 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 01, 2013 |
| Title |
P1 RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Blood lymphocytes
|
| Organism |
Homo sapiens |
| Characteristics |
individual type: patient
gender: male
mutation type: Frame shift
cell type: blood lymphocyte
phenotype: intellectual disability
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Blood lymphocytes were extracted using the PAXgeneTM Blood System (Becton Dickinson, Heidelberg, Germany). 20 ng total RNA was amplified using the Ovation RNA-Seq system (NuGEN, San Carlos, CA, USA).
The Beckman Coulter SPRIworks (Beckman Coulter, Danvers, MA, USA) platform was used for the automated library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Data processing |
RNA-seq reads were mapped to the hg19 reference genome using Bowtie version 0.12.7 with a SNP fraction of 0.001.
Mapped reads were assigned to transcripts of the March 9 2012 version of the Illumina iGenomes transcriptome (http://cufflinks.cbcb.umd.edu/igenomes.html) using HTSeq (http://www-huber.embl.de/users/anders/HTSeq/) version 0.5.3p9 with default settings.
Differential expression between patients and controls was determined using the count-based DESeq R package. A Benjamini & Hochberg multiple testing-adjusted P-value cut-off of 0.05 was used.
Gene expression levels were calculated as the DESeq-normalized number of reads per kilobase of gene exon model length (normalized reads per kilobase; NRPK). Gene exon model length was determined by overlapping the genomic ranges of all exons assigned to a gene in the iGenomes GTF file with BedTools, and summing up their total genomic coverage. The NRPK value was scaled to a “reads per kilobase per million mapped reads” (RPKM) value by dividing it by the mean number of reads per individual in millions.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated RPKM expression matrix containing gene Ensembl ID, Entrez gene ID, HUGO gene symbol, and the RPKM values for the 3 patients and 8 controls. Where one measurement corresponds to multiple gene IDs, these are sepatered by semicolons.
|
| |
|
| Submission date |
May 10, 2013 |
| Last update date |
Jun 14, 2022 |
| Contact name |
Jo Huiqing Zhou |
| E-mail(s) |
jo.zhou@radboudumc.nl
|
| Organization name |
Radboud University
|
| Street address |
Geert Grooteplein 26/28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525GA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL13393 |
| Series (2) |
| GSE46831 |
De novo mutations in the genome organizer CTCF cause Intellectual Disability (RNA-Seq) |
| GSE46833 |
De novo mutations in the genome organizer CTCF cause Intellectual Disability |
|
| Relations |
| BioSample |
SAMN02142002 |
| SRA |
SRX276986 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
