|
| Status |
Public on Jan 01, 2017 |
| Title |
HEXIM1+DMSO iCLIP Biological Replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
A375 melanoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A375
treatment: DMSO
|
| Treatment protocol |
A375 cells were treated with DMSO or 25 μM A771726. Drugs used were DMSO (Sigma) and A771726 (Enzo Life Sciences). After a 48 hr treatment, cells were UV-C crosslinked to a total of 0.3J/cm2. Each iCLIP experiment was normalized for total protein amount, typically 2.5mg, and partially digested with RNaseI (Life Technologies) for 10 minutes at 37°C and quenched on ice.
|
| Growth protocol |
Human A375 malignant melanoma cells (ATCC) are grown on standard tissue culture plates in filter sterilized DMEM (Life Technologies) with 10% heat-inactivated FBS (Atlanta Biologicals), 1X GlutaMAX (Life Technologies) and 1% Penicillin-Streptomycin (Life Technologies).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To isolate HEXIM-bound RNAs HEXIM1 antibody (Abcam, ab25388) conjugated to Protein A Dynabeads (Life Technologies) were incubated with RNaseI-digested lysate overnight at 4°C on rotation.
Libraries were prepared according to the FAST-iCLIP protocol (PMID: 25411354)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Protein enriched RNA
|
| Data processing |
Library strategy: iCLIPseq
Sequencing reads were trimmed of 3' adaptors, collapsed for PCR duplicates, stripped of the 5' barcode, and mapped to the human (hg19) genome using bowtie2
RT stop identificaiton, gene assignment, and peak calling was performed as in FAST-iCLIP (PMID: 25411354)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file containing unique RT stops from the high confidence intersection of biological replicates of HEXIM1 iCLIP
|
| |
|
| Submission date |
Apr 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Leonard Zon |
| E-mail(s) |
zon@enders.tch.harvard.edu
|
| Organization name |
Boston Children's Hospital
|
| Department |
Oncology/Hematology
|
| Street address |
1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE68045 |
Nucleotide stress induction of HEXIM1 suppresses melanoma by modulating cancer cell-specific gene transcription [FAST-iCLIP] |
| GSE68053 |
Nucleotide stress induction of HEXIM1 suppresses melanoma by modulating cancer cell-specific gene transcription |
|
| Relations |
| BioSample |
SAMN03492287 |
| SRA |
SRX1000219 |
