Weber 2014, Nucleosomes, H2A.Z and RNA in S2-DRSC knockdown cells.

Nucleosomes, H2A.Z maps in S2-DRSC with two knockdown genes (H2Av and YL1). PolII map at nucleotide resolution is done using a novel technique (3NT, mapping of the 3' end of nascent transcripts).

• Raw data was downloaded from: GSE49106
• Input file format: SRA
• Download date: 21-03-2016

From D. melanogaster (Apr 2006 BDGP R5/dm3).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM1193874.sga	S2-DRSC|H2AvPD|GFP-RNAi	H2AvPD	GSM1193874
2	GSM1193878.sga	S2-DRSC|H2AvPD|H2Av-RNAi	H2AvPD	GSM1193878
3	GSM1193882.sga	S2-DRSC|H2AvPD|YL1-RNAi	H2AvPD	GSM1193882

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	GSM1193876.sga	S2-DRSC|Nucleosomes|GFP-RNAi	MNase	GSM1193876
2	GSM1193880.sga	S2-DRSC|Nucleosomes|H2Av-RNAi	MNase	GSM1193880
3	GSM1193875.sga	S2-DRSC|Input|GFP-RNAi	IN	GSM1193875
4	GSM1193879.sga	S2-DRSC|Input|H2Av-RNAi	IN	GSM1193879
5	GSM1193883.sga	S2-DRSC|Input|YL1-RNAi	IN	GSM1193883

Transcription Profiling data:

	Filename	Description	Feature	GEO-ID
1	GSM1193873.sga	S2-DRSC|3NT|GFP-RNAi	3NT	GSM1193873
2	GSM1193877.sga	S2-DRSC|3NT|H2Av-RNAi	3NT	GSM1193877
3	GSM1319858.sga	S2-DRSC|3NT|TFIIS-RNAi	3NT	GSM1319858
4	GSM1193881.sga	S2-DRSC|3NT|YL1-RNAi	3NT	GSM1193881

Notes on samples nomenclature:

• H2Av: in D. melanogasper the H2A variant corresponding to H2A.Z is H2Av
• YL1: Chromatin remodelling factor that bind H2Av
• 3NT: mapping of the 3' end of nascent transcripts
• H2Av-RNAi: S2-DRSC cells with H2Av gene knockdown
• YL1-RNAi: S2-DRSC cells with YL1 gene knockdown
• GFP-RNAi: S2-DRSC cells with GFP gene knockdown (a control of the other two)

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. 1.5.2).

• Weber CM, Ramachandran S, Henikoff S
  Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase. Mol Cell. 2014 Mar 6;53(5):819-30. doi: 10.1016/j.molcel.2014.02.014. 24606920
• GEO series GSE49106: Nucleosomes are context-specific, H2A.Z modulated barriers to RNA polymerase