 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 15, 2013 |
| Title |
RNA-Seq analysis of placenta (trophoblast) tissue from CTL02 (A19261) |
| Sample type |
SRA |
| |
|
| Source name |
A19261-1
|
| Organism |
Homo sapiens |
| Characteristics |
submitted sample id: JOC218-RNA
donor_id: CTL02
Sex: male
body site: Placenta
histological type: Trophoblast
is tumor: No
biomaterial_type: primary tissue
tissue_type: placenta (trophoblast) tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
library construction protocol: Refer to document 'Strand Specific 96-well Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
design description: RNA-Seq analysis of placenta (trophoblast) tissue from CTL02 (A19261) using Illumina HiSeq 2000
library name: A19261
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 7.5
RNA_PREPARATION_INITIAL_RNA_QNTY: 4 ug
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 312-531 bp
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
|
| Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM1127106_UCSF-UBC.Placenta_Trophoblast_Primary_Cells.mRNA-Seq.CTL02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19261-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Trophoblast Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Placenta Trophoblast Primary Cells, Donor CTL02 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16990
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 312,136,881
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.34
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM1127106_UCSF-UBC.Placenta_Trophoblast_Primary_Cells.mRNA-Seq.CTL02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19261-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Trophoblast Primary Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Placenta Trophoblast Primary Cells, Donor CTL02 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17006
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PT mRNA 02 61
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Trophoblast Primary Cells mRNA-Seq Donor CTL02 Library A19261 EA Release 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 312,136,881
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.34
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
|
| |
|
| Submission date |
Apr 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
UCSF-UBC CENTER |
| Organization name |
UCSF-UBC
|
| Street address |
UCSF-UBC
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE16368 |
UCSF-UBC Human Reference Epigenome Mapping Project |
|
| Relations |
| Named Annotation |
GSM1127106_UCSF-UBC.Placenta_Trophoblast_Primary_Cells.mRNA-Seq.CTL02.wig.gz |
| SRA |
SRX1158080 |
| BioSample |
SAMN03416729 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1127106_UCSF-UBC.Placenta_Trophoblast_Primary_Cells.mRNA-Seq.CTL02.bed.gz |
3.2 Gb |
(ftp)(http) |
BED |
| GSM1127106_UCSF-UBC.Placenta_Trophoblast_Primary_Cells.mRNA-Seq.CTL02.wig.gz |
27.1 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
|
|
|
|
 |
