|
| Status |
Public on Jul 29, 2019 |
| Title |
hiPSC4_H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
single-cell CVB derived hiPSC#4 subline (genome editing: PSEN1 deltaE9 -/-, IB12)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Craig Venter-B (CVB) hiPSC subline
chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification): H3K4me3 (Millipore, 07-473)
|
| Treatment protocol |
No particular treatments were applied.
|
| Growth protocol |
CVB and CVI lines and sublines as well as HUES9 hESC line and sublines were cultured on a feeder layer of gamma-irradiated mouse embryonic fibroblasts (MEFs), and maintained in hESC media made with knockout (KO) Dulbecco’s modified Eagle’s Medium (DMEM) (Gibco) supplemented with 10% Plasmanate from Talecris Biotherapeutics; 10% Knockout serum replacement (KOSR) from Gibco; 20 mM GlutaMax, 20 mM nonessential amino acids (NEAA) and 20 mM Pen/Strep from Invitrogen; and, 20 ng/µL FGF from Millipore. Mouse ESCs were prepared in feeder free condition with DMEM-KO supplemented with 15% ESC qualified-fetal bovine serum, 2 mM nonessential amino acids, glutamx, penicillin/streptomycin, 2-mercaptoethanol and 1000u/ml LIF.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 2mM disuccinimidyl glutarate (DSG) for 45 mins and 1% formaldehyde for 10mins, and followed by glycine for 5 mins. Chromatin DNA was sheared to 200–500 bp average in size by sonication and chromatin was immunoprecipitated with antibodies. Protein A/G beads Sigma were added and incubated overnight at 4°C. After washing and elution, the protein–DNA complex was reverse-crosslinked by heating at 65°C, and immunoprecipitated DNA was purified by using QIAquick Spin column.
ChIP-seq libraries were prepared using the KAPA Library Preparation Kit (KK8201)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were aligned to the hg18 human genome with bowtie2 (–very-sensitive option) and tophat. One mismatch was allowed.
Artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data
Read counts were calculated with HOMER 3.9 considering only exonic regions of human RefSeq genes
The bedGraph and bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18 and mm9
Supplementary_files_format_and_content: bedGraph
|
| |
|
| Submission date |
Nov 14, 2017 |
| Last update date |
Jul 30, 2019 |
| Contact name |
Daria Merkurjev |
| E-mail(s) |
dashamerkurjev@gmail.com
|
| Phone |
858-534-5858
|
| Organization name |
UCSD
|
| Department |
Medicine
|
| Lab |
Michael G. Rosenfeld Laboratory
|
| Street address |
9500 Gilman Drive, Mail Code 0648
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE106870 |
Analysis of the Clustered Protocadherin (cPcdh) Locus in Human Pluripotent Stem and Derived Cells (ChIP-seq I out of II) |
| GSE106872 |
Analysis of the Clustered Protocadherin (cPcdh) Locus in Human Pluripotent Stem and Derived Cells |
|
| Relations |
| BioSample |
SAMN08024860 |
| SRA |
SRX3390396 |
