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.

• Raw data was downloaded from SRA: SRP073105
• Input file format: SRA
• Download date: 12-11-2020

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.

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.

• Raborn RT, Spitze K, Brendel VP, Lynch M. Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex Genetics. 2016 Oct;204(2):593-612. doi: 10.1534/genetics.116.193334. 27585846
• GEO series GSE80141: CAGE sequences from three developmental states in the microcrustacean Daphnia pulex.