|
| Status |
Public on Oct 20, 2013 |
| Title |
CD4_resting_binding_sites |
| Sample type |
SRA |
| |
|
| Source name |
Primary CD4+ purified from PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: CD4+ T cells
cell type: primary human CD4+ purified from PBMC
condition: Resting
|
| Treatment protocol |
JSL1 cells were either untreated for 24 hours (resting samples) or activated with 20ng/mL PMA for 60 hours, and CD4+ cells were either untreated for 24 hours (resting samples) or activated with 10ug anti-CD3/CD28 antibodies
|
| Growth protocol |
Cells were cultured in RPMI + 10% FBS at 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were UV crosslinked on ice, and lysates were immunprecipitated with anti-hnRNP L antibody (4D11) on Protein G Dynabeads, and RNAs from protein-RNA complexes were isolated and subjected to CLIP-seq library preparation.
Biological triplicate libraries were individually barcoded by two-step PCR, pooled, and sequenced on Hi-Seq 2000 (CD4 samples) or GA-Iix (JSL1 samples).
Single-end, 76 cycles (JSL1 samples) or 100 cycles (CD4 samples)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
hnRNP L-bound RNA
Binding profile from resting CD4 combined CLIP-seq experiments, this sample represents 3 CD4 resting samples
|
| Data processing |
Raw reads were trimmed from the 3' end for basecall quality score of 0 (PHRED score) with Perl 5.16.2
3' sequencing adaptor (RL3) was removed with cutadapt version 0.9.4
Homopolymeric ends (6+ identical bases at the 3' end of the read) were trimmed with Perl 5.16.2
Reads were aligned to the human genome (hg19) with bowtie 0.12.7, keeping only one copy of each alignment position (start and end) that aligned to no other position in the genome.
Peaks were called empirically using 100 iterations of randomization of aligned reads within each transcript at an FDR threshold of 0.001, then merged within 50nt.
Genome_build: hg19
Supplementary_files_format_and_content: BED6, score field is total number of alignments per binding site
|
| |
|
| Submission date |
Jun 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kristen Lynch |
| E-mail(s) |
klync@pennmedicine.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Department |
Biochemistry and Molecular Biophysics
|
| Lab |
Kristen Lynch
|
| Street address |
906 Stellar Chance Labs 422 Curie Blvd
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE47604 |
Transcriptome-wide interaction mapping of hnRNP L in human T cells with CLIP-seq |
|
| Relations |
| BioSample |
SAMN02189841 |
| SRA |
SRX286284 |
| SRA |
SRX286285 |
| SRA |
SRX286286 |
