Antigen

Antigen Class

Unclassified

Antigen

Unclassified

Cell type

Cell type Class

Lung

Cell type

Alveolar Epithelial Cells

MeSH Description

Large flat epithelial cells that line the PULMONARY ALVEOLI and are involved in PULMONARY GAS EXCHANGE.

Sample

source_name

Alveolar epithelial cells

tissue

lung

cell type

Alveolar epithelial cells

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Chomatin of freshly isolated AT2 cells was prepared as previously described (Marconett et al., PLoS Genetics, 2013). INPUT DNA was collected after sonication and supernatant collection but before IP stage. FAIRE was performed on supernanant removed after ChIP immunoprecipiation. ChIPseq libraries were made by the USC Epigenome Center. The NEB Ultra Kit was used for library construction according to manufacturer's reccomendations. Adapter sequences were obtained from BioScientific. Barcodes were attached. Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1. Sample underwent Single End 50 cycling. Libraries were plated using the Illumina cBot and run on the Hi-Seq 2000 according to manufacturer’s instructions using HSCS v 1.5.15.1. Sample underwent Single End 50 cycling.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

hg38

Number of total reads

143424035

Reads aligned (%)

73.2

Duplicates removed (%)

19.3

Number of peaks

1797 (qval < 1E-05)

hg19

Number of total reads

143424035

Reads aligned (%)

72.7

Duplicates removed (%)

20.1

Number of peaks

1642 (qval < 1E-05)