{"text_format":"5","workbook":"xlsx","n_sheets":5,"sheets":["dataset","datasource","sample","expdesign","method"],"props":{"creator":"Sudhansu Dash","last_modified_by":"Sudhansu Dash","company":"NCGR"},"read":"whole","wrapped":"gz","date_system":"1904"}

{"sheet":"dataset","index":0,"n_rows":32,"n_cols":3,"rows_kept":32}
["#","#DATASET"]
["#","#SECTION: For DataStore and LIS database"]
["#","#"]
["#","#accession_no"]
[null,"ACCESSION_NO","cicar1"]
["#","#Name:Title"]
[null,"NAME","Chickpea flower development gene expression atlas (ICC4958  Deshi cultivar type)"]
["#","#Shortname: For label in website"]
[null,"SHORTNAME","Chickpea flower development atlas"]
["#","#As in DataStore Expected to be the same in LIS Chado)"]
[null,"GENOME","cicar.ICC4958.gnm2.ann1"]
["#","#Description for LIS"]
[null,"DESCRIPTION","Gene expression during flower development was studied in chickpea, Deshi cultivar type ICC4958, using 11 tissue samples at various stages of flower development.  For comparison, the samples include 2 vegetative stages. This dataset at LIS uses reads mapped to the ICC4958 chickpea reference genome cicar.ICC4958.gnm2.ann1."]
["#","#Date data analysed"]
[null,"ANALYSIS_DATE","2016 Nov"]
["#","#????Only after loading OR should be in database auto-updated. **Think and change"]
[null,"LOAD_DATE"]
["#","#"]
["#"]
["#"]
["#","#SECTION: For G/Jbrowse"]
["#","#"]
["#","#Browser dir name:  **Is DATASET_SHORTNAME in scripts"]
[null,"BROW_DIRNAME","cicer_flower_devp_atlas"]
["#","#"]
["#","#Browser dataset name: May use SHORTNAME.  **Is DATASET_LONGNAME in scripts"]
["#","#Browser genome version: Is  GENOME_VERSION in scripts"]
[null,"BROW_GENOME_VER","Ca2.0"]
["#","#Browser LG_ABBREVIATION: Pseudomolecule abbreviation in GBrowse. Ex: Pv or Ca or Cc, etc."]
[null," LG_ABBREVIATION","Ca"]
["#","#Local working dir: Location of data and file processing"]
[null,"LOCAL_WORKING_DIR","cicar-SRP017394"]

{"sheet":"datasource","index":1,"n_rows":26,"n_cols":3,"rows_kept":26}
["#","#DATASOURCE"]
["#","#"]
["#","#Name, descriptive (max 250 char)"]
[null,"NAME","A global view of transcriptome dynamics during flower development in chickpea (Desi) by deep sequencing"]
["#","#Shortname: max 64 char"]
[null,"SHORTNAME","Chickpea (Desi) flower development atlas"]
["#","#Origin: ex. SRA, GEO, A labname, etc."]
[null,"ORIGIN","SRA"]
["# ","#Description: our description if needed"]
[null,"DESCRIPTION","A global view of transcriptome dynamics during flower development in chickpea (Desi) by deep sequencing has been presented by generating reads from eight flower development stages and three vegetative tissues for comparison. Platform:  Illumina high-throughput sequencing GAII platform"]
["#","#NCBI BioProj acc"]
[null,"BIOPROJ_ACC","PRJNA182724"]
["#","#NCBI BioProj Title"]
[null,"BIOPROJ_TITLE","Title:Chickpea Transcriptome Atlas - I (chickpea)"]
["#","#NCBI BioProj description/ abstract(?)"]
[null,"BIOPROJ_DESCRIPTION","Abstaract: In this study, we aim to present a global view of transcriptome dynamics during flower development in chickpea. We generated around 234 million high-quality reads for eight flower development stages (ranging from 16 to 40 million reads for each stage) and 91 million high-quality reads from three vegetative tissues using Illumina high-throughput sequencing GAII platform. Because of non-availability of reference genome sequence, we mapped the reads to chickpea transcriptome comprised of 34,760 transcripts for estimation of their transcriptional activity in different tissue samples. The transcriptome dynamics was studied by comparison of gene expression during flower development stages with vegetative tissues. Overall design: We collected different tissue samples used in this study and total RNA isolated was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to 34760 chickpea transcripts and reads per kilobase per million (RPKM) was calculated for each gene in all the sample to measure their gene expression. Differential expression analysis was performed using DESeq software. The genes preferentially expression during various stages of flower development as compared to vegetative stages and those with speciifc expression were identified."]
["#","#NCBI SRP number"]
[null,"SRA_PROJ_ACC","SRP017394"]
["#","# GEO series if exists"]
[null,"GEO_SERIES","GSE42679"]
["#","#Associated publication at NCBI"]
[null,"BIOPROJ_PUBLICATION","Singh VK, Garg R, Jain M. A global view of transcriptome dynamics during flower development in chickpea by deep sequencing. Plant Biotechnol J 2013 Aug;11(6):691-701. PMID: 23551980"]
["#","#Link to Pub"]
[null,"PUB_LINK","http://www.ncbi.nlm.nih.gov/pubmed/23551980"]
["#","#Link to full publication"]
[null,"PUB_FULLLINK","http://onlinelibrary.wiley.com/doi/10.1111/pbi.12059/full"]

{"sheet":"sample","index":2,"n_rows":16,"n_cols":17,"rows_kept":16}
["#SAMPLE"]
["#"]
["#Hints:"]
["#sample display name","Lookup key for data column (=SRR no)","unique name for LIS Chado","Descriptive","Exp design: factors-rep combinations","tissue/organ/plant part",null,null,"Chado spelling","sub-spp, cv-type","strain, line, cultivar, genotype","Other_attributes, place-holder, add extra columns","SRR(not in recc)","SAMN number","SRS number","PRJN number","SRP number"]
["sample_name","key","sample_uniquename","description","treatment","tissue","dev_stage","age","organism","infraspecies","cultivar","other","sra_run","biosample_accession","sra_accession","bioproject_accession","sra_study"]
["Germinating seedling (SRR627762)","SRR627762","Germinating seedling (SRR627762)","Germinating seedling","Germinating seedling","Germinating seedling","Seedling",null,"cicer arietinum","Deshi","ICC4958",null,"SRR627762","SAMN01822058","SRS377931","PRJNA182724","SRP017394"]
["Young leaves (SRR627763)","SRR627763","Young leaves (SRR627763)","Young leaves","Young leaves","Young leaves","Mature plant",null,"cicer arietinum","Deshi","ICC4958",null,"SRR627763","SAMN01822059","SRS377932","PRJNA182724","SRP017394"]
["Shoot apical meristem (SRR627764)","SRR627764","Shoot apical meristem (SRR627764)","Shoot apical meristem","Shoot apical meristem","Shoot apical meristem","20-day-old plants",null,"cicer arietinum","Deshi","ICC4958",null,"SRR627764","SAMN01822060","SRS377933","PRJNA182724","SRP017394"]
["Flower bud 1 (SRR627765)","SRR627765","Flower bud 1 (SRR627765)","Flower bud 1","Flower bud 1","Flower bud 1","Mature plant",null,"cicer arietinum","Deshi","ICC4958",null,"SRR627765","SAMN01822061","SRS377934","PRJNA182724","SRP017394"]
["Flower bud 2 (SRR627766)","SRR627766","Flower bud 2 (SRR627766)","Flower bud 2","Flower bud 2","Flower bud 2","Mature plant",null,"cicer arietinum","Deshi","ICC4958",null,"SRR627766","SAMN01822062","SRS377935","PRJNA182724","SRP017394"]
["Flower bud 3 (SRR627767)","SRR627767","Flower bud 3 (SRR627767)","Flower bud 3","Flower bud 3","Flower bud 3","Mature plant",null,"cicer arietinum","Deshi","ICC4958",null,"SRR627767","SAMN01822063","SRS377936","PRJNA182724","SRP017394"]
["Flower bud 4 (SRR627768)","SRR627768","Flower bud 4 (SRR627768)","Flower bud 4","Flower bud 4","Flower bud 4","Mature plant",null,"cicer arietinum","Deshi","ICC4958",null,"SRR627768","SAMN01822064","SRS377937","PRJNA182724","SRP017394"]
["Flower 1 (SRR627769)","SRR627769","Flower 1 (SRR627769)","Flower 1","Flower 1","Flower 1","Mature plant",null,"cicer arietinum","Deshi","ICC4958",null,"SRR627769","SAMN01822065","SRS377938","PRJNA182724","SRP017394"]
["Flower 2 (SRR627770)","SRR627770","Flower 2 (SRR627770)","Flower 2","Flower 2","Flower 2","Mature plant",null,"cicer arietinum","Deshi","ICC4958",null,"SRR627770","SAMN01822066","SRS377939","PRJNA182724","SRP017394"]
["Flower 3 (SRR627771)","SRR627771","Flower 3 (SRR627771)","Flower 3","Flower 3","Flower 3","Mature plant",null,"cicer arietinum","Deshi","ICC4958",null,"SRR627771","SAMN01822067","SRS377940","PRJNA182724","SRP017394"]
["Flower 4 (SRR627772)","SRR627772","Flower 4 (SRR627772)","Flower 4","Flower 4","Flower 4","Mature plant",null,"cicer arietinum","Deshi","ICC4958",null,"SRR627772","SAMN01822068","SRS377941","PRJNA182724","SRP017394"]

{"sheet":"expdesign","index":3,"n_rows":23,"n_cols":4,"rows_kept":23}
["#EXPT DESIGN (This page is not fully thought yet)"]
[]
["#","#Factors","Total","Factor Names; ':' separated; in order"]
[null,null,1,"tissue"]
[]
["#","#Factor Levels"]
["#","#Factor Name","Total levels","Factor Level Names; ':' separated; in order"]
[null,"tissue",11,"Germinating seedling:Young leaves:Shoot apical meristem:Flower bud 1:Flower bud 2:Flower bud 3:Flower bud 4:Flower 1:Flower 2:Flower 3:Flower 4"]
[]
[]
["#","Treatments (Factor combinations)"]
["#","Treatment Name","Reps"]
[null,"Germinating seedling",1]
[null,"Young leaves",1]
[null,"Shoot apical meristem",1]
[null,"Flower bud 1",1]
[null,"Flower bud 2",1]
[null,"Flower bud 3",1]
[null,"Flower bud 4",1]
[null,"Flower 1",1]
[null,"Flower 2",1]
[null,"Flower 3",1]
[null,"Flower 4",1]

{"sheet":"method","index":4,"n_rows":13,"n_cols":3,"rows_kept":13}
["#METHOD"]
["#","#Name:Title"]
[null,"NAME","TPM values per gene from HTSeq raw read counts on exons"]
["#","#Shortname: For label in website"]
[null,"SHORTNAME","TPM from HTSeq Count"]
["#","#Version if any"]
[null,"VERSION"]
["#","#Description: for LIS website"]
[null,"DESCRIPTION","TPM values calculated from HTSeq read counts mapped to exons only per gene.  "]
["#","#Details:"]
[null,"DETAILS","Reads were mapped to reference genome using GSNAP.  HTSeq counts were generated from read alignments only to exons aggregated over a gene. TPM was calculated from these exonic read counts."]
["#","#Notes: For curation, private"]
[null,"NOTES","**Provide later: GSNAP parameters and ref. HTSeq count parameters and ref. Refine description and details. TPM explain and reference."]