|
| Status |
Public on Oct 21, 2012 |
| Title |
HeLa eIF4AIII CLIP-seq 2 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa eIF4AIII CLIP-seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
|
| Treatment protocol |
HeLa cells were crosslinked on ice with UV-C (254 nm) at 400 mJ per cm2 in presence of cold PBS (4 ml per 15 cm dish).
|
| Growth protocol |
HeLa cells were cultivated in 15 cm dishes in Dulbecco’s modified Eagle’s medium (DMEM) with 4,5g l-1 D-glucose supplemented with 10% FCS and antibiotics (streptomycin 100 ug ml-1 and penicillin 100 U ml-1).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
HeLa cell lysate were treated with RNAse T1 and mRNP-containing eIF4AIII were immunoprecipitated by using rabbit polyclonal anti-human eIF4AIII antibodies. eIF4AIII-RNAs complexes were resolved on SDS-PAGE and transferred to nitrocellulose membrane. RNAs were extracted by proteinase K treatment. cDNAs libraries were prepared with the small RNA kit (v1.5, Illumina).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Library strategy: CLIP-seq
Illumina Casava1.7 software used for basecalling.
CLIP-seq reads were trimmed for adaptor sequence (Adapter 5’ 5'-AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACGATC-3'; Adapter 3’
5'-ATCTCGTATGCCGTCTTCTGCTTG-3) using the Btrim software (parameters -3 -v7 -l 15).
CLIP-seq and mRNA-seq reads were mapped to hg19 genome assembly (Ensembl 63) using Novoalign V2.07.11 (parameters -F ILMFQ -o SAM) and BLAT version 34 (parameter -minScore=15).
All uniquely mapped reads with Novoalign and BLAT were used in subsequent processing.
bedGraph files were generated using the genomeCoverageBed function v2.12.0 from BEDTools.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files
|
| |
|
| Submission date |
Sep 11, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Herve LE HIR |
| E-mail(s) |
lehir@ens.fr
|
| Organization name |
IBENS
|
| Department |
Functional Genomics
|
| Lab |
Le Hir lab
|
| Street address |
46 rue d'Ulm
|
| City |
PARIS |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE40778 |
CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex |
|
| Relations |
| SRA |
SRX186078 |
| BioSample |
SAMN01164167 |
