|
| Status |
Public on Jan 24, 2013 |
| Title |
TAF15_2_L |
| Sample type |
SRA |
| |
|
| Source name |
Temporal cortices
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Temporal cortex
origin: Brain
antibodies: TAF15 (Bethyl Lab, A300-308A)
|
| Treatment protocol |
High-throughput sequencing of immunoprecipitated and crosslinked RNA (HITS-CLIP) from normal human brain was performed using anti-TAF15 antibody (Bethyl; A300-308A). HITS-CLIP was performed as previously described (Chi et al., 2009; Vourekas et al., 2012).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sample preparation for HITS-CLIP: Frozen brain tissues were homogenized and irradiated by UV. Cells were lysed, treated with RNaseT1 and DNaseI. Cleared lysates were used for IPs using anti-TAF15 antibodies (A300-308A) that were cojugated with ProteinA Dynabeads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
HITS-CLIP of TAF15 prepared from human brain-2 main signal
Illumina Genome Analyzer IIe
|
| Data processing |
The 3’-adaptor was removed from the sequences using the cutadapt software and a 0.25 acceptable error rate for the alignment of the adaptor on the tag.
Reads shorter than 15nt were removed
Reads were aligned to the human (hg19) and mouse (mm9) genomes respectively using BWA with default program parameters
Aligned reads shorter than 20nt that align to more than 1 position on the genome were removed
Aligned reads mapping on repeat elements as defined by RepeatMasker were removed
Peaks were defined by merging overlapping tags into single merged regions and selecting the point with the highest number of aligned reads within each region as the actual peak position. The height of each peak was defined as the total number of tags within the merged region. Only peaks with score higher than 2 were used in further analysis
Genome_build: hg19
Supplementary_files_format_and_content: BED files contain the defined peaks. Scores represent the score of the peaks.
Supplementary_files_format_and_content: The column names for the bed files are: 1. chromosome 2. start 3. stop 4. name 5. score 6. strand
|
| |
|
| Submission date |
Jan 04, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Manolis Maragkakis |
| E-mail(s) |
emmanouil.maragkakis@nih.gov
|
| Organization name |
National Institute on Aging
|
| Street address |
251 Bayview Blvd
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE43294 |
Identification of in vivo, conserved, TAF15 RNA binding sites and the impact of TAF15 on the neuronal transcriptome |
|
| Relations |
| SRA |
SRX214274 |
| BioSample |
SAMN01882354 |
