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hputnam / Montipora_Spawn_Timing

Time series gene expression analysis (RNAseq) of Montipora capitata spawning
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Montipora_Spawn_Timing

This repository includes data and analysis scripts to accompany:

Authors: Journal:
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Description: This project examines gene expression during the normal spawning timing of corals that did and did not spawn. Samples were collected from 3 replicate Montipora capitata colonies for each condition at 18:00, 20:00 and 00:00 the night of 6/6/16. RNA extracted from samples was prepped using Illumina TruSeq Sample Prep v2 Guide and sequenced 2x150bp on the Illumina MiSeq.

Data Description

NCBI PRJNA376841

Sample.ID Date Time Spawn Read.ID File.ID Read.Count SRA.ID MD5Sum
T4-1 6/6/16 18:00 NO Read1 T4-1_S1_L001_R1_001.fastq.gz 3438991 SRR5311171 0d034de745024ef1f3a0a808fb814da2
T4-1 6/6/16 18:00 NO Read2 T4-1_S1_L001_R2_001.fastq.gz 3438991 SRR5311171 e6a8619819ae4ebbda76fab1c16d2ee5
T4-6 6/6/16 18:00 NO Read1 T4-6_S1_L001_R1_001.fastq.gz 4070019 SRR5311306 d2524a6fd255b15b3e3fb2dfe04b8912
T4-6 6/6/16 18:00 NO Read2 T4-6_S1_L001_R2_001.fastq.gz 4070019 SRR5311306 9eddbe1ab57021043a2971c07c3f9285
T4-8 6/6/16 18:00 YES Read1 T4-8_S1_L001_R1_001.fastq.gz 5059437 SRR5311307 ecb64ffbedac95c4e3cbe0d473ef2236
T4-8 6/6/16 18:00 YES Read2 T4-8_S1_L001_R2_001.fastq.gz 5059437 SRR5311307 68755f4a785e6b5723674370dfc3974d
T4-10 6/6/16 18:00 YES Read1 T4-10_S1_L001_R1_001.fastq.gz 4192400 SRR5311255 ee119a26764c90fc2f958d104a75fd9f
T4-10 6/6/16 18:00 YES Read2 T4-10_S1_L001_R2_001.fastq.gz 4192400 SRR5311255 3c572aa147718915633c86e707269aba
T4-16 6/6/16 18:00 YES Read1 T4-16_S1_L001_R1_001.fastq.gz 5728309 23369f48d9c8a09cdcbf3360c5d98af9
T4-16 6/6/16 18:00 YES Read2 T4-16_S1_L001_R2_001.fastq.gz 5728309 e3a48c6186b0869b94ccc70df65310cd
T4-17 6/6/16 18:00 NO Read1 T4-17_S1_L001_R1_001.fastq.gz 5685333 SRR5311305 42e199deae9b280dc0c4c46c3eace29b
T4-17 6/6/16 18:00 NO Read2 T4-17_S1_L001_R2_001.fastq.gz 5685333 SRR5311305 c539fd52b0e5835007b81949bec37898
T5-1 6/6/16 20:00 NO Read1 T5-1_S2_L001_R1_001.fastq.gz 3278023 SRR5311308 06eed3df093f468027e006cd61b71c1a
T5-1 6/6/16 20:00 NO Read2 T5-1_S2_L001_R2_001.fastq.gz 3278023 SRR5311308 f462023d1207004cd4d0e1145407bbff
T5-6 6/6/16 20:00 NO Read1 T5-6_S2_L001_R1_001.fastq.gz 4508425 SRR5311313 2eeb28b45c5a000577755c830e36b7be
T5-6 6/6/16 20:00 NO Read2 T5-6_S2_L001_R2_001.fastq.gz 4508425 SRR5311313 020049d0cda29af60e90925afaa3b0c7
T5-8 6/6/16 20:00 YES Read1 T5-8_S2_L001_R1_001.fastq.gz 5257196 SRR5311342 4e62cb401dadfff0b8ebdd5e79a67348
T5-8 6/6/16 20:00 YES Read2 T5-8_S2_L001_R2_001.fastq.gz 5257196 SRR5311342
T5-10 6/6/16 20:00 YES Read1 T5-10_S2_L001_R1_001.fastq.gz 5182807 SRR5311310 82cfe360bbba75e543aa89824e0beab4
T5-10 6/6/16 20:00 YES Read2 T5-10_S2_L001_R2_001.fastq.gz 5182807 SRR5311310 324d781e5a9897b745311d258871ebf3
T5-16 6/6/16 20:00 YES Read1 T5-16_S2_L001_R1_001.fastq.gz 5054983 SRR5311311 c7b6251c673bad1a5c41358afb6432d8
T5-16 6/6/16 20:00 YES Read2 T5-16_S2_L001_R2_001.fastq.gz 5054983 SRR5311311 1e97f1615681b512901abc1a791617ae
T5-17 6/6/16 20:00 NO Read1 T5-17_S2_L001_R1_001.fastq.gz 4777150 SRR5311312 e28b444af3380762f8181e49b3ec8639
T5-17 6/6/16 20:00 NO Read2 T5-17_S2_L001_R2_001.fastq.gz 4777150 SRR5311312 a862e594e4c8a2f0ef0901d9f833777b
T7-1 6/7/16 00:00 NO Read1 T7-1_S3_L001_R1_001.fastq.gz 3480865 SRR5311343 0a1c2963ed23888ee7fa18ce00f52497
T7-1 6/7/16 00:00 NO Read2 T7-1_S3_L001_R2_001.fastq.gz 3480865 SRR5311343 608079eadce5498ccab50c72d4ebef2c
T7-6 6/7/16 00:00 NO Read1 T7-6_S3_L001_R1_001.fastq.gz 4179337 SRR5311347 0722ee9f7a97367403667f878329b9ba
T7-6 6/7/16 00:00 NO Read2 T7-6_S3_L001_R2_001.fastq.gz 4179337 SRR5311347 0202e6a634547b3275d318ebdf20dfe1
T7-8 6/7/16 00:00 YES Read1 T7-8_S3_L001_R1_001.fastq.gz 4055930 SRR5311348 820397dbcc084832ad34ba177cea411a
T7-8 6/7/16 00:00 YES Read2 T7-8_S3_L001_R2_001.fastq.gz 4055930 SRR5311348 5c8792e297e619d97a8f65cc1d2e6b24
T7-10 6/7/16 00:00 YES Read1 T7-10_S3_L001_R1_001.fastq.gz 3767511 SRR5311344 072e8d420b9cfb6939ffde8f5c264f5e
T7-10 6/7/16 00:00 YES Read2 T7-10_S3_L001_R2_001.fastq.gz 3767511 SRR5311344 7a2e6ae58b0c6e77ced5cb2fae082d4f
T7-16 6/7/16 00:00 YES Read1 T7-16_S3_L001_R1_001.fastq.gz 4661903 SRR5311345 ef4537d0d48b7dd8b27f0abe4cbd17fd
T7-16 6/7/16 00:00 YES Read2 T7-16_S3_L001_R2_001.fastq.gz 4661903 SRR5311345 a3ab869746c91eaacb6d402d47c7523b
T7-17 6/7/16 00:00 NO Read1 T7-17_S3_L001_R1_001.fastq.gz 4349113 SRR5311346 f94c1468d7de02729c98b93f5f38347a
T7-17 6/7/16 00:00 NO Read2 T7-17_S3_L001_R2_001.fastq.gz 4349113 SRR5311346 3446a006926122041431f708cd6291d8

6 lanes with 3 samples per lane for library prep and sequencing 2 x 150 on MiSeq at HIMB Samples submitted: 20160629 Sequencing completed: December 2016

Notes about Files

Sequence files submitted to NCBI under BioProject ID: PRJNA376841

Directory Structure

notebooks:

Jupyter Notebook files for bioinformatic analysis

Processing:

Quality and quantity results from RNA extraction and library preparation

Protocols:

Sample processing protocols for RNA extraction and library preparation

RAnalysis:

### Data
### Output
### Scripts

SEQ_Data:

### Clean_Data
### Cleaned_QC_Files
### Raw_Data
### Raw_QC_Files