 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 10, 2017 |
| Title |
H3K36me3_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
hES H1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H1
chip antibody: H3K36me3, Abcam, ab9050
|
| Growth protocol |
H1 hES cells were expanded in mTeSR1 medium (Stem Cell Technologies) on Matrigel
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed with the Millipore ChIP Assay Kit (Millipore, 17-295)
Libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, E7370S) and sequenced on NextSeq500
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Data were analysed using in-house pipeline that automatically assesses the quality of data, trims adaptors, merges short reads, maps reads to the reference genome, and filters data for duplicates :
mapping : bowtie -m 2 --maxIns 350
for un-mapping reads : trim_galore -- length 10, flash -m 9 -x 0.125
combining trimmed+flashed and originally mapped reads, mapping again with bowtie -m 2 --maxIns 350
removing read pairs overlapping Duke Blacklisted regions
removing duplicates : samtools rmdup
reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
pileup of fragments (bedtools genomecov -counts)
generating bigwig tracks (ucsctools bedGraphToBigWig)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig : un-normalised coverage of filtered fragments (reconstructing fragments, filtering : see above)
|
| |
|
| Submission date |
Jul 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jim Hughes |
| E-mail(s) |
jim.hughes@imm.ox.ac.uk
|
| Phone |
1865222113
|
| Organization name |
University of Oxford
|
| Department |
MHU
|
| Lab |
Genome Biology Group
|
| Street address |
Weatherall Institute Of Molecular Me
|
| City |
oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE84352 |
Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs [H3K36me3_ChIP-seq] |
| GSE84355 |
Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs |
|
| Relations |
| BioSample |
SAMN05388840 |
| SRA |
SRX1942804 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2232660_H3K36me3_DJ_filtered_pileup.bw |
415.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
