Weber 2014, Nucleosomes, H2A.Z and RNA in S2-DRSC knockdown cells. LiftOver from dm3.

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 for the dm3 assembly was downloaded from: GSE49106
• Input file format: SRA
• Download date: 21-03-2016

From D. melanogaster (Aug 2014 BDGP Rel6 + ISO1 MT/dm6).

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
• 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)

This dataset was lifted over from dm3.

• 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