Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MYC

Cell type

Cell type Class
Lung
Cell type
SW 1271
Primary Tissue
Lung
Tissue Diagnosis
Carcinoma Small Cell

Attributes by original data submitter

Sample

source_name
SW1271
cell type
small cell lung cancer
mutation
MYC amplifcation
antibody
c-Myc (D3N8F) Rabbit mAb

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Total RNA was extracted using Trizol and QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit. ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit PRO-seq was performed according to the previously published protocol (Mahat et al., 2016a) with minor modifications. All 4 biotinylated nucleotides were used at 25 μM each final concentration for the run-on reaction. RPPH (NEB) was used to remove the 5' RNA cap. Libraries were size selected using a 2% agarose gel on a Pippin HT programmed to elute 140–350 bp. 4sU-seq Cell Labeling with 4sU, RNA Extraction and Fragmentation 20-50 million cells were treated with flavopiridol for 1 hour and washed with PBS twice. The cells were labeled in media with 500 μM 4-thiouridine (4sU, Sigma-Aldrich, St. Louis, MO, USA.) and harvested through centrifugation for 3 min at 3,000 rpm. RNA was extracted with 4 mL Trizol (Invitrogen) and 5 μL 20 mg/mL glycogen. The extracted RNA was further fragmented by base hydrolysis in 0.2 M NaOH on ice for 18 min, neutralized by adding 1x volume of 1 M Tris-HCl pH 6.8 and precipitated with isopropanol.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
46285021
Reads aligned (%)
85.1
Duplicates removed (%)
11.4
Number of peaks
56533 (qval < 1E-05)

hg38

Number of total reads
46285021
Reads aligned (%)
85.9
Duplicates removed (%)
11.0
Number of peaks
56673 (qval < 1E-05)

Base call quality data from DBCLS SRA