Antigen

Antigen Class

Bisulfite-Seq

Antigen

Bisulfite-Seq

Cell type

Cell type Class

Lung

Cell type

Lung

MeSH Description

Either of the pair of organs occupying the cavity of the thorax that effect the aeration of the blood.

Sample

source_name

Lung

biomaterial_provider

UCLA

strain

C57BL/6J

tissue

Lung

age

2mo

Sex

male

Sequenced DNA Library

library_strategy

Bisulfite-Seq

library_source

GENOMIC

library_selection

RANDOM

library_construction_protocol

(UCLA Data) For each sample 50-100 ng of purified genomic DNA was digested with 20 U of MspI (NEB, cat # R0106L) at 37°C o/n in the presence of RNase Cocktail Mix (Ambion, cat # AM2286). End-repair and dA-tailing was performed by the addition of Klenow Fragment 3'->5' exo- (NEB, cat # M0212L) in the presence of dATP, dGTP and d5mCTP (Fermentas). Adapter Ligation was performed by the addition of 0.3 µl of Illumina TruSeq methylated Adapters (Illumina, TruSeq Nano cat# FC-121-4001) and 2 µl of Illumina Ligation Mix 2 (Illumina, TruSeq Nano cat# FC-121-4001). Samples were pooled and purified using an equal volume of SPRI beads (Beckman Coulter, cat # B23318). Size-selection was performed using SPRI beads to enrich for fragments from 200 to 300 bp. Bisulfite treatment was performed using Epitect Bisulfite kit (QIAGEN, cat # 59104) according to manufacturer's protocol, except that two consecutive rounds of conversion are performed, for a total of 10 hr of incubation. Purified converted DNA was PCR amplified using MyTaq HS Mix (Bioline, cat# BIO-25045) and TruSeq PCR Primer Cocktail (Illumina, TruSeq Nano cat# FC-121-4001) according to the following protocol: initial denaturation at 98°C for 30s; 12 cycles of 98°C for 15s, 60°C for 30s, 72°C for 30s; final extension at 72°C for 5 min. Amplified libraries were purified twice with an equal amount of SPRI beads to remove primer and adapter dimers. Libraries were sequenced 100 bp single-end on an Illumina HiSeq4000.

Sequencing Platform

instrument_model

Illumina HiSeq 4000

mm10

Number of total reads

20114132

Reads aligned (%)

70.6

Coverage rate (×)

1.0

Number of hyper MRs

103586 (qval < 1E-05)

mm9

Number of total reads

20114132

Reads aligned (%)

70.6

Coverage rate (×)

1.0

Number of hyper MRs

103431 (qval < 1E-05)