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Status |
Public on Aug 10, 2017 |
Title |
sonication INPUT_ChIPseq |
Sample type |
SRA |
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Source name |
hES H1
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Organism |
Homo sapiens |
Characteristics |
cell line: H1 chip antibody: none
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Growth protocol |
H1 hES cells were expanded in mTeSR1 medium (Stem Cell Technologies) on Matrigel
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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
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NextSeq 500 |
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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)
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Submission date |
Jul 13, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Jim Hughes |
E-mail(s) |
jim.hughes@imm.ox.ac.uk
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Phone |
1865222113
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Organization name |
University of Oxford
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Department |
MHU
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Lab |
Genome Biology Group
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Street address |
Weatherall Institute Of Molecular Me
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City |
oxford |
ZIP/Postal code |
OX3 9DS |
Country |
United Kingdom |
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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 |
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Relations |
BioSample |
SAMN05388841 |
SRA |
SRX1942805 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2232661_INPUT_H3K36me3_DJ_filtered_pileup.bw |
518.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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