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| Status |
Public on Jan 04, 2012 |
| Title |
[E-MTAB-684] GENCODE PCR-Seq Batch IV |
| Project |
ENCODE
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| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing. This is batch IV, based on chromosome 3, 4 and 5 annotations from Gencode 4 (January 2010). The sequences in this submission were obtained from two different RNA amplifications of the same original RNA for each tissue (called cdna1 and cdna2 in the assay names). In addition testis cDNA1 and lung cDNA2 were sequenced twice (rep1, rep2), and sequences originated from a new dilution of brain and testis cDNA1 (newdil) have also been included.
ArrayExpress Release Date: 2011-08-22
Publication Title: GENCODE: producing a reference annotation for ENCODE
Publication Author List: Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R
Person Roles: submitter
Person Last Name: Gonzalez
Person First Name: Jose
Person Mid Initials: M
Person Email: jmg@sanger.ac.uk
Person Phone: -498006
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute
Person Roles: investigator
Person Last Name: Hubbard
Person First Name: Tim
Person Mid Initials:
Person Email: th@sanger.ac.uk
Person Phone: -498055
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute
Person Roles: investigator
Person Last Name: Reymond
Person First Name: Alexandre
Person Mid Initials:
Person Email: Alexandre.Reymond@unil.ch
Person Phone:
Person Address: Lausanne, Switzerland
Person Affiliation: University of Lausanne
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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| Overall design |
Experimental Design: organism_part_comparison_design
Experimental Design: reference_design
Experimental Design: co-expression_design
Experimental Factor Name: ORGANISMPART
Experimental Factor Type: organism_part
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| Web link |
http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
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| Citation(s) |
16925838 |
| Submission date |
Dec 30, 2011 |
| Last update date |
May 15, 2019 |
| Organization |
European Bioinformatics Institute |
| E-mail(s) |
miamexpress@ebi.ac.uk
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| Lab |
ArrayExpress
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| Street address |
Wellcome Trust Genome Campus
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| City |
Hinxton |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB10 1SD |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
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| Samples (20)
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| GSM855562 |
[E-MTAB-684] polyA+_brain_6120217, Batch_4_brain_cdna1 |
| GSM855563 |
[E-MTAB-684] polyA+_heart_7082801A, Batch_4_heart_cdna1 |
| GSM855564 |
[E-MTAB-684] polyA+_kidney_7110096, Batch_4_kidney_cdna1 |
| GSM855565 |
[E-MTAB-684] polyA+_liver_6100188, Batch_4_liver_cdna1 |
| GSM855566 |
[E-MTAB-684] polyA+_lung_1100350, Batch_4_lung_cdna1 |
| GSM855567 |
[E-MTAB-684] polyA+_muscle_7040106, Batch_4_muscle_cdna1 |
| GSM855568 |
[E-MTAB-684] polyA+_spleen_6090097, Batch_4_spleen_cdna1 |
| GSM855569 |
[E-MTAB-684] polyA+_testis_7060321, Batch_4_testis_cdna1_rep1 |
| GSM855570 |
[E-MTAB-684] polyA+_testis_7060321, Batch_4_testis_cdna1_rep2 |
| GSM855571 |
[E-MTAB-684] polyA+_brain_6120217, Batch_4_brain_cdna1_newdil |
| GSM855572 |
[E-MTAB-684] polyA+_testis_7060321, Batch_4_testis_cdna1_newdil |
| GSM855573 |
[E-MTAB-684] polyA+_brain_6120217, Batch_4_brain_cdna2 |
| GSM855574 |
[E-MTAB-684] polyA+_heart_7082801A, Batch_4_heart_cdna2 |
| GSM855575 |
[E-MTAB-684] polyA+_kidney_7110096, Batch_4_kidney_cdna2 |
| GSM855576 |
[E-MTAB-684] polyA+_liver_6100188, Batch_4_liver_cdna2 |
| GSM855577 |
[E-MTAB-684] polyA+_lung_1100350, Batch_4_lung_cdna2_rep1 |
| GSM855578 |
[E-MTAB-684] polyA+_lung_1100350, Batch_4_lung_cdna2_rep2 |
| GSM855579 |
[E-MTAB-684] polyA+_muscle_7040106, Batch_4_muscle_cdna2 |
| GSM855580 |
[E-MTAB-684] polyA+_spleen_6090097, Batch_4_spleen_cdna2 |
| GSM855581 |
[E-MTAB-684] polyA+_testis_7060321, Batch_4_testis_cdna2 |
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| Relations |
| SRA |
ERP000774 |
| ArrayExpress |
E-MTAB-684 |
| BioProject |
PRJNA151121 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data not provided for this record |
| Raw data are available in SRA |
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