|
| Status |
Public on Dec 20, 2017 |
| Title |
pLD567_3xFLAG_elution_1 |
| Sample type |
SRA |
| |
|
| Source name |
pLD567_3xFLAG_elution
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T_LD
rip antibody: anti-FLAG; Sigma #F1804
growth: suspension
|
| Growth protocol |
Suspension growth as described in DOI: 10.1007/978-1-4939-3372-3_20
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cryomilling and affinity capture as descibed DOI: 10.1007/978-1-4939-3372-3_20 ; and 10.3791/54518. RNAs were further extracted and purified in a multi-stage procedure as described in the main research article, see summary, above.
5 µl of purified RNA was used directly in RNA fragmentation. Libraries were prepared according to Illumina's instructions with unique barcodes and were pooled at equimolar ratios.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Processed_RNA-Seq_combined.xlxs
6_567-3xFlag-1
|
| Data processing |
FASTAQ files were trimmed via trimmomatic (Bolger et al, 2014) using the following parameters: -phred33 -threads 8, LEADING:3 TRAILING:3 SLIDINGWINDOW:4:16 MINLEN:25
mapping was performed via STAR (Dobin et al, 2013) version 2.5.3a (https://github.com/alexdobin/STAR) using the following parameters: -runThreadN 8, --quantMode GeneCounts, --outSAMtype BAM SortedByCoordinate, --outFilterMatchNmin 30
the results were output to one binary alignment map file for each sample matched to the reference
genes with the coverage of 10 or more reads in at least 3 experiments were selected
data was normalized using the ‘DESeq2’ (Love et al, 2014) R package version 1.14.1.
Genome_build: Human genome hg19 GRCh37.87 (FASTA) and annotation (GTF file) were downloaded from ENSEMBL (ftp://ftp.ensembl.org/pub/grch37/release-90) and reference FASTA and GTF files were created by combining the human genome and ORFeus-Hs from pLD401 (DOI: 10.1016/j.cell.2013.10.021)
Supplementary_files_format_and_content: Single Excel spreadsheet
|
| |
|
| Submission date |
Dec 19, 2017 |
| Last update date |
Dec 20, 2017 |
| Contact name |
John LaCava |
| E-mail(s) |
jlacava@rockefeller.edu
|
| Organization name |
The Rockefeller University
|
| Street address |
1230 York ave
|
| City |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE108270 |
RNAs associated with affinity captured LINE-1 ribonucleoproteins |
|
| Relations |
| BioSample |
SAMN08203192 |
| SRA |
SRX3482572 |
