|
| Status |
Public on Dec 27, 2018 |
| Title |
ETO2_Chip_input1 |
| Sample type |
SRA |
| |
|
| Source name |
FLK1+mesoderm
|
| Organism |
Mus musculus |
| Characteristics |
cell type: ES cell-derived embryoid bodies
strain: C57Bl/6 X Sv129
ebs stage: day 4
antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Complexes were eluted from beads in a thermomixer at 65 degres for 15 min and the eluates and reserved inputs were reverse cross-linked overnight at 65C. The samples were then treated with RNaseA, proteinase K and phenol/chloroform purified.
ChIP samples were submitted to library preparation using NEBNext Ultra DNA Library prep kit for Illumina (NEB 7370) and multiplexing barcodes (NEB E7500) following Illumina’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Base calling performed on illumina 1.9 platform
Chipseq reads were aligned to the mm9 genome reference. 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: http://userweb.molbiol.ox.ac.uk/public/telenius/PipeSite.html
mapping : bowtie -m 1 --maxIns 350 --lanes 4
for un-mapping reads : trim_galore -- length 10, --noFlash
removing duplicates : samtools rmdup
no ploidy region (bedtools pairtobed )
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)
peak calling were performed using Macs2 v2.0.10 with the following parameters -B -q 0.05 --to-large
Genome_build: mm9
Supplementary_files_format_and_content: narrowPeak files were generated with macs2
Supplementary_files_format_and_content: bed file: tab delimited text file containing peakcalling union of replicate 1 and 2
|
| |
|
| Submission date |
Oct 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Hedia Chagraoui |
| E-mail(s) |
hedia.chagraoui@imm.ox.ac.uk
|
| Phone |
00441865222309
|
| Organization name |
Weatherall Institute of Molecular Medicine
|
| Department |
Molecular Hematology Unit
|
| Lab |
PORCHER/VYAS lab
|
| Street address |
john radcliffe hospital headley way headington
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE104845 |
SCL establishes a global repressive environment and cooperates with Polycomb RYBP-PRC1 to suppress alternative lineages in blood-fated cells [ETO2 ChIP-seq] |
| GSE104883 |
SCL establishes a global repressive environment and cooperates with Polycomb RYBP-PRC1 to suppress alternative lineages in blood-fated cells |
|
| Relations |
| BioSample |
SAMN07775384 |
| SRA |
SRX3272225 |
