|
| Status |
Public on Dec 31, 2017 |
| Title |
H3K4me1_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
airway smooth muscle
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: airway smooth muscle
passages: 3
chip antibody: H3K4me1 (Abcam ab8895)
|
| Growth protocol |
ASM cells were generated by re-plating confluent cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic I
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were prepared from Mnase-treated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg18 genome assembly using Novoalign version 2.07.11 with the default configuration and the output written in SAM format
The aligned reads were subjected to quality control by omitting reads with 0 mapping quality and removing the redundant reads using samtools
peaks were called using SICER version 1.1 with the following settings: Fragment size=150bp, window size=200 for K4me1 and K4me3 while 500 for K27me3, FDR=1E-5
Genome_build: hg18
Supplementary_files_format_and_content: wig files were generated in variable step with a span size of 200bp for K4me1 and K4me3 and 500bp for K27me3. The wig files were then converted to bigWig format using “WigToBigWig” utility from UCSC tools. These files contain amplitude of the ChIP-seq signal as number of reads without normalizing to tags per million reads.
|
| |
|
| Submission date |
Jan 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Paul Lavender |
| E-mail(s) |
paul.lavender@kcl.ac.uk
|
| Organization name |
King's College London
|
| Department |
School of Immunology and Microbial Sciences
|
| Street address |
5th Floor, Tower Wing, Great Maze Pond
|
| City |
London |
| ZIP/Postal code |
SE1 9RT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE43357 |
Genome-wide maps of chromatin state in human primary airway smooth muscle cells. |
|
| Relations |
| SRA |
SRX215595 |
| BioSample |
SAMN01883266 |
