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GSE107768

GSE GEO
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Best practices for eCLIP experiments and analysis

Organism: Homo sapiens
Platform: GPL20301
Samples: 378
Experiment Types:
Other
Submitted: Dec 06 2017
Last Updated: Aug 24 2020
Status: Public on Jun 08 2018
Contact: Gene,,Yeo (UCSD)

Relations

SuperSeries of: GSE107766 SuperSeries of: GSE107767 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA421341

Summary

This SuperSeries is composed of the SubSeries listed below.

Overall Design

Refer to individual Series

Analysis (33 steps)

View Data Processing
Processing steps for GSE107768
  1. Library strategy: eCLIP-seq
  2. Takes output from raw files.
  3. Run to trim off both 5’ and 3’ adapters on both reads.
  4. Command: quality-cutoff 6 -m 18 -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
  5. Takes output from cutadapt round 1.
  6. Run to trim off the 3’ adapters on read 2, to control for double ligation events.
  7. Command: cutadapt -f fastq --match-read-wildcards --times 1 -e 0.1 -O 5 --quality-cutoff 6 -m 18 -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
  8. Takes output from cutadapt round 2.
Showing first 8 steps.

Supplementary Files (1)

GSE107768_RAW.tar Download
GEO Samples (378)
GSM2878474 GSM2878475 GSM2878476 GSM2878477 GSM2878478 GSM2878479 GSM2878480 GSM2878481 GSM2878482 GSM2878483 GSM2878484 GSM2878485 GSM2878486 GSM2878487 GSM2878488 GSM2878489 GSM2878490 GSM2878491 GSM2878492 GSM2878493 GSM2878494 GSM2878495 GSM2878496 GSM2878497 GSM2878498 GSM2878499 GSM2878500 GSM2878501 GSM2878502 GSM2878503 GSM2878504 GSM2878505 GSM2878506 GSM2878507 GSM2878508 GSM2878509 GSM2878510 GSM2878511 GSM2878512 GSM2878513 GSM2878514 GSM2878515 GSM2878516 GSM2878517 GSM2878518 GSM2878519 GSM2878520 GSM2878521 GSM2878522 GSM2878523 GSM2878524 GSM2878525 GSM2878526 GSM2878527 GSM2878528 GSM2878529 GSM2878530 GSM2878531 GSM2878532 GSM2878533 GSM2878534 GSM2878535 GSM2878536 GSM2878537 GSM2878538 GSM2878539 GSM2878540 GSM2878541 GSM2878542 GSM2878543 GSM2878544 GSM2878545 GSM2878546 GSM2878547 GSM2878548 GSM2878549 GSM2878550 GSM2878551 GSM2878552 GSM2878553 GSM2878554 GSM2878555 GSM2878556 GSM2878557 GSM2878558 GSM2878559 GSM2878560 GSM2878561 GSM2878562 GSM2878563 GSM2878564 GSM2878565 GSM2878566 GSM2878567 GSM2878568 GSM2878569 GSM2878570 GSM2878571 GSM2878572 GSM2878573 GSM2878574 GSM2878575 GSM2878576 GSM2878577 GSM2878578 GSM2878579 GSM2878580 GSM2878581 GSM2878582 GSM2878583 GSM2878584 GSM2878585 GSM2878586 GSM2878587 GSM2878588 GSM2878589 GSM2878590 GSM2878591 GSM2878592 GSM2878593 GSM2878594 GSM2878595 GSM2878596 GSM2878597 GSM2878598 GSM2878599 GSM2878600 GSM2878601 GSM2878602 GSM2878603 GSM2878604 GSM2878605 GSM2878606 GSM2878607 GSM2878608 GSM2878609 GSM2878610 GSM2878611 GSM2878612 GSM2878613 GSM2878614 GSM2878615 GSM2878616 GSM2878617 GSM2878618 GSM2878619 GSM2878620 GSM2878621 GSM2878622 GSM2878623 GSM2878624 GSM2878625 GSM2878626 GSM2878627 GSM2878628 GSM2878629 GSM2878630 GSM2878631 GSM2878632 GSM2878633 GSM2878634 GSM2878635 GSM2878636 GSM2878637 GSM2878638 GSM2878639 GSM2878640 GSM2878641 GSM2878642 GSM2878643 GSM2878644 GSM2878645 GSM2878646 GSM2878647 GSM2878648 GSM2878649 GSM2878650 GSM2878651 GSM2878652 GSM2878653 GSM2878654 GSM2878655 GSM2878656 GSM2878657 GSM2878658 GSM2878659 GSM2878660 GSM2878661 GSM2878662 GSM2878663 GSM2878664 GSM2878665 GSM2878666 GSM2878667 GSM2878668 GSM2878669 GSM2878670 GSM2878671 GSM2878672 GSM2878673 GSM2878674 GSM2878675 GSM2878676 GSM2878677 GSM2878678 GSM2878679 GSM2878680 GSM2878681 GSM2878682 GSM2878683 GSM2878684 GSM2878685 GSM2878686 GSM2878687 GSM2878688 GSM2878689 GSM2878690 GSM2878691 GSM2878692 GSM2878693 GSM2878694 GSM2878695 GSM2878696 GSM2878697 GSM2878698 GSM2878699 GSM2878700 GSM2878701 GSM2878702 GSM2878703 GSM2878704 GSM2878705 GSM2878706 GSM2878707 GSM2878708 GSM2878709 GSM2878710 GSM2878713 GSM2878714 GSM2878715 GSM2878716 GSM2878717 GSM2878718 GSM2878719 GSM2878720 GSM2878721 GSM2878722 GSM2878723 GSM2878724 GSM2878725 GSM2878726 GSM2878727 GSM2878728 GSM2878729 GSM2878730 GSM2878731 GSM2878732 GSM2878733 GSM2878734 GSM2878735 GSM2878736 GSM2878737 GSM2878738 GSM2878739 GSM2878740 GSM2878741 GSM2878742 GSM2878743 GSM2878744 GSM2878745 GSM2878746 GSM2878747 GSM2878748 GSM2878749 GSM2878750 GSM2878751 GSM2878752 GSM2878753 GSM2878754 GSM2878755 GSM2878756 GSM2878757 GSM2878758 GSM2878759 GSM2878760 GSM2878761 GSM2878762 GSM2878763 GSM2878764 GSM2878765 GSM2878766 GSM2878767 GSM2878768 GSM2878769 GSM2878770 GSM2878771 GSM2878772 GSM2878773 GSM2878774 GSM2878775 GSM2878776 GSM2878777 GSM2878778 GSM2878779 GSM2878780 GSM2878781 GSM2878782 GSM2878783 GSM2878785 GSM2878786 GSM2878787 GSM2878788 GSM2878789 GSM2878790 GSM2878791 GSM2878792 GSM2878793 GSM2878794 GSM2878795 GSM2878796 GSM2878797 GSM2878798 GSM2878799 GSM2878800 GSM2878801 GSM2878802 GSM2878803 GSM3396755 GSM3396756 GSM3396757 GSM3396758 GSM3396759 GSM3396760 GSM3398052 GSM3398053 GSM3398054 GSM3398055 GSM3398056 GSM3398057 GSM3398058 GSM3398059 GSM3398060 GSM3398061 GSM3398062 GSM3398063 GSM3398064 GSM3398065 GSM3398066 GSM3398067 GSM3398068 GSM3398069 GSM3398070 GSM3398071 GSM3398072 GSM3398073 GSM3398074 GSM3398075 GSM3398076 GSM3398077 GSM3398078 GSM3398079 GSM3398080 GSM3398081 GSM3398082 GSM3398083 GSM3398084 GSM3398085 GSM3398086 GSM3398087 GSM3398088 GSM3398089 GSM3398090 GSM3398091 GSM3398092 GSM3398093 GSM3398094 GSM3398095 GSM3398096

Dataset Citations (2)

A protein-RNA interaction atlas of the ribosome biogenesis factor AATF.
PMID 31363146 · 2019 · Scientific reports
Rainer W J Kaiser, Michael Ignarski, Eric L Van Nostrand, Christian K Frese, Manaswita Jain, Sadrija Cukoski, Heide Heinen, Melanie Schaechter, Lisa Seufert, Konstantin Bunte, Peter Frommolt, Patrick Keller, Mark Helm, Katrin Bohl, Martin Höhne, Bernhard Schermer, Thomas Benzing, Katja Höpker, Christoph Dieterich, Gene W Yeo, Roman-Ulrich Müller, Francesca Fabretti
A large-scale binding and functional map of human RNA-binding proteins.
PMID 32728246 · 2020 · Nature
Eric L Van Nostrand, Peter Freese, Gabriel A Pratt, Xiaofeng Wang, Xintao Wei, Rui Xiao, Steven M Blue, Jia-Yu Chen, Neal A L Cody, Daniel Dominguez, Sara Olson, Balaji Sundararaman, Lijun Zhan, Cassandra Bazile, Louis Philip Benoit Bouvrette, Julie Bergalet, Michael O Duff, Keri E Garcia, Chelsea Gelboin-Burkhart, Myles Hochman, Nicole J Lambert, Hairi Li, Michael P McGurk, Thai B Nguyen, Tsultrim Palden, Ines Rabano, Shashank Sathe, Rebecca Stanton, Amanda Su, Ruth Wang, Brian A Yee, Bing Zhou, Ashley L Louie, Stefan Aigner, Xiang-Dong Fu, Eric Lécuyer, Christopher B Burge, Brenton R Graveley, Gene W Yeo

Linked Publications (2)

A large-scale binding and functional map of human RNA-binding proteins.
Nature · 2020
A protein-RNA interaction atlas of the ribosome biogenesis factor AATF.
Scientific reports · 2019