|
Status |
Public on Apr 10, 2023 |
Title |
G1E CTCF [2628] |
Sample type |
SRA |
|
|
Source name |
cell line
|
Organism |
Mus musculus |
Characteristics |
cell type: G1E strain: C57BL/6 chip antibody: CTCF
|
Growth protocol |
G1E and G1E-ER4 cells were grown in IMDM media + 15% FBS, kit ligand, and erythropoietin in a standard tissue culture incubator at 37°C with 5% CO2.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Lysates were prepared from sonicated nuclei and protein-DNA complexes were isolated with antibody. ChIP-seq samples were prepared by end repair, 3’ adenylation, and adaptor ligation using Illumina’s TruSeq ChIP-seq Sample Preparation Kit.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Basecalls using bcl2fastq-1.8.4, and parameters --no-eamss --mismatches 1 Mapping to reference genome mm10 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam Wiggle and peaks called using MACS with parameters --format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1 Filter blacklist regions from peaks, and convert the *peaks.xls file from MACs to broadpeak format (see UCSC Genome Browser for format specs) Assembly: mm10 Supplementary files format and content: bigWigs, signal from MACS
|
|
|
Submission date |
Apr 06, 2023 |
Last update date |
Apr 11, 2023 |
Contact name |
Ross Hardison |
E-mail(s) |
rch8@psu.edu
|
Organization name |
Pennsylvania State University
|
Street address |
303 Wartik Lab
|
City |
University Park |
State/province |
PA |
ZIP/Postal code |
16802 |
Country |
USA |
|
|
Platform ID |
GPL19057 |
Series (2) |
GSE229100 |
Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes [mouse TFbs] |
GSE229101 |
Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes |
|
Relations |
BioSample |
SAMN34091135 |
SRA |
SRX19892449 |