|
| Status |
Public on Mar 26, 2013 |
| Title |
HeLaS3.S.SFMBT1 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa S3
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HeLa S3
cell cycle phase: S
antibody: SFMBT1
antibody information: custom (rb4731 LOT#110518)
internal reference: 130104_lane4_VLB2
|
| 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 |
| |
|
| Description |
Harvested 5 hours after release (double thymidine)
|
| 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 |
GPL11154 |
| 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 |
|
| Relations |
| SRA |
SRX254623 |
| BioSample |
SAMN01986092 |
