sample 8 - SRA

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SRX1092172: sample 8
1 ILLUMINA (Illumina HiSeq 2000) run: 8.3M spots, 751M bases, 465Mb downloads

Design: Ten micrograms of high molecular weight genomic DNA per individual was submitted to Floragenex Inc. (Eugene, OR) for library preparation and high-throughput sequencing. Individual sample specific identifying barcodes and sequencing adaptors were ligated to total genomic DNA that was digested using a high-fidelity SbfI restriction enzyme. Five base pair sequence tags were added as unique barcodes. The resulting fragments were multiplexed and sequenced on an Illumina HiSeq 2000 platform using single-end 100 bp reads. Samples were de-multiplexed, separated by individual, and barcode sequences removed, leaving RAD tags of 90 basepairs. Sequences were aligned to de novo RAD pseudo-reference genomes for each genus. The two RAD references came from a single individual per genus after preliminary analysis identified which had the greatest number of unique RAD tag clusters. Custom perl scripts were used to group identical sequences represented by 5 to 500x coverage. Reads for each individual were aligned to the RAD pseudo-reference genome using BOWTIE [33], using sequence quality information that allowed a maximum of three mismatches. Alignment to no more than one reference region per read was allowed. SAMTOOLS algorithms and custom Floragenex scripts were used to detect SNPs and determine genotypes. Initial filters for genotyping required a minimum Phred quality score of 15, a minimum of 4x, 6x, or 10x sequence coverage, and a minimum of 65–85% of the population genotyped across samples. The different sequence coverage cutoffs provided three different genotyped data sets that were tabulated and formatted in the variant call format.

Submitted by: City College, City Univeristy of New York

Study: Single-end RAD libraries for Hylomyscus denniae and Sylvisorex granti groups for phylogeographic analysis Albertine Rift and Kenyan Highlands populations.

PRJNA289595 • SRP060689 • All experiments • All runs

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We analyzed restriction-site associated DNA-sequences (RAD-Seq) to study recent historical processes in co-distributed mouse (Hylomyscus) and shrew (Sylvisorex) species complexes, with an aim to better determine how historical paleoenvironmental processes might have contributed to the EABH’s high diversity.

Sample:

SAMN03851948 • SRS987776 • All experiments • All runs

Organism: Hylomyscus kerbispeterhansi

Library:

Instrument: Illumina HiSeq 2000

Strategy: WGS

Source: GENOMIC

Selection: Restriction Digest

Layout: SINGLE

Spot descriptor:

1 forward

Runs: 1 run, 8.3M spots, 751M bases, 465Mb

Run	# of Spots	# of Bases	Size	Published
SRR2098377	8,252,784	751M	465Mb	2016-07-08

ID:: 1597724

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Sequence Read Archive

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