Kruesi 2013, Pol-II controls to achive X-chromosome compensation.

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.

• Raw data was downloaded from: GEO
• Input file format: SRA
• Download date: n/a

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	-

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).

• 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. doi: 10.7554/eLife.00808. 23795297
• GEO series GSE43087: Condensin Controls Recruitment of RNA Polymerase II to Achieve X-Chromosome Dosage Compensation