Kruesi13, Pol-II controls to achive X-chromosome compensation

Description

Sequencing of cap RNA (5'-end) of C. elebans transcripts. Samples marked as 'short' refer to nascent transcrips before they are transpliced. The scientist isolated short (20-100nt) nuclear RNA with a 5' cap from embryos. 'Long' samples are capped RNA longher than 200nt that are already transpliced and can be used to validate the 'short' samples. Original sample GSM1050559 was discarded die to very poor mapping.

Source

Data can be downloaded from: GEO dataset GSE43087

Samples

From C. elegans genome WC190 (ce6).

Filename Description Feature GEO-ID
1 GSM1056279.sga wild type - GRO-seq - none GRO-seq GSM1056279
2 GSM1056283.sga wild type - GRO-seq - none GRO-seq GSM1056283
3 GSM1056281.sga sdc-2 - GRO-seq - sdc-2 RNAi GRO-seq GSM1056281
4 GSM1056282.sga wild type - GRO-seq - starved GRO-seq GSM1056282
5 GSM1056280.sga wild type - GRO-seq - L4440 control siRNA GRO-seq GSM1056280
6 GSM1056284.sga wild type - GRO-cap - none GRO-cap GSM1056284
7 GSM1056285.sga wild type - GRO-cap - none GRO-cap GSM1056285
8 GSM1056290.sga wild type - GRO-cap - none GRO-cap GSM1056290
9 GSM1056291.sga wild type - GRO-cap - none GRO-cap GSM1056291
10 GSM1056286.sga sdc-2 - GRO-cap - sdc-2 RNAi GRO-cap GSM1056286
11 GSM1056287.sga sdc-2 - GRO-cap - sdc-2 RNAi GRO-cap GSM1056287
12 GSM1056288.sga wild type - GRO-cap - starved GRO-cap GSM1056288
13 GSM1056289.sga wild type - GRO-cap - starved GRO-cap GSM1056289
14 GSM1056292.sga wild type - DPY-27 - none DPY-27 GSM1056292
15 GSM1056293.sga wild type - IgG - none IgG GSM1056293

Technical Notes

SRA files were downloaded from GEO GSE43087 and converted in FASTQ using fastq-dump program from sratoolkit. Mapping was done using Bowtie and sam files were converted in sga files using samtools and chipseq.

References

  1. Kruesi WS, Core LJ, Waters CT, Lis JT, Meyer BJ.
    Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation. Elife. 2013 Jun 18;2:e00808. PMID: 23795297

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