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| Status |
Public on Sep 05, 2012 |
| Title |
RpL12-Myc |
| Sample type |
SRA |
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| Source name |
pools of wing imaginal discs
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Wing imaginal discs
developmental stage: Third instar larvae
genotype: sd::Gal4>UAS::FH-cortoCD
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| Extracted molecule |
total RNA |
| Extraction protocol |
Wing imaginal discs of third instar larvae (one disc per larva) were dissected by batches of 50 in PBS and frozen in liquid nitrogen. 300 discs (6 batches) were pooled and homogenized in lysis buffer using a FastPrep-24 during 20 s at 4m.s-1 (MP Biomedicals, Lysing Matrix D). Total RNA were extracted using RNeasy® kit (Quiagen). Library preparation and Illumina sequencing (multiplexed 50 bp paired-end sequencing on HiSeq 2000) were performed at the BC Cancer Agency Genome Sciences Center (Canada) following the manufacturer's protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava 1.7 was used for basecalling.
Before mapping, poly N read tails were trimmed, reads ≤11 bases were removed, and reads with quality mean ≤12 were discarded.
Reads were then aligned against the D. melanogaster genome (dm3 genome assembly, BDGP Release 5.38) using Bowtie mapper (version 0.12.7)
Alignments from reads matching more than once on the reference genome were removed using Java version of samtools.
To compute gene expression, D. melanogaster GFF3 genome annotation from FlyBase (version 5.38) was used. All overlapping regions between alignments and referenced exons were counted.
Technical replicates coming from paired-end reads were first summed. Then, all samples were normalized together. Data were normalized according to the scaling normalization proposed by Robinson and Oshlack and implemented in the edgeR package version 1.6.10
A Fisher's Exact Test was then performed using the sage.test function of the statmod package version 1.4.6. Finally, a Benjamini and Hochberg (BH) P-value adjustment was made.
Genome_build: dm3 genome assembly, BDGP Release 5.38
Supplementary_files_format_and_content: tab-delimited text files include abundance estimation for each Sample. ID: transcript ID from modEncode Drosophila database, Type: feature annotation type according to the GFF format definition, Chromosome: chromsome reference, Start: genomic start position of the feature, End: genomic end position of the feature, Strand: genomic strand position + or - of the feature, length: full length of the feature, FullCovered: boolean that indicates is the feature is fully covered by reads, BasesNotCovered: the number of bases not covered by any reads after mapping, Ratio: the feature abundance among all the feature list, Count: the raw read count covering the feature
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| Submission date |
Jun 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Stéphane LE CROM |
| Organization name |
École normale supérieure
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| Department |
Biology Institute - IBENS
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| Lab |
Genomic platform
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| Street address |
46 rue d'Ulm
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| City |
Paris |
| ZIP/Postal code |
75013 |
| Country |
France |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE38435 |
New partners in regulation of gene expression: the Enhancer of Trithorax and Polycomb Corto interacts with methylated Ribosomal Protein L12 via its chromodomain. |
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| Relations |
| Reanalyzed by |
GSM3278124 |
| SRA |
SRX151345 |
| BioSample |
SAMN01036608 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM942042_rpl12m2_1.txt.gz |
662.5 Kb |
(ftp)(http) |
TXT |
| GSM942042_rpl12m2_2.txt.gz |
663.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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