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

Samples

From C. elegans (May 2008 WS190/ce6).

Genome Annotation:

Filename Description Feature GEO-ID
1 kruesi13_tss_ce6.sga TSS from Kruesi et al, 2013 TSS -

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM1056292.sga wild type - DPY-27 - none DPY-27 GSM1056292
2 GSM1056293.sga wild type - IgG - none IgG GSM1056293

:

Filename Description Feature GEO-ID
1 GSM1056279.sga wild type - GRO-seq - none - rep1 GRO-seq GSM1056279
2 GSM1056283.sga wild type - GRO-seq - none - rep2 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 - rep1 GRO-cap GSM1056284
7 GSM1056285.sga wild type - GRO-cap - none - rep2 GRO-cap GSM1056285
8 GSM1056290.sga wild type - GRO-cap - none - rep3 GRO-cap GSM1056290
9 GSM1056291.sga wild type - GRO-cap - none - rep4 GRO-cap GSM1056291
10 GSM1056286.sga sdc-2 - GRO-cap - sdc-2 RNAi - rep1 GRO-cap GSM1056286
11 GSM1056287.sga sdc-2 - GRO-cap - sdc-2 RNAi - rep2 GRO-cap GSM1056287
12 GSM1056288.sga wild type - GRO-cap - starved - rep1 GRO-cap GSM1056288
13 GSM1056289.sga wild type - GRO-cap - starved - rep2 GRO-cap GSM1056289
14 wt_GRO_seq_all.sga wild type - GRO-seq - all GRO-seq -
15 wt_GRO_cap_all.sga wild type - GRO-cap - all GRO-cap -

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.3).

References

Last update: 11 Oct 2017