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1 | 33 | ProjectID | Task | Paper | Paper-URL | Data-URL | notes1 | notes2 | notes3 | Hypatia file location | |||||||||||||||||||
2 | Panagiota Stamatopoulou | 1 | Replicate RNAseq analysis | Human β Cell Transcriptome Analysis Uncovers lncRNAs That Are Tissue-Specific, Dynamically Regulated, and Abnormally Expressed in Type 2 Diabetes | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3475176/ | https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1294/samples/ | ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR173/ERR173280/ERR173280_1.fastq.gz | ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR173/ERR173280/ERR173280_2.fastq.gz | ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR173/ERR173261/ERR173261_1.fastq.gz | ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR173/ERR173261/ERR173261_2.fastq.gz | https://www.ebi.ac.uk/ena/browser/view/PRJEB3293?show=reads | ||||||||||||||||||
3 | Konstantinos Kapelios | 2 | Replicate ChIPseq analysis | Human β Cell Transcriptome Analysis Uncovers lncRNAs That Are Tissue-Specific, Dynamically Regulated, and Abnormally Expressed in Type 2 Diabetes | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3475176/ | https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1294/samples/ | ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR173/ERR173267/ERR173267.fastq.gz | ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR173/ERR173277/ERR173277.fastq.gz | ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR173/ERR173272/ERR173272.fastq.gz | ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR191/ERR191518/ERR191518.fastq.gz | |||||||||||||||||||
4 | Eva Mikraki-Petroula | 3 | Replicate ChIPseq analysis | Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3477283/ | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36994 | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM908038 | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM970257 | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM970259 | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM970262 | /data/ncbi_data/project3 | please do not copy the files to your folder ! | |||||||||||||||||
5 | Sofia Rossiou | 4 | Replicate ChIPseq analysis | Gene induction and repression during terminal erythropoiesis are mediated by distinct epigenetic changes | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204918/ | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27893 | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM688808 | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM688811 | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM688815 | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM688824 | https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?exp=SRX461538&cmd=search&m=downloads&s=seq | /data/ncbi_data/project4 | |||||||||||||||||
6 | Glykeria Spyrou | 5 | Replicate RNAseq analysis | TAF10 Interacts with the GATA1 Transcription Factor and Controls Mouse Erythropoiesis | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438247/ | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68083 | all 7 samples | /data/ncbi_data/project5 | |||||||||||||||||||||
7 | Eirini Tsiouni | 6 | Replicate ChIPseq analysis | Kmt5a Controls Hepatic Metabolic Pathways by Facilitating RNA Pol II Release from Promoter-Proximal Regions | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5542855/ | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97338 | GSM2561922 to GSM2561944 (only replicate1) | /data/ncbi_data/project6 | |||||||||||||||||||||
8 | Foteini Papageorgiou | 7 | Replicate ChIPseq analysis | Kmt5a Controls Hepatic Metabolic Pathways by Facilitating RNA Pol II Release from Promoter-Proximal Regions | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5542855/ | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97338 | GSM2561923 to GSM2561945 (only replicate2) | /data/ncbi_data/project7 | |||||||||||||||||||||
9 | Maria Chasapi | 8 | Replicate RNAseq analysis | Kmt5a Controls Hepatic Metabolic Pathways by Facilitating RNA Pol II Release from Promoter-Proximal Regions | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5542855/ | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97338 | GSM2561916 to GSM2561921 | /data/ncbi_data/project8 | |||||||||||||||||||||
10 | Stamati Konstantina-Maria | 9 | Replicate ChIPseq analysis | High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4216921/ | https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2326/ | ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR435/ERR435987/ERR435987.fastq.gz | ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR435/ERR435999/ERR435999.fastq.gz | ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR435/ERR435998/ERR435998.fastq.gz | ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR436/ERR436005/ERR436005.fastq.gz | |||||||||||||||||||
11 | Sotirios Dimitriadis | 10 | Replicate RNAseq analysis (PairedEnd data!) | High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4216921/ | https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2328/ | ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR435/ERR435946/ERR435946_2.fastq.gz | ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR435/ERR435947/ERR435947_1.fastq.gz | ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR435/ERR435937/ERR435937_1.fastq.gz | ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR435/ERR435939/ERR435939_1.fastq.gz | |||||||||||||||||||
12 | Konstantinos Giatras | 11 | Replicate GATK Variant calling analysis | Germline short variant discovery (SNPs + Indels) | https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- | ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/ | samples: HG00100 - HG00114 | chromosome 11 only | exome_alignment | ||||||||||||||||||||
13 | Marina Akarepi | 12 | Replicate GATK Variant calling analysis | Germline short variant discovery (SNPs + Indels) | https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- | ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/ | samples: HG00115 - HG00129 | chromosome 11 only | exome_alignment | ||||||||||||||||||||
14 | Asimenia Giagli | 13 | Replicate GATK Variant calling analysis | Germline short variant discovery (SNPs + Indels) | https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- | ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/ | samples: HG00130 - HG00148 | chromosome 11 only | exome_alignment | ||||||||||||||||||||
15 | Eleni Panagiotopoulou | 14 | Replicate GATK Variant calling analysis | Germline short variant discovery (SNPs + Indels) | https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- | ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/ | samples: HG00149 - HG00178 | chromosome 11 only | exome_alignment | ||||||||||||||||||||
16 | 15 | Replicate GATK Variant calling analysis | Germline short variant discovery (SNPs + Indels) | https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- | ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/ | samples: HG00179 - HG00233 | chromosome 11 only | exome_alignment | |||||||||||||||||||||
17 | Asimakopoulos Giannis | 16 | Replicate GATK Variant calling analysis | Germline short variant discovery (SNPs + Indels) | https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- | ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/ | samples: HG00234 - HG00251 | chromosome 11 only | exome_alignment | ||||||||||||||||||||
18 | 17 | Replicate GATK Variant calling analysis | Germline short variant discovery (SNPs + Indels) | https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- | ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/ | samples: HG00252 - HG00266 | chromosome 11 only | exome_alignment | |||||||||||||||||||||
19 | Liassa Maria Despoina | 18 | Replicate GATK Variant calling analysis | Germline short variant discovery (SNPs + Indels) | https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- | ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/ | samples: HG00267 - HG00282 | chromosome 11 only | exome_alignment | ||||||||||||||||||||
20 | 19 | Replicate GATK Variant calling analysis | Germline short variant discovery (SNPs + Indels) | https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- | ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/ | samples: HG00284 - HG00320 | chromosome 11 only | exome_alignment | |||||||||||||||||||||
21 | Izabella Gogaeva | 20 | Replicate GATK Variant calling analysis | Germline short variant discovery (SNPs + Indels) | https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- | ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/ | samples: HG00321 - HG00337 | chromosome 11 only | exome_alignment | ||||||||||||||||||||
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23 | Instructions: See https://docs.google.com/document/d/e/2PACX-1vQqHL1YK7foWo89PVXH-v2ETLhavdZNK-crpuBKbEZgIIKCVghJJn5GPtQ-hsCXTwqRyYb1YC5zWYQH/pub | ||||||||||||||||||||||||||||
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