|
| Status |
Public on Dec 01, 2013 |
| Title |
HMGD1 ChIP-seq replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
late embryonic stage cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: late embryonic cells
passages: 10--15
strain: S2
antibody: customized antibody
|
| Growth protocol |
D. Melanogaster S2-DRSC cells (obtained from the Drosophila Genomics Resource Center) were cultured in Schneider's Drosophila medium (Invitrogen) supplemented with 10% FCS (Hyclone).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
MNase digested nuclei and histone-DNA complexes were isolated with specific antibody.
Libraries were prepared according to Applied Biosystems protocol for SOLiD fragment paired-end sequencing. Briefly, DNA was end-repaired and 5’-phosphorylated by incubation in DNATerminator end-repair kits, as recommended by the manufacturer (Lucigen Corp., Middleton, WI). SOLiD adapters were ligated and the DNA molecules PCR amplified (very low cycle number) and sequenced by using the Applied Biosystems protocol for SOLiD fragment paired-end sequencing. After adapter ligation DNA was PCR amplified with SoLiD primers for less than 12 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on a SoLid flow cell for cluster generation.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Data processing |
HMGD1 SOLiD output files were converted to fastq using custom script
Mapped HMGD1 reads to the Drosophila genome using BWA v0.6.1
Estimated the mean HMGD1 fragment length of each replicate by computing the offset that gave the highest covariation of read depth between the forward and reverse strands
Estimated HMGD1 nucleosome midpoint locations as the read start plus the offset (or minus the offset for those that mapped to the reverse strand.
Aligned the MNase-seq and H1 paired-end reads to the genome using the standard SOLiD pipeline and discarded those where only one side of pair mapped
Estimated the distribution of H1 and MNase-seq fragment sizes from separation of read pairs, and discarded read pairs outside of the central 95% of distribution (101-191bp)
Estimated H1 and MNase-seq nucleosome midpoints as the midpoint between read pairs
Genome_build: dm3
Supplementary_files_format_and_content: wig files containing counts of mapped fragment midpoints at each genomic position
|
| |
|
| Submission date |
Aug 02, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Graham McVicker |
| E-mail(s) |
gmcvicker@salk.edu
|
| Organization name |
Salk Institute
|
| Lab |
McVicker
|
| Street address |
10010 N Torrey Pines Rd
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL10942 |
| Series (1) |
| GSE49526 |
Genome-wide maps of HMGD1 and H1-bound nucleosomes. |
|
| Relations |
| BioSample |
SAMN02302776 |
| SRA |
SRX331677 |
