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| Status |
Public on Jul 29, 2020 |
| Title |
Input_IgG |
| Sample type |
SRA |
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| Source name |
Melanoma
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| Organism |
Homo sapiens |
| Characteristics |
cell line: A375
cell type: Melanoma cell line
passages: 14-18
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| Extracted molecule |
total RNA |
| Extraction protocol |
HNRNPH1-RNA interactions were stabilized with UV crosslinking (254 nm, 400 mJ/cm2), followed by lysis in iCLIP lysis buffer, limited digestion with RNase I (Ambion), immunoprecipitation of HNRNPH1-RNA complexes with a HNRNPH1 primary antibody (Bethyl Labs #A300-511A, at 10 μg per mL of lysate). Sample was dephosphorylated with FastAP (ThermoFisher) and T4 PNK (NEB).
A barcoded RNA adapter was ligated to the 3′ end (T4 RNA Ligase, NEB). RNA was reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter was then ligated to the cDNA fragment 3′ end. Sample was PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis. Samples were sequenced on the Illumina HiSeq 4000 platform.
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Ha3_12_input_S30_L007
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| Data processing |
Reads were adapter trimmed (cutadapt v1.9.dev1) and reads less than 18 bp were discarded.
Mapping was performed against the full human genome (hg38) including a database of splice junctions with STAR (v 2.4.0i). Uniquely mapping reads were then run through a custom-built PCR duplicate removal script.
eCLIP data sets with multiple in-line barcodes were merged at the usable read stage, and cluster identification was performed on usable reads using CLIPper11 (available at https://github.com/YeoLab/clipper/releases/tag/1.0).
Genome_build: hg38
Supplementary_files_format_and_content: file include Chromosome, Start position, Stop position, -log10(P-value), Log2 fold enrichment in eCLIP vs. input, Strand (+ or -)
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| Submission date |
Sep 16, 2019 |
| Last update date |
Jul 29, 2020 |
| Contact name |
Marco Mineo |
| E-mail(s) |
mmineo@bwh.harvard.edu
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| Phone |
6175255656
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| Organization name |
Brigham and Women's Hospital
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| Street address |
60 Fenwood Rd, BTM 8012
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE137489 |
Long noncoding RNA INCA1 regulates tumor interferon signaling. |
| GSE137526 |
Long noncoding RNA INCA1 regulates tumor interferon signaling [CLIP-seq] |
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| Relations |
| BioSample |
SAMN12768232 |
| SRA |
SRX6854811 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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