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| Status |
Public on Jan 22, 2019 |
| Title |
HA_control_Rep1 |
| Sample type |
SRA |
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| Source name |
ChIP Seq of HA tag alone
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2R+
cell type: Embryonic
chip antibody: F-7 (anti-HA), Santa Cruz
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| Treatment protocol |
S2R+ cells were fixed with 1% formaldehyde for 10 min at room temperature, and harvested in SDS buffer resuspended in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and lysed by sonication. The lysate was cleared by centrifugation, and incubated with respective antibodies overnight at 4¡C. Antibody complexes bound to protein G beads, were washed once with 140mM RIPA, four times with 500mM RIPA, one with LiCl buffer and twice with T.E buffer for 10 minutes each at 4¡C.
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| Growth protocol |
Drosophila S2R+ cells were cultured in Schneider Cell’s Medium (GIBCO, Cat No-21720) supplemented with 10% FBS and 2% Penicillin/Streptomycin
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was recovered after reverse crosslinking and phenol chloroform extraction. After precipitating and pelleting, DNA was dissolved in 30 _l of TE
After checking enrichment the recovered DNA was converted into libraries using NebNext Ultra DNA library preperation kit, following manufacturer's protocol
NebNext UltraII
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Samples were sequencing on an Illumian NextSeq500 and demultiplexed using bcl2fastq v2.19. The libraries contain a Yeast spike in.
Mapping was done using bowtie2 (v. 2.2.8) against BDGP6 fo the Drosophila genome
Bigwig tracks were produced using bedTools (v.2.25) and bedGraphToBigwig
Genome_build: BDGP6
Supplementary_files_format_and_content: sequencing depth normalised bigwig tracks
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| Submission date |
Nov 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jean-Yves Roignant |
| Organization name |
Institute of molecular Biology
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| Lab |
Roignant
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| Street address |
Ackermannweg 4
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| City |
Mainz |
| ZIP/Postal code |
55128 |
| Country |
Germany |
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| Platform ID |
GPL19132 |
| Series (2) |
| GSE92389 |
Promoter-proximal pausing mediated by the exon junction complex regulates splicing |
| GSE106905 |
ChIP of eif4AIII_HA and Y14_HA with Ctrl_HA [Promoter-proximal pausing mediated by the exon junction complex regulates splicing] |
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| Relations |
| BioSample |
SAMN08027403 |
| SRA |
SRX3393641 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2857411_HA_control_Rep1.bw |
63.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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