Raborn 2016, CAGE analysis of Daphnia pulex RNA from three developmental stages.


This series contains CAGE data for three developmental states of the water flea Daphnia pulex: sexual females, asexual females, and males.



From D. pulex (Sep 2019 PA42 4.1/dpu2).

Transcription Profiling data:

Filename Description Feature GEO-ID
1 Asexual_Females_rep1.sga Asexual females|CAGE||rep1 CAGE GSM2113454
2 Asexual_Females_rep2.sga Asexual females|CAGE||rep2 CAGE GSM2113455
3 Asexual_Females_rep3.sga Asexual females|CAGE||rep3 CAGE GSM2113456
4 Sexual_Females_rep1.sga Sexual females|CAGE||rep1 CAGE GSM2113457
5 Sexual_Females_rep2.sga Sexual females|CAGE||rep2 CAGE GSM2113458
6 Sexual_Females_rep3.sga Sexual females|CAGE||rep3 CAGE GSM2113459
7 Males_rep1.sga Males|CAGE||rep1 CAGE GSM2113460
8 Males_rep2.sga Males|CAGE||rep2 CAGE GSM2213461
9 Asexual_Females_merged.sga Asexual females|CAGE||merged CAGE GSM2113454, GSM2113455, GSM2113456
10 Sexual_Females_merged.sga Sexual females|CAGE||merged CAGE GSM2113457, GSM2113458, GSM2113459
11 Males_merged.sga Males|CAGE||merged CAGE GSM2113460, GSM2113461
12 all_samples.sga All samples|CAGE||merged CAGE GSM2113454, GSM2113455, GSM2113456, GSM2113457, GSM2113458, GSM2113459, GSM2113460, GSM2113461

Merged samples:

This series contains both merged and individual replicates samples.

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v1.2.2. SAM files were then converted to BAM using samtools v1.9 and to BED using bamToBed v2.27.0 from bedtools. BED to SGA conversion was carried out using bed2sga v1.5.4 from ChIP-Seq.


Last update: 18 Mar 2021