Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Lung
Cell type
NCI-H1299
Primary Tissue
Lung
Tissue Diagnosis
Carcinoma Non-Small Cell

Attributes by original data submitter

Sample

source_name
H1299
cell
H1299 cells
treatment
Input
antibody
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20. ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20. mRNA was prepared using the RNeasy Plus kit (Qiagen) and reverse-transcribed using the iScript™ cDNA Synthesis Kit (Bio-Rad). For ChIP-seq, sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using paired-end sequencing technology on Illumina HiSeq 2000 platform. For RNA-seq, samples were prepared as instructed using the TruSeq mRNA Sample Preparation Kit v2 (Illumina, San Diego, CA) in accordance with the manufacturer's instructions. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles, DNA fragments were sequenced using single-end sequencing technology on Illumina paried-end on Illumina HiSeq2000 .

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
69991113
Reads aligned (%)
95.4
Duplicates removed (%)
2.4
Number of peaks
1407 (qval < 1E-05)

hg19

Number of total reads
69991113
Reads aligned (%)
94.6
Duplicates removed (%)
4.1
Number of peaks
1617 (qval < 1E-05)

Base call quality data from DBCLS SRA