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).



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:

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 (ChIP-Seq v. 1.5.2).


Last update: 1 Oct 2018