|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jan 08, 2020 |
Title |
100169 ERY input |
Sample type |
SRA |
|
|
Source name |
bone marrow
|
Organism |
Mus musculus |
Characteristics |
chip ab: none strain: C57BL6 developmental stage: adult cell isolation markers: CD4-, CD8-, IL7Ra-, CD11b-, Ly6g-, CD45R-, Ter119+, CD44+, FSCLow cell type: erythroblast
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying TruSeq ChIP-seq Sample Preparation Kit. (Part# IP-202-1012). In brief, ChIP-enriched, fragmented DNA was subjected to end repair to generate blunt-end double stranded DNA, adenylation of 3’ ends, and adaptor ligation. Following ligation, SPRIselect (Beckman Coulter) beads were used at 0.9X and 0.6X for left and right side selection, respectively, to obtain an average library target size of ~300 bp. After size selection, fragments were amplified for 16 cycles, and PCR products were purified using Agencourt AMPureXP beads (Beckman Coulter).
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
Mapping to reference genome 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 generated with MACS using parameters --nomodel --shiftsize=120--format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1 Peaks called with Sicer V1.1 using parameters mm10 1 200 150 0.74 600 0.01 Filter blacklist regions from peaks, and convert to broadpeak format (see UCSC Genome Browser for format specs) UCSC's wigToBigWig to convert wiggle track Genome_build: mm10 Supplementary_files_format_and_content: bigWig, signal from Macs Supplementary_files_format_and_content: broadpeak, peaks from Sicer
|
|
|
Submission date |
Jan 07, 2020 |
Last update date |
Jan 08, 2020 |
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 |
GPL17021 |
Series (2) |
GSE143265 |
An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis [histones] |
GSE143271 |
An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis |
|
Relations |
BioSample |
SAMN13750833 |
SRA |
SRX7517442 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4255722_100169.mm10.bw |
2.3 Gb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|