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| Status |
Public on Feb 07, 2023 |
| Title |
Kdm3 GLKD biol rep 3 |
| Sample type |
SRA |
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| Source name |
ovary
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: ovary
cell line: na
cell type: germinal + somatic
genotype: Kdm3 germline knock down
treatment: none
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| Growth protocol |
Flies were raised at 25°C on cornmeal medium.
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| Extracted molecule |
total RNA |
| Extraction protocol |
small RNA-seq: Total RNA was extracted from 10-20 pairs of ovaries using TRIzol (Life Technologies). A small RNA fraction of 15 nt to 30 nt in length was obtained following separation of total RNA on a denaturing polyacrylamide gel.
This fraction was used to generate multiplexed libraries with Illumina TruSeq Small RNA library preparation kits (RS-200-0012, RS200-0024, RS-200-036 or RS-200-048) at Fasteris (http://www.fasteris.com).
A house protocol based on TruSeq, which reduces 2S RNA (30 nt) contamination in the final library, was performed.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
small RNA-seq
Sequence reads in fastq format were trimmed from the adapter sequence 5’-TGGAATTCTCGGGTGCCAAG-3’ and matched to the D. melanogaster genome release 6 (dm6) using Bowtie
Sequence length distributions, small RNA mapping and small RNA overlap signatures were generated from bowtie alignments using Python and R (http://www.r- project.org/) scripts, which were wrapped and run in Galaxy instance publicly from ARTbio platform available at http://mississippi.fr.
For library comparisons, read counts were normalized to one million reads
unique mapper reads were obtained using sR_Bowtie -m0 (Galaxy Version 2.1.1)
For alignments we used a cleaned version of r6.36 version of Drosophila melanogaster genome (dm6, Flybase) in which sequences corresponding to unmapped (chrU), Y chromosome (chrY) and mitochondrial chromosome (chrM) were removed (dm6_clean).
Assembly: dm6_clean
Supplementary files format and content: bigWig, DEseq2 result for biological triplicates as a tab-delimited text file
RNA-seq
A DeSEq2 analyze on all D. mel. genes (release 6.36) was performed using the three biological replicates for each genotype, control or Kdm3 GLKD.
Assembly: dm6_clean
Supplementary files format and content: bigWig, DEseq2 result for biological triplicates as a tab-delimited text file
ChIP-Seq
reads were mapped on dm6_clean reference genome with BWA (Galaxy Version 0.7.17.4).
PCR duplicates were discarded using Picard tool (Galaxy Version 2.18.2.1)
Peak calling was made on mapped reads with MACS2 (Galaxy Version 2.1.1.20160309.6) using following parameters : --gsize ‘120000000’ --keep-dup ‘1’ --qvalue ‘0.05’ --nomodel --extsize ‘200’ --shift ‘0’. Narrowpeak was used for libraries obtained with Rhino antibody and broadpeak calling was used for libraries obtained with H3K9me2 and H3K9me3 antibodies ( --broad --broadcutoff=’0.1’).
Assembly: dm6_clean
Supplementary files format and content: bigWig and MACS2 files, broadpeak for H3K9me2 and H3K9me3, narrowpeak for Rhino
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| Submission date |
May 18, 2022 |
| Last update date |
Feb 08, 2023 |
| Contact name |
Antoine Boivin |
| E-mail(s) |
[email protected]
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| Organization name |
Sorbonne Universite CNRS
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| Department |
IBPS
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| Lab |
LBD UMR7622
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| Street address |
9 quai St Bernard
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| City |
PARIS |
| ZIP/Postal code |
75005 |
| Country |
France |
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| Platform ID |
GPL17275 |
| Series (1) |
| GSE203279 |
The histone demethylase KDM3 prevents auto-immune piRNAs production in Drosophila |
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| Relations |
| BioSample |
SAMN28525466 |
| SRA |
SRX15329061 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6165860_bamCoverage_smallRNAseq_KDM3GLKD3.bigwig |
2.2 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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