|
| Status |
Public on Dec 30, 2014 |
| Title |
Colo829_MNase-seq |
| Sample type |
SRA |
| |
|
| Source name |
Human Colo829 melanoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Colo829
treatment: none
|
| Treatment protocol |
For ChIP-seq, Cells are fixed in 1% Formaldehyde and stoped by lysine. For Mnase-seq, Chromatin was processed by optimizing a previously published protocol (Ozsolak et al., 2007) with 200 units of MNase (Worthington Biochemical Corp.) and incubation at 25 degree for 5 min, which typically yielded 80-90% mononucleosomal DNA.
|
| Growth protocol |
Cells are maintained in standard mouse stem cells medium with Lif. Purimycin was added to the medium for transfected cells.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells are lysed in 1% SDS lysis buffer and sonicated for ChIP analysis. RNA extraction and amplification from preimplantation embryos and ICM were carried out as described before (Xie et al., 2010).
For ChIP-seq, the libraries were prepared with Illumina's 'TruSeq DNAseq Sample Prep kit'. The libraries were then pooled and quantitated by qPCR. Each pool each was sequenced on one lane for 101 cycles on a HiSeq2000 using a TruSeq SBS sequencing kit version 3. For RNA-seq of ICM and blastocyst, there are two-round of RNA Amplification. The amplified RNAs were subjected to sequencing using Illumina’s small sample RNA-seq protocol.
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
The ChIP-seq data were mapped back into mm9 genome by Bowtie 0.12.7, with unique alignment and ≤ 1 mismatch
Raw RNA-seq data were aligned to mouse (mm9) genome using Tophat with unique alignment and ≤ 1 mismatch. Cufflinks with default parameters was used to estimate the expression levels.
Raw MNase-seq data were mapped to mouse (mm9) and human(hg19) genome using Bowtie 0.12.7 allowing 2 mis-matches and unique alignment only.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: BED files for mapped data of Mnase-seq and ChIP-seq experiment;
|
| |
|
| Submission date |
Mar 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Pengfei Yu |
| E-mail(s) |
yupf05@gmail.com
|
| Organization name |
University of California San Diego
|
| Department |
Bioengineering
|
| Lab |
Dr. Sheng Zhong
|
| Street address |
9500 Gilman Drive MC 0419
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0419 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE47802 |
SMARCAD1 Regulates Nucleosome Positioning and Maintenance of the Naïve Pluripotent State |
|
| Relations |
| BioSample |
SAMN01984918 |
| SRA |
SRX302126 |
| Named Annotation |
GSM1102665_Colo829_MNase-seq.bed.gz |
