fresh tissue was homogenized using a hand-held dounce homogenizer, cross-linked in Phosphate buffer saline (PBS) containing 1% formaldehyde for 10 minutes, quenched with 125mM Glycine for 5 minutes and washed three times with PBS. Cross-linked tissue pellet was processed further for chromatin immuoprecipitation using the 'Low cell Chip Kit' (Diagenode; catalog number C01010072) following the manufacturer's protocol. An S. pyogenes Cas9 polyclonal antibody (Diagenode; catalog number C15310258) and an S.aureus Cas9 monoclonal antibody (Diagenode; catalog number C15200230) were used for the pull down. RNA-seq - Nugen Ovations and Nextera XT, ChIP-seq - Rubicon Genomics ThruPLEX DNA-seq kit

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
3406272
Reads aligned (%)
94.1
Duplicates removed (%)
28.8
Number of peaks
163 (qval < 1E-05)

mm9

Number of total reads
3406272
Reads aligned (%)
93.6
Duplicates removed (%)
29.4
Number of peaks
172 (qval < 1E-05)

Base call quality data from DBCLS SRA