Transcription Profiling data:
Filename | Description | Feature | GEO-ID | |
1 | SRR1582004_ACAGAT.sga | Brain|CAGE|Nurse|Rep 1 | CAGE | GSM1568470 |
2 | SRR1582004_ATCGTG.sga | Brain|CAGE|Nurse|Rep 2 | CAGE | GSM1568470 |
3 | SRR1582004_CACGAT.sga | Brain|CAGE|Nurse|Rep 3 | CAGE | GSM1568470 |
4 | SRR1582004_CACTGA.sga | Brain|CAGE|Nurse|Rep 4 | CAGE | GSM1568470 |
5 | SRR1582004_CTGACG.sga | Brain|CAGE|Nurse|Rep 5 | CAGE | GSM1568470 |
6 | SRR1582004_GAGTGA.sga | Brain|CAGE|Nurse|Rep 6 | CAGE | GSM1568470 |
7 | SRR1582004_GTATAC.sga | Brain|CAGE|Nurse|Rep 7 | CAGE | GSM1568470 |
8 | SRR1582004_TCGAGC.sga | Brain|CAGE|Nurse|Rep 8 | CAGE | GSM1568470 |
9 | SRR1582203_ACAGAT.sga | Brain|CAGE|Forager|Rep 1 | CAGE | GSM1568471 |
10 | SRR1582203_ATCGTG.sga | Brain|CAGE|Forager|Rep 2 | CAGE | GSM1568471 |
11 | SRR1582203_CACGAT.sga | Brain|CAGE|Forager|Rep 3 | CAGE | GSM1568471 |
12 | SRR1582203_CACTGA.sga | Brain|CAGE|Forager|Rep 4 | CAGE | GSM1568471 |
13 | SRR1582203_CTGACG.sga | Brain|CAGE|Forager|Rep 5 | CAGE | GSM1568471 |
14 | SRR1582203_GAGTGA.sga | Brain|CAGE|Forager|Rep 6 | CAGE | GSM1568471 |
15 | SRR1582203_GTATAC.sga | Brain|CAGE|Forager|Rep 7 | CAGE | GSM1568471 |
16 | SRR1582203_TCGAGC.sga | Brain|CAGE|Forager|Rep 8 | CAGE | GSM1568471 |
Each biological replica was extracted form the ame sequencing run as described in the Techniacal Notes.
FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0). Following manuscript protocol, paired-end reads were grouped according to 8 different barcodes into the biological replicas. Subsequently, reads were trimmed of the 21 bp long adapter at the 5' end and mapped to the genome using Bowtie2 v2.2.9. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.2).