GEO series

PAR-CLIP analysis of YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 and SRSF10 in human HeLa cells

GSE71096 Homo sapiens (human) Other 9 samples Submitted 2016/02/17 Platform GPL11154

At a glance

human · 9 samples

Organism: Homo sapiens (human)
Samples: 9 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

Label the cells overexpressed Flag tagged YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 and SRSF10 with 4-SU, the RNA bound by YTHDC1 and SRSF proteins can be got by Flag IP followed by RNA isolation by using the TRIzol (Invitrogen) reagent by following the company manual.the RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 101 bp.

Read the full summary ↓

Sequencing chemistry v2 (Illumina) was used and samples were multiplexed in two samples per lane.

This dataset

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Download · which file do I need?

Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE71096_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA290341 and SRA study SRP061321. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 26876937) ↗

Samples in this study

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+ 9 more — browse all 9 samples with per-sample file links →

Datasets on a similar topic

GSE71095 Transcriptomics analysis of gene expression in normal and YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 or SRSF10 deficient human HeLa cells 12 samples shares ythdc1, srsf10, srsf1, srsf3, srsf7, srsf9, hela
GSE272166 The regulation of transcriptome in HCC cells by SRSF10 [Huh7_shSRSF10_RNAseq] 6 samples shares srsf10, srsf1
GSE336266 RNA-seq of THP1 cells with SRSF10 knockdown 6 samples shares srsf10, srsf1
GSE29943 Unstressed HeLa cells and ELAVL1/HuR knock down conditions: polyA RNA-Seq, small RNA-Seq, and PAR-CLIP 9 samples shares par-clip, hela
GSE287825 The METTL3-YTHDC1 axis mediates architectural RNA m6A modification to modulate the integrity of chromatin TADs in MLLr+ AML genome 36 samples shares ythdc1
GSE283317 YTHDC1 cooperates with the THO complex to prevent RNA damage-induced DNA breaks 30 samples shares ythdc1
GSE21578 Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP 29 samples shares par-clip
GSE239333 YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response 21 samples shares ythdc1

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