SRX2410149
GSM2421490: ChIP-seq from A549 (ENCLB884HRT); Homo sapiens; ChIP-Seq

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Lung
Cell type
A549
Primary Tissue
Lung
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

dev stage
adult
cell line
A549
treatments
treatment_term_id: CHEBI:41879; treatment_term_name: dexamethasone; treatment_type: chemical; duration: 3; duration_units: hour;
sex
male
sample type
immortalized cell line
donor ID
ENCDO000AAZ
age
58 year
lab
Tim Reddy, Duke

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
general protocol: https://www.encodeproject.org/documents/e21fb833-cd54-4c37-a3b6-440732909433/@@download/attachment/01_ChIP_DEX_Harvest_Reddy_GGR.pdf extraction protocol: https://www.encodeproject.org/documents/4ac7e9ce-4a92-42da-a1ab-299d4205eb96/@@download/attachment/02_ChIP_shearing_IP_reverse_v.2_Reddy_GGR.pdf treatment protocol: https://www.encodeproject.org/documents/1bca5eae-b9ce-4df0-b401-612924dc53a4/@@download/attachment/03_KAPA_Hyper_Prep_Kit_KR0961-TDSv2.15_final_24%20rxn_Reddy_GGR.pdf general protocol: https://www.encodeproject.org/documents/0d841e8a-a32d-416e-8f99-9db162bd09be/@@download/attachment/03_notes_Reddy_GGR.pdf

Sequencing Platform

instrument_model
Illumina HiSeq 2000

Where can I get the processing logs?

Read processing pipeline log

hg38

Number of total reads
47873801
Reads aligned (%)
98.6
Duplicates removed (%)
3.9
Number of peaks
25368 (qval < 1E-05)

hg19

Number of total reads
47873801
Reads aligned (%)
98.2
Duplicates removed (%)
4.3
Number of peaks
25123 (qval < 1E-05)

Base call quality data from DBCLS SRA