|
| Status |
Public on Oct 21, 2011 |
| Title |
MDA-231_HOTAIR_even |
| Sample type |
SRA |
| |
|
| Source name |
MDA-231_HOTAIR
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-231
cell type: MDA-231 cell line overexpressing human HOTAIR
lincrna probes: HOTAIR
|
| Growth protocol |
Drosophila cell line: 10% Heat-Inactivated FBS in Schneider medium (pen/strep). Human cell lines: 10% FBS in DMEM (pen/strep)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells are crosslinked in 1% glutaraldehyde and lysates clarified by sonication. lincRNA:chromatin adducts are isolated using specific probes. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 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 an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
ChIRP-seq of HOTAIR from MDA-231 cells
|
| Data processing |
Briefly, raw reads from "even" and "odd" in each samples were aligned using "Bowtie," and merged so that only signals common in both "even" and "odd" are retained (merge.wig files). These files were then converted into SAM formats for peaking calling by MACS. For complete methods please refer to the paper.
|
| |
|
| Submission date |
Oct 20, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Kun Qu |
| E-mail(s) |
[email protected]
|
| Organization name |
Stanford University
|
| Department |
Dermatology
|
| Lab |
Howard Chang
|
| Street address |
269 Campus Dr. CCSR 2150
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE31332 |
Genomic maps of lincRNA occupancy reveal principles of RNA-chromatin interactions. |
|
| Relations |
| SRA |
SRX101819 |
| BioSample |
SAMN00740107 |
