Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Neural
Cell type
Intermediate pituitary
NA
NA

Attributes by original data submitter

Sample

source_name
ATACseq in Tpit Knockout intermediate pituitary
strain background
mixed background 129sv X Balb/C
genotype/variation
Pax7+/-;Tpit-/-
tissue/cell type
Neuro-intermediate pituitary

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Mouse pituitary intermediate or anterior lobes were dissected pituitaries were separated into intermediate and anterior lobes and kept during the dissections in 300µl of dissection buffer (DMEM, 10% FBS, HEPES 10mM and DNase 100 U/ml). Anterior lobes were cut in pieces using a scalpel to facilitate tissue dissociation and digested at 37°C using 5mg/ml Trypsin for 10 minutes. We then added 2mM EDTA and incubated 5 minutes more. 50 000 cells were washed in PBS and incubated on ice for 30 minute in a hypotonic cell lysis buffer (0.1% w/v sodium citrate tribasic dehydrate and 0.1% v/v Triton X100) and centrifuged (5 minutes at 2000g at 4°C). Cells were then incubated 30 minutes on ice in cell lysis buffer (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% v/v IGEPAL CA-630). After centrifugation, the nuclei pellets were resuspended in transposase Master Mix (1.25 µl 10x TD buffer, 5 µl H2O and 6.5 µl of Tn5: Illumina Nextera Kit; FC-121-1031) and incubated for 30 minutes at 37°C. Samples were purified using the DCC purification columns (Zymo). The eluted DNA was barcoded for multiplexing of samples using Nextera barcodes and PCR-enriched using the Phusion kit. Libraries were recovered with GeneRead Purification columns. Samples were then evaluated by qPCR to test enrichments and sequenced on Illumina Hiseq 2500 with 50bp or 125bp paired-end reads according to Illumina's recommendation.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
61087617
Reads aligned (%)
60.0
Duplicates removed (%)
7.8
Number of peaks
22630 (qval < 1E-05)

mm9

Number of total reads
61087617
Reads aligned (%)
59.9
Duplicates removed (%)
7.8
Number of peaks
22614 (qval < 1E-05)

Base call quality data from DBCLS SRA