|
| Status |
Public on Aug 22, 2012 |
| Title |
Chr-IgG |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells (ATCC)
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Chromatin
antibody: IgG
cell line: HeLa
sample fraction: immunoprecipitation
|
| Treatment protocol |
Hela cells were UV cross-linked (400 mJ/cm2) and subfractionated as described in Ameyar et al., (2012) Nat Struc Mol Biol in press. Inputs and immunoprecipitated extracts (incubated with either IgG as negative control or with anti-AGO2 antibodies) from cytoplasmic (EC) and chromatin (Chr) fractions were treated with Proteinase K, and RNA was extracted with phenol-chlorophorm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Following digestion with DNase (RNase free), short RNAs below 100 bp were gel-purified, poly(A)-tailed using poly(A) polymerase, treated with tobacco acid pyrophosphastase, and RNA adapters were ligated to the 5’phosphate of the RNA. cDNA was synthesized and PCR-amplified.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
immunoprecipitation of the chromatin extract by rabbit non immun IgG (Sigma Aldrich)) linked to protein-A-dynabeads (Invitrogen) and rat non immun IgG (Sigma Aldrich) linked to protein-G-dynabeads (Invitrogen)
|
| Data processing |
Sequences were aligned to the genome (GRCh37) using oligomap (Berninger, P., Gaidatzis, D., van Nimwegen, E. & Zavolan, M. 2008. Computational analysis of small RNA cloning data. Methods 44, 13-21) to find alignments with up to 1 error (replacement, insertion, or deletion). Alignments were filtered to include only the best matches for each sequence. Sequences with >5 alignments were filtered out.
BED tracks were calculated. For each reads their number were indicated followed by an underscore and the length (in nucleotide) of the considered read. Number of clones of the same sequence is indicated in the score label of the BED tracks. sRNAs bound to AGO2 appear in red, sRNAs bound to the control IgG are in blue, and Input are in black.
Genome_build: GRCh37 / hg19
Supplementary_files_format_and_content: BED tracks were calculated. For each reads their number were indicated followed by an underscore and the length (in nucleotide) of the considered read. Number of clones of the same sequence is indicated in the score label of the BED tracks. sRNAs bound to
|
| |
|
| Submission date |
Jul 30, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Eric Batsche |
| Phone |
(33)1 44 27 34 77
|
| Organization name |
IBPS - Institut Biologie Paris Seine
|
| Department |
B2A Biological Adaptation and Ageing - UMR8256 CNRS
|
| Lab |
Epigenetics and RNA metabolism in human diseases
|
| Street address |
7-9, Quai Saint Bernard
|
| City |
Paris |
| ZIP/Postal code |
75006 |
| Country |
France |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE39748 |
Argonaute proteins couple chromatin silencing to alternative splicing (RNA IP-Seq) |
| GSE39749 |
Argonaute proteins couple chromatin silencing to alternative splicing |
|
| Relations |
| SRA |
SRX171601 |
| BioSample |
SAMN01096079 |
