Curated Sample Data


Genome
dm3
Antigen Class
Input control
Antigen
Input control
Cell type Class
Adult
Cell type
Dopaminergic Neurons

Cell type information


MeSH Description
Neurons whose primary neurotransmitter is DOPAMINE.

Attributes by Original Data Submitter


source_name
H3K4me3_GH_input_ChIPseq
strain
Canton S
condition
4 days group-housing (20 males/vial)

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For each ChIP-seq reaction ~10,000-15,000 mini-INTACT isolated bead-bound nuclei were processed using Low Cell # ChIP kit (Diagenode: C01010070) as per manufacturer's instructions. In brief, nuclei were fixed in 1% formaldehyde for 2 minutes, immediately quenched with Glycine and then lysed using nuclear lysis buffer with protease inhibitor cocktail at room temperature for 5 minutes. PBS was added to dilute the lysate-bead mix and loaded in AFA tubes (Covaris Inc.: 520045) for sonication. Ultra-sonicator (Covaris Inc.: E220) was used to sheer chromatin to ~200 bp length and chromatin was recovered from the supernatant after magnetic separation. We isolated cell bodies of dopaminergic neurons using Fluorescence Activated Cell Sorting (FACS) during the flies' morning activity peak. In brief, brains were dissected from socially-isolated or group-housed flies expressing membrane-tagged GFP and nuclear tdTomato in their dopaminergic neurons. The flies were obtained by crossing flies carrying TH-GAL4 with a stock carrying pJFRC105-10XUAS-IVS-nlstdTomato in VK40 (gift of Barret D. Pfeiffer, Rubin Lab, Janelia Research Campus) and pJFRC29-10XUAS-IVS-myr::GFP-p10 in AttP40. To account for possible manual bias, dissectors switched their handling of group- or single-housed flies in each session. Dissected brains were digested using Liberase DH (Roche: 5401054001), manually triturated using glass pipettes, and filtered using a Falcon 35 μm cell strainer (Corning: 352235) before sorting. Approximately 1500 dopaminergic neurons were obtained from approximately 30 brains using a BD FACSAria II sorter (BD Biosciences, USA). Total RNA was extracted using the Arctus, PicoPure RNA Isolation Kit (Thermo Fisher Scientific: 12204-01), ERCC spike-in controls were added and cDNA libraries from this material were prepared. ChIP-seq libraries for sequencing were prepared using MicroPlex Library Preparation kit (Diagenode: C05010012) as per manufacturer's instruction. Ovation RNA-seq System V2 (Nugen: 7102) as per manufacturer's instructions.

Platform Information


instrument_model
Illumina HiSeq 2500

External Database Query

Logs in read processing pipeline


Number of total reads
14881875
Reads aligned (%)
95.2
Duplicates removed (%)
10.0
Number of peaks
1640 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA