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| Status |
Public on Aug 30, 2019 |
| Title |
ABO_NC0_R2_B1_L2 |
| Sample type |
SRA |
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| Source name |
Single Embryo
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| Organism |
Drosophila melanogaster |
| Characteristics |
treatment: abo mutation; Histone overexpression
developmental stage: Unfertilized
embryo/ biological replicate: Replicate 2
sequencing batch/ lane/ technical replicate: abo timecourse experiment: Batch 1 Lane 2
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| Growth protocol |
Drosophila stocks grown and embryos collected in 18°C (Slbp experiment) or 25°C (abo experiment). Embryos staged and imaged at 22°C.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
The appropriately staged embryos were placed into an RNase free tube, lysed with a sterile needle. Then 100 μl of lysis buffer (Applied Biosystems, KIT0214) was added, and embryos were flash-frozen in liquid nitrogen, then stored at -80°C
For the Slbp comparison: rRNA depletion was performed using the Ribo-Zero rRNA Removal (Human, Mouse, Rat) Kit (Illumina, MRZH11124) followed by converting the poly-A containing RNA transcripts to cDNA using oligo-dT adaptor and further amplified by PCR following the Smart-seq2 method (Picelli et al, 2014). Illumina sequencing libraries were made from the amplified cDNA samples using the Nextera DNA library prep kit (Illumina, FC-121-1031). For the abo single time point comparison: poly-A containing RNA transcripts were enriched using oligo-dT bead and further converted to cDNA and Illumina sequencing library using PrepX RNA-seq library kit on the automated Apollo 324 NGS Library Prep System (Wafergen Biosystems) following the manufacturer's protocol. For the abo timecourse comparison: poly-A containing RNA transcripts were converted to cDNA using oligo-dT adaptor and further amplified by PCR following the Smart-seq2 method (Picelli et al, 2014). Illumina sequencing libraries were made from the amplified cDNA samples using the Nextera DNA library prep kit (Illumina, FC-121-1031). The RNA-seq libraries were sequenced on Illumina HiSeq 2500 Rapid flow-cells as single-end 75nt reads, following the standard Illumina protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Single end 75bp reads
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| Data processing |
Raw sequencing reads were filtered by Illumina HiSeq Control Software and only the Pass-Filter reads were used for further analysis.
Sequenced raw reads were demultiplexed using fastq-multx (v 1.3.1) and trimmed using Trim Galore (v 0.5.0) default parameters.
Trimmed reads were mapped to the Drosophila melanogaster transcriptome (r6.19) and quantified using default parameters in Salmon (0.10.2).
Normalization and differnetial gene expression analysis were performed using DESeq2 (v 1.20.0) after collapsing the technical replicates (same library sequenced in different batches/ lanes).
Genome_build: Drosophila melanogaster Trranscriptome r6.19
Supplementary_files_format_and_content: Tab-delimited raw quantfication output from Salmon. Tab-delimited files for DESeq2 normalized gene counts as well as DE analysis outputs for each of the Slbp, abo pooled and abo timecourse experiments.
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| Submission date |
Aug 29, 2019 |
| Last update date |
Aug 30, 2019 |
| Contact name |
Amanda Amodeo |
| E-mail(s) |
aamodeo@princeton.edu
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| Phone |
6092589406
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| Organization name |
Princeton University
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| Department |
Lewis-Sigler Institute for Integrative Genomics
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| Street address |
Carl Ichan Laboratory, Washington Rd
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| City |
Princeton |
| State/province |
NJ |
| ZIP/Postal code |
08544 |
| Country |
USA |
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| Platform ID |
GPL17275 |
| Series (1) |
| GSE136631 |
Histone concentration times the cell cycle and transcription in early development. |
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| Relations |
| BioSample |
SAMN12658246 |
| SRA |
SRX6771445 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4053484_ABO_NC0_R2_B1_L2_salmon_quant.txt.gz |
352.6 Kb |
(ftp)(http) |
TXT |
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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