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Sample GSM1104365 Query DataSets for GSM1104365
Status Public on Mar 26, 2013
Title pachynema.input
Sample type SRA
Source name pachynema cells
Organism Mus musculus
Characteristics cell type: pachynema cells
antibody: none (input)
antibody information: NA
internal reference: 120504B_lane8_VLB1
Extracted molecule genomic DNA
Extraction protocol Isolated nuclei (HeLaS3) or whole cells (germ cells) were sonicated using a Diagenode Bioruptor to an average size of 200 bp. Chromatin was pre-cleared with BSA-blocked protein G sepharose (Roche) and incubated with antibodies at 4C overnight. The chromatin immunocomplexes were recovered with BSA-blocked protein G beads. After 5 washes in RIPA buffer, immunocomplexes were eluted in 1% SDS and DNA was decrosslinked at 65C for 16h.
Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with LigaFast (Promega, city, state #M8225). Fragments of 300±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Data processing Trimmed sequences in 3' to 36 nts
mapped to hg19 (HeLa S3 data) or mm9 (germ cell data) with BOWTIE -m4 -v2
duplicates were removed with SAMTOOLS RMDUP (except cell cycle ChIP-seq)
WIGs were generated with IGVtools count extending fragments to 200 nts
WIGs were normalized to 10,000,000 mapped reads (RP10M) using a shell script
normalized WIGs were converted to bigWigs with wigToBigWig
for the cell cycle data, the IgG bigWig profiles were subtracted from each IP profile using a custom script, IgG and input are provided before subtraction
Genome_build: hg19 (HeLaS3) or mm9 (germ cells)
Supplementary_files_format_and_content: RP10M-normalized bigWigs
Submission date Mar 22, 2013
Last update date Feb 04, 2022
Contact name Roberto Bonasio
Organization name University of Pennsylvania
Department Cell and Developmental Biology
Lab Bonasio
Street address 3400 Civic Center Blvd - SCTR 9-111
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platform ID GPL13112
Series (2)
GSE45441 SFMBT1 Functions with LSD1 to Regulate Expression of Canonical Histone Genes and Chromatin-Related Factors [ChIP-Seq]
GSE45489 SFMBT1 Functions with LSD1 to Regulate Expression of Canonical Histone Genes and Chromatin-Related Factors
SRA SRX254626
BioSample SAMN01986095

Supplementary file Size Download File type/resource 250.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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