|
| Status |
Public on Sep 08, 2015 |
| Title |
IP Ig on involved psoriatic skin sample |
| Sample type |
SRA |
| |
|
| Source name |
involved psoriatic skin biopsies, IgG IP
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: skin
disease status: psoriasis
ip antibody: mouse IgG1 isotype control
|
| Growth protocol |
Five different patients were used for both uninvolved and involved psoriatic skin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen skin biopsies were disrupted using the MagNA Pure Instrument (Roche). Immunoprecipitations of endogenous RNA-protein complexes for involved and uninvolved psoriatic skin were carried out as previously described (Peritz T et al. Nat Protoc. 2006 (PMID 17406284 )) using protein-A-agarose that had been pre-coated with anti-HuR (clone 3A2, Santa Cruz Biotechnology, catalog number sc-5261, Lot# F1710) or with isotype control (mock; clone G3A1, Cell Signaling, catalog number 5415, Lot# 1) antibodies.
Illumina TruSeq RNA Sample Prep Kit (RS-122-1001) was used with 10 ng of each RNA sample for the construction of sequencing libraries, as per manufacturer's recommendations.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Mix of 5 biopsies from 5 patients.
IgG-binding RNA.
|
| Data processing |
Library strategy: RIP-Seq
Image analyses and basecalling were performed using the HiSeq Control Software (HCS 1.4.8) and Real-Time Analysis component (RTA 1.12.4.0).
Demultiplexing, alignments and RNA counting were performed using CASAVA 1.8.1 (Illumina).
Alignment was made with eland_rna on the UCSC hg19 version of the human genome and on several contaminants (the ribosomal RNA sequences RN28S1, RN18S1 and RN5S1, the mitochondrial chromosome, the PhiX genome and the Illumina adaptors).
The transcript annotation ("exonic") was retrieved from UCSC (refFlat file) on January 22, 2012. Sequences were also aligned on intronic regions (downloaded from UCSC, refGene table).
Genome_build: GRCh37
Supplementary_files_format_and_content: Exonic.xls: Tab-delimited text file of HuR mature RNAs binding for uninvolved and involved psoriatic skin HuR RIP-Seq. 'HuR IP involved' and 'HuR IP uninvolved' are normalized counts. Transcripts with less than 10 reads in both uninvolved and involved skin HuR IPs were filtered and thus removed from the analysis. Transcripts with a ratio (HuR IP)/(mock IP) inferior to 0.5 log2 were also excluded. To avoid contamination of mature RNA transcripts with pre-mature RNA, values represent an "exonic relative read". Both in the 'HuR IP involved' and 'Hur IP uninvolved' columns, "exonic relative read" is calculated as follows: "exonic relative count" = (("exonic count" divided by "mRNA length") minus ("intronic count" divided by ("gene length" minus "mRNA length")) multiplied by "mRNA length", where "gene length" was as indicated in the UCSC table and "mRNA length" was as given in the RPKM formulation. We kept transcripts in the exonic listing when the ratio between "exonic relative count" and "intronic count" was superior or equal to 2 log2.
Supplementary_files_format_and_content: Intronic.txt: Tab-delimited text file of HuR pre-mature RNAs binding for uninvolved and involved psoriatic skin HuR RIP-Seq. 'HuR IP involved' and 'HuR IP uninvolved' are normalized counts. Transcripts with less than 10 reads in both uninvolved and involved skin HuR IPs were filtered and thus removed from the analysis. Transcripts with a ratio (HuR IP)/(mock IP) inferior to 0.5 log2 were also excluded.
|
| |
|
| Submission date |
Sep 04, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Geneviève Garcin |
| E-mail(s) |
genevieve.garcin@univ-montp2.fr
|
| Organization name |
CNRS UMR5235
|
| Lab |
DIMNP
|
| Street address |
UM2. Place Eugene Bataillon. Bat 24.
|
| City |
Montpellier |
| ZIP/Postal code |
34095 |
| Country |
France |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE50598 |
AMPK epidermal inhibition promotes HuR cytoplasmic localization eliciting post-transcriptional inflammatory response in psoriasis |
|
| Relations |
| BioSample |
SAMN02345629 |
| SRA |
SRX345295 |
