Genome sequencing September 2015

kubu4 edited this page Jun 21, 2017 · 16 revisions

Sample collection and DNA preparations were performed by members of the Roberts Lab.

Sequencing and draft genome assembly will be performed by Beijing Genomics Institute (BGI).


Sequencing Details

BGI Contract (F15FTSUSAT0327)

  • Sequencing & Assembly
  • 100x coverage
  • HiSeq4000
  • Library paired-end insert sizes (bp): 300, 500, 800
  • Library mate-pair insert sizes (bp): 2000, 5000, 10000
  • Sequencing: PE150, PE50
Notebook(s):
Sample(s):
  • Individual adult Ostrea lurida
Sample collection date(s) and personnel:
DNA extraction date(s), tissue(s), method(s), and personnel:
Sample submission date(s):
  • 20150921
  • 20151006
  • 20151201
QC Report(s) and brief summaries:
Data receipt date(s), format(s), description, and storage location:
Data: FASTQ sequencing files

Received: 20160127

Format: FASTQ (Illumina HiSeq4000)

Location: http://owl.fish.washington.edu/nightingales/O_lurida/

Files:

FILENAME READS INSERT SIZE SEQUENCING SRA BIOPROJECT BIOSAMPLE SRA_EXPERIMENT
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz 61253141 500bp PE150 SRP072461 PRJNA316624 SRS1365663 SRX1667397
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz 61253141 500bp PE150 SRP072461 PRJNA316624 SRS1365663 SRX1667397
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz 58755925 800bp PE150 SRP072461 PRJNA316624 SRS1365663
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz 53307837 800bp PE150 SRP072461 PRJNA316624 SRS1365663
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz 27731148 300bp PE150 SRP072461 PRJNA316624 SRS1365663
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz 43938762 300bp PE150 SRP072461 PRJNA316624 SRS1365663
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq.gz 87198584 5000bp PE50 SRP072461 PRJNA316624 SRS1365663 SRX1667400
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.gz 87198584 5000bp PE50 SRP072461 PRJNA316624 SRS1365663 SRX1667400
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq.gz 43766527 10000bp PE50 SRP072461 PRJNA316624 SRS1365663 SRX1667401
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.gz 43766527 10000bp PE50 SRP072461 PRJNA316624 SRS1365663 SRX1667401
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq.gz 87135961 5000bp PE50 SRP072461 PRJNA316624 SRS1365663 SRX1667400
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.gz 87135961 5000bp PE50 SRP072461 PRJNA316624 SRS1365663 SRX1667400
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq.gz 43138844 10000bp PE50 SRP072461 PRJNA316624 SRS1365663 SRX1667401
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.gz 43138844 10000bp PE50 SRP072461 PRJNA316624 SRS1365663 SRX1667401
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq.gz 95270180 2000bp PE50 SRP072461 PRJNA316624 SRS1365663 SRX1667402
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz 95270180 2000bp PE50 SRP072461 PRJNA316624 SRS1365663 SRX1667402
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq.gz 92524416 2000bp PE50 SRP072461 PRJNA316624 SRS1365663 SRX1667402
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.gz 92524416 2000bp PE50 SRP072461 PRJNA316624 SRS1365663 SRX1667402

Data: Initial genome assembly

Received: 20160314

Formats: TXT, FASTA

Location: http://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20160314/

Files:

FILENAME DESCRIPTION
md5.txt Checksum file to verify integrity of files after downloading.
N50.txt Contains limited stats on scaffolds provided.
scaffold.fa.fill A FASTA file of scaffolds.

Data: Genome assembly

Received: 20160512

Formats: TXT, FASTA, PDF, PNG, FASTQ

Location: http://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20160512/

Files:

FASTQ Files

FILENAME READS
51114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz.clean.dup.clean.gz 61253141
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz.clean.dup.clean.gz 61253141
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz.clean.dup.clean.gz 58755925
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz.clean.dup.clean.gz 58755925
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz.clean.dup.clean.gz 43938762
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz.clean.dup.clean.gz 43938762