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| Status |
Public on Jun 22, 2013 |
| Title |
RNA-Seq analysis of cDNA_Lib 2 derived from human hippocampus middle cells; cDNA_Lib 2 |
| Sample type |
SRA |
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| Source name |
specified brain region obtained by post-mortem collection in a longitudinal study; cDNA_Lib 2
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| Organism |
Homo sapiens |
| Characteristics |
sample common name: Brain, Hippocampus Middle
sra sample accession: SRS255276
collection_method: Post-Mortem
donor_health_status: no AD evident at demise
disease: no AD evident at demise
tissue_type: Hippocampus Middle
donor_ethnicity: NA
donor_sex: Male
biomaterial_type: Primary Tissue
tissue_depot: Brain
donor_id: 149
biomaterial_provider: Rush University Medical Center
donor_age: 81.0 Years
rna_preparation_5'_rna_adapter_ligation_protocol: NA
rna_preparation_3'_rna adapter_ligation_protocol: NA
rna_preparation_5'_rna_adapter_sequence: NA
library_generation_pcr_f_primer_sequence: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
rna_preparation_3'_rna_adapter_sequence: NA
mrna_preparation_initial_mrna_qnty: 200ng
library_generation_pcr_product_isolation_protocol: 1.8X SPRI cleanup (no size selection)
rna_preparation_5'_dephosphorylation: NA
extraction_protocol_mrna_enrichment: Dynabeads mRNA purification kit (Invitrogen)
library_generation_pcr_thermocycling_program: 95C 2mins, 10 cycles of: 98C for 30 sec, 55C for 30 sec, 72C for 1 min, then 72C for 10 min, hold 4C
rna_preparation_reverse_transcription_primer_sequence: NNNNNN
extraction_protocol: Qiagen AllPrep DNA/RNA/Protein Mini Kit
library_generation_pcr_template: Adapter ligated cDNA made by reverse transcription of RNA
library_generation_pcr_polymerase_type: PFU Ultra II
library_generation_pcr_number_cycles: 10
library_generation_pcr_primer_conc: 0.83 uM
library_generation_pcr_r_primer_sequence: CAAGCAGAAGACGGCATACGAGAT
extraction_protocol_fragmentation: 98C for 40 min in 0.2 mM sodium citrate, pH 6.4 (Ambion), followed by concentrating it to 3.5 ul, mixing with 1 ul 2 uM SMART tagged random primer, incubating at 70deg C for 10 min and chilling on ice for 2 min.
rna_preparation_5'_phosphorylation: NA
experiment_type: mRNA-Seq
rna_preparation_reverse_transcription_protocol: We synthesized first-strand cDNA with this RNA primer mix by adding 4 ul 5x first-strand buffer, 2 ul 100 mM DTT, 1 ul 10 mM dNTPs, 4 ug of actinomycin D, 200 U SuperScript III and 20 U SUPERase-In, incubating at room temperature for 10 min followed by 1 h at 55degC. We cleaned up first-strand cDNA by PCIA extraction twice, ethanol precipitation with 0.1 volumes 5 M ammonium acetate to remove dNTPs and resuspension in 104 ul H2O. We synthesized second-strand cDNA by adding 4 ul of 5x first-strand buffer, 2 ul of 100 mM DTT, 4 ul of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 ul of 5x second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16degC for 2 h.
mrna_preparation_fragment_size_range: 400bp
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| Extracted molecule |
total RNA |
| Extraction protocol |
Library construction protocol: Strand specific cDNA libraries were constructed for Illumina sequencing using the dUTP method essentially as described in S. Zhong et al, Cold Spring Harbor Protoc 8, 940 - 949 (2011).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
sample_term_id: EFO_0000530
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: mRNA-Seq for REMC on Illumina
Library name: cDNA_Lib 2
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15433
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9441
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
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| Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM1112836_BI.Brain_Hippocampus_Middle.mRNA-Seq.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 2.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Brain Hippocampus Middle, Donor 149 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.16656
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: 103,897,010
PERCENT_READS_MAPPING_TO_UCSC_GENES: 69.68
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 1
MAXIMUM_REPLICATE_CORRELATION: 0.58
**********************************************************************
ANALYSIS FILE NAME: GSM1112836_BI.Brain_Hippocampus_Middle.mRNA-Seq.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 2.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Brain Hippocampus Middle, Donor 149 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.16665
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: BHM mRNA 49
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle mRNA-Seq Donor 149 Library cDNA_Lib 2 EA Release 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 103,897,010
PERCENT_READS_MAPPING_TO_UCSC_GENES: 69.68
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 1
MAXIMUM_REPLICATE_CORRELATION: 0.58
**********************************************************************
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| Submission date |
Apr 02, 2013 |
| Last update date |
Jun 25, 2019 |
| Contact name |
BROAD INSTITUTE |
| E-mail(s) |
rharris1@bcm.tmc.edu
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| Organization name |
Broad Institute
|
| Street address |
-
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE17312 |
BI Human Reference Epigenome Mapping Project |
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| Relations |
| Reanalyzed by |
GSE87112 |
| BioSample |
SAMN00691454 |
| Named Annotation |
GSM1112836_BI.Brain_Hippocampus_Middle.mRNA-Seq.149.wig.gz |
| SRA |
SRX533052 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1112836_BI.Brain_Hippocampus_Middle.mRNA-Seq.149.bed.gz |
908.2 Mb |
(ftp)(http) |
BED |
| GSM1112836_BI.Brain_Hippocampus_Middle.mRNA-Seq.149.wig.gz |
14.4 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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