|
| Status |
Public on Feb 21, 2012 |
| Title |
IgG control KE |
| Sample type |
SRA |
| |
|
| Source name |
adult testis
|
| Organism |
Mus musculus |
| Characteristics |
age: adult
gender: male
genetic background: 9R female x 13R male F1
chip antibody: IgG
|
| Growth protocol |
Cells were extracted from testis of euthanized mice and subjected to immunoprecipitation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates from mouse testis cells were crosslinked, sonicated and immunoprecipitated with anti-DMC1 or anti-RAD51 antibodies. Library construction was done using enzymes from New England Biolabs or Illumina and standard Illumina protocol. Size selection of library fragments of 150~250 bp was performed after PCR amplification. “Klenow exo(-)” sample was prepared by substituting Klenow fragment and T4 DNA polymerase from the end repair step of the standard protocol with Klenow exo(-) enzyme and performing end repair at 37 °C for 1h. “Klenow exo(-), 12 °C“ sample was prepared the same way followed by incubation at 20 °C for 2h and at 12 °C overnight. "Kinetic enrichment" samples were denatured and quickly renatured before adapter ligation.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Kinetic Enrichment (KE) protocol. Samples were denatured and quickly renatured before adapter ligation.
|
| Data processing |
IgG_KE.sorted.ssDNA_type1.bed; genome build: mm9
IgG_KE.sorted.ssDNA_type2.bed; genome build: mm9
IgG_KE.sorted.dsDNA.bed; genome build: mm9
IgG_KE.sorted.1K_100.wig; genome build: mm9
BED: Quality-filtered sequencing reads were mapped to mm9 version of mouse genome assembly using BWA (first end) (http://bio-bwa.sourceforge.net/) or BWA-RA (second end). BWA-RA is modification of BWA that iteratevily seeks longest aligning suffux of the query. Obtained alignments were further processed to generate ssDNA type 1, ssDNA type 2 and dsDNA subsets of fragments. Fourths field in the BED file is (ITR_length)_(microhomology_lenght) and fifth field is BWA-calculated alignment quality. PHRED alignment qualities for both ends (0-30) were added and then re-scaled to 0-1000.
WIG: type1 ssDNA, type2 ssDNA and dsDNA subsets were combined and read coverage was calculated in sliding windows of 1Kb with 100 bp step. Counts were normalized to total numer of reads in the dataset and are given in reads per million.
|
| |
|
| Submission date |
Dec 20, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Pavel P Khil |
| E-mail(s) |
pk94j@nih.gov
|
| Phone |
301-496-4638
|
| Fax |
(301)-496-9878
|
| Organization name |
NIDDK
|
| Department |
|
| Lab |
Genetics and Biochemistry Branch
|
| Street address |
5 Memorial Dr.
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE34592 |
Sequencing-based ssDNA detection |
|
| Relations |
| Reanalyzed by |
GSM869789 |
| SRA |
SRX112541 |
| BioSample |
SAMN00767724 |
